Scholars@Duke
Hashim Al-Hashimi

Hashim Al-Hashimi

Adjunct Professor in the Department of Biochemistry
Biochemistry

Selected Publications

Insights into the A-C Mismatch Conformational Ensemble in Duplex DNA and its Role in Genetic Processes through a Structure-based Review.

Journal Article J Mol Biol · September 15, 2024 Knowing the conformational ensembles formed by mismatches is crucial for understanding how they are generated and repaired and how they contribute to genomic instability. Here, we review structural and energetic studies of the A-C mismatch in duplex DNA an ... Full text Link to item Cite

RNA dynamics from experimental and computational approaches.

Journal Article Structure · September 5, 2024 Conformational dynamics is crucial for the biological function of RNA molecules and for their potential as therapeutic targets. This meeting report outlines key "take-home" messages that emerged from the presentations and discussions during the CECAM works ... Full text Link to item Cite

Direct Measurement of 8OG Syn-Anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics Using 1H CEST NMR.

Journal Article J Phys Chem B · May 2, 2024 Elucidating how damage impacts DNA dynamics is essential for understanding the mechanisms of damage recognition and repair. Many DNA lesions alter their propensities to form low-populated and short-lived conformational states. However, NMR methods to measu ... Full text Link to item Cite

NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing.

Journal Article Nucleic Acids Res · March 21, 2024 Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of ... Full text Link to item Cite

An RNA excited conformational state at atomic resolution.

Journal Article Nat Commun · December 19, 2023 Sparse and short-lived excited RNA conformational states are essential players in cell physiology, disease, and therapeutic development, yet determining their 3D structures remains challenging. Combining mutagenesis, NMR spectroscopy, and computational mod ... Full text Link to item Cite

Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.

Journal Article J Am Chem Soc · October 25, 2023 Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and funct ... Full text Link to item Cite

Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs.

Journal Article Nat Chem Biol · July 2023 Replicative errors contribute to the genetic diversity needed for evolution but in high frequency can lead to genomic instability. Here, we show that DNA dynamics determine the frequency of misincorporating the A•G mismatch, and altered dynamics explain th ... Full text Link to item Cite

Turing, von Neumann, and the computational architecture of biological machines.

Journal Article Proc Natl Acad Sci U S A · June 20, 2023 In the mid-1930s, the English mathematician and logician Alan Turing invented an imaginary machine which could emulate the process of manipulating finite symbolic configurations by human computers. His machine launched the field of computer science and pro ... Full text Link to item Cite

RNA conformational propensities determine cellular activity.

Journal Article Nature · May 2023 Cellular processes are the product of interactions between biomolecules, which associate to form biologically active complexes1. These interactions are mediated by intermolecular contacts, which if disrupted, lead to alterations in cell physiology. Neverth ... Full text Link to item Cite

Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements.

Journal Article Front Mol Biosci · 2023 Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be ... Full text Link to item Cite

RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs.

Journal Article Cell Rep · August 30, 2022 N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the m ... Full text Link to item Cite

Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy.

Journal Article Proc Natl Acad Sci U S A · July 26, 2022 The majority of base pairs in double-stranded DNA exist in the canonical Watson-Crick geometry. However, they can also adopt alternate Hoogsteen conformations in various complexes of DNA with proteins and small molecules, which are key for biological funct ... Full text Link to item Cite

Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.

Journal Article Proc Natl Acad Sci U S A · June 14, 2022 Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abu ... Full text Link to item Cite

Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis.

Journal Article Proc Natl Acad Sci U S A · March 8, 2022 SignificanceUnderstanding and treating neurological disorders are global priorities. Some of these diseases are engendered by mutations that cause defects in the cellular synthesis of transfer RNAs (tRNAs), which function as adapter molecules that translat ... Full text Link to item Cite

Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.

Journal Article Nucleic Acids Res · December 2, 2021 Watson-Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative 'Hoogsteen' bps, expanding the functional complexity of DNA. We developed 'Hoog-fi ... Full text Link to item Cite

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.

Journal Article Curr Opin Struct Biol · October 2021 Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to describe their propensities to cycle between different conformations when performing cellular functions. We review recent advances in solution-state nuclear magnetic ... Full text Link to item Cite

A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions.

Journal Article Nat Commun · August 31, 2021 N6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using temperature-dependent (20 ... Full text Link to item Cite

Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.

Journal Article RNA · January 2021 Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that m ... Full text Link to item Cite

Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST.

Journal Article Magn Reson (Gott) · 2021 In duplex DNA, Watson-Crick A-T and G-C base pairs (bp's) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low in abundance and short-lived. Measuring how the Hoogsteen dynamics varies across different DNA sequences, struct ... Full text Link to item Cite

2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.

Journal Article Nucleic Acids Res · December 2, 2020 2'-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribo ... Full text Link to item Cite

Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.

Journal Article J Biol Chem · November 20, 2020 As the Watson-Crick faces of nucleobases are protected in dsDNA, it is commonly assumed that deleterious alkylation damage to the Watson-Crick faces of nucleobases predominantly occurs when DNA becomes single-stranded during replication and transcription. ... Full text Link to item Cite

Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.

Journal Article Nat Commun · November 2, 2020 Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands ... Full text Link to item Cite

DNA mismatches reveal conformational penalties in protein-DNA recognition.

Journal Article Nature · November 2020 Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, so ... Full text Open Access Link to item Cite

Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion.

Journal Article J Biomol NMR · September 2020 NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson-Crick-like con ... Full text Link to item Cite

Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields.

Journal Article Angew Chem Int Ed Engl · July 6, 2020 Biomolecules undergo motions on the micro-to-millisecond timescale to adopt low-populated transient states that play important roles in folding, recognition, and catalysis. NMR techniques, such as Carr-Purcell-Meiboom-Gill (CPMG), chemical exchange saturat ... Full text Link to item Cite

Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

Journal Article J Am Chem Soc · June 24, 2020 DNA bases can adopt energetically unfavorable tautomeric forms that enable the formation of Watson-Crick-like (WC-like) mispairs, which have been proposed to give rise to spontaneous mutations in DNA and misincorporation errors in DNA replication and trans ... Full text Link to item Cite

Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.

Journal Article Biochemistry · June 16, 2020 Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for the transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes' behaviors at chemical ... Full text Link to item Cite

Publisher Correction: High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.

Journal Article Nat Struct Mol Biol · June 2020 An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Full text Link to item Cite

Probing RNA Conformational Equilibria within the Functional Cellular Context.

Journal Article Cell Rep · February 25, 2020 Low-abundance short-lived non-native conformations referred to as excited states (ESs) are increasingly observed in vitro and implicated in the folding and biological activities of regulatory RNAs. We developed an approach for assessing the relative abunda ... Full text Link to item Cite

Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States.

Journal Article J Mol Biol · February 14, 2020 Many promising RNA drug targets have functions that require the formation of RNA-protein complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules. Regulatory RNAs have been shown to transiently form excited conformationa ... Full text Link to item Cite

Exposing Hidden High-Affinity RNA Conformational States.

Journal Article J Am Chem Soc · January 15, 2020 RNA recognition frequently results in conformational changes that optimize intermolecular binding. As a consequence, the overall binding affinity of RNA to its binding partners depends not only on the intermolecular interactions formed in the bound state b ... Full text Link to item Cite

Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields

Journal Article Advanced Materials · January 1, 2020 Biomolecules undergo motions on the micro-tomillisecond timescale to adopt low-populated transient states that play important roles in folding, recognition, and catalysis. NMR techniques, such as Carr–Purcell–Meiboom–Gill (CPMG), chemical exchange saturati ... Full text Cite

NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing.

Journal Article J Am Chem Soc · December 26, 2019 N6-Methyladenosine (m6A) is an abundant epitranscriptomic modification that plays important roles in many aspects of RNA metabolism. While m6A is thought to mainly function by recruiting reader proteins to specific RNA sites, the modification can also resh ... Full text Link to item Cite

Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements.

Journal Article J Magn Reson · November 2019 NMR relaxation dispersion studies have shown that Watson-Crick G-C and A-T base pairs in duplex DNA exist in dynamic equilibrium with their Hoogsteen counterparts. Hoogsteen base pairs form through concurrent rotation of the purine base about the glycosidi ... Full text Link to item Cite

Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.

Journal Article Angew Chem Int Ed Engl · August 26, 2019 Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson-Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X-ray structures of protein-DNA complexes. However, there are ... Full text Open Access Link to item Cite

The roles of structural dynamics in the cellular functions of RNAs.

Journal Article Nat Rev Mol Cell Biol · August 2019 RNAs fold into 3D structures that range from simple helical elements to complex tertiary structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory RNAs depend on how their 3D structure changes in response to a diverse array o ... Full text Link to item Cite

Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site.

Journal Article Nucleic Acids Res · July 26, 2019 The HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooper ... Full text Link to item Cite

Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.

Journal Article Biochemistry · April 23, 2019 The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-ade ... Full text Link to item Cite

Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA.

Journal Article Biochemistry · April 16, 2019 A( syn)-T and G( syn)-C+ Hoogsteen base pairs in protein-bound DNA duplexes can be difficult to resolve by X-ray crystallography due to ambiguous electron density and by nuclear magnetic resonance (NMR) spectroscopy due to poor chemical shift dispersion an ... Full text Link to item Cite

The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA.

Journal Article Nucleic Acids Res · February 28, 2019 Kinetoplastid RNA (kRNA) editing takes place in the mitochondria of kinetoplastid protists and creates translatable mRNAs by uridine insertion/deletion. Extensively edited (pan-edited) transcripts contain quadruplex forming guanine stretches, which must be ... Full text Link to item Cite

Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion.

Journal Article Prog Nucl Magn Reson Spectrosc · 2019 This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments ... Full text Link to item Cite

m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB.

Journal Article PLoS One · 2019 N6-methyladenosine (m6A) is a ubiquitous RNA post-transcriptional modification found in coding as well as non-coding RNAs. m6A has also been found in viral RNAs where it is proposed to modulate host-pathogen interactions. Two m6A sites have been reported i ... Full text Link to item Cite

5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo5 U-G Base Pairs.

Journal Article Chemistry · December 17, 2018 Watson-Crick like G-U mismatches with tautomeric Genol or Uenol bases can evade fidelity checkpoints and thereby contribute to translational errors. The 5-oxyacetic acid uridine (cmo5 U) modification is a base modification at the wobble position on tRNAs a ... Full text Link to item Cite

Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?

Journal Article Nucleic Acids Res · November 16, 2018 A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson-Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical mel ... Full text Link to item Cite

Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.

Journal Article RNA · October 2018 Helical elements separated by bulges frequently undergo transitions between unstacked and coaxially stacked conformations during the folding and function of noncoding RNAs. Here, we examine the dynamic properties of poly-pyrimidine bulges of varying length ... Full text Open Access Link to item Cite

A potentially abundant junctional RNA motif stabilized by m6A and Mg2.

Journal Article Nat Commun · July 17, 2018 N6-Methyladenosine (m6A) is an abundant post-transcriptional RNA modification that influences multiple aspects of gene expression. In addition to recruiting proteins, m6A can modulate RNA function by destabilizing base pairing. Here, we show that when neig ... Full text Link to item Cite

Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.

Journal Article Biochemistry · July 3, 2018 The C-terminal domain of cobalamin-dependent methionine synthase (MetH) has an essential role in catalyzing the reactivation of the enzyme following the oxidation of its cobalamin cofactor. This reactivation occurs through reductive methylation of the coba ... Full text Link to item Cite

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.

Journal Article Nat Struct Mol Biol · May 2018 Dynamic ensembles hold great promise in advancing RNA-targeted drug discovery. Here we subjected the transactivation response element (TAR) RNA from human immunodeficiency virus type-1 to experimental high-throughput screening against ~100,000 drug-like sm ... Full text Link to item Cite

Modulation of Hoogsteen dynamics on DNA recognition.

Journal Article Nat Commun · April 16, 2018 In naked duplex DNA, G-C and A-T Watson-Crick base pairs exist in dynamic equilibrium with their Hoogsteen counterparts. Here, we used nuclear magnetic resonance (NMR) relaxation dispersion and molecular dynamics (MD) simulations to examine how Watson-Cric ... Full text Link to item Cite

Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.

Journal Article J Biomol NMR · April 2018 NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson-Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occu ... Full text Open Access Link to item Cite

Hidden Structural Modules in a Cooperative RNA Folding Transition.

Journal Article Cell Rep · March 20, 2018 Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly concerted rearra ... Full text Link to item Cite

Dynamic basis for dG•dT misincorporation via tautomerization and ionization.

Journal Article Nature · February 8, 2018 Tautomeric and anionic Watson-Crick-like mismatches have important roles in replication and translation errors through mechanisms that are not fully understood. Here, using NMR relaxation dispersion, we resolve a sequence-dependent kinetic network connecti ... Full text Link to item Cite

The Mechanism of HdeA Unfolding and Chaperone Activation.

Journal Article J Mol Biol · January 5, 2018 HdeA is a periplasmic chaperone that is rapidly activated upon shifting the pH to acidic conditions. This activation is thought to involve monomerization of HdeA. There is evidence that monomerization and partial unfolding allow the chaperone to bind to pr ... Full text Link to item Cite

Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.

Journal Article Nucleic Acids Res · August 21, 2017 Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical mo ... Full text Link to item Cite

Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA.

Journal Article FEBS Lett · June 2017 Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine ... Full text Link to item Cite

Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

Journal Article Nucleic Acids Res · May 19, 2017 In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-sta ... Full text Open Access Link to item Cite

Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions.

Journal Article RNA · May 2017 RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant noncoding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the ... Full text Link to item Cite

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR.

Journal Article Medchemcomm · May 1, 2017 Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic route ... Full text Link to item Cite

Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs.

Journal Article J Am Chem Soc · March 29, 2017 The replicative and translational machinery utilizes the unique geometry of canonical G·C and A·T/U Watson-Crick base pairs to discriminate against DNA and RNA mismatches in order to ensure high fidelity replication, transcription, and translation. There i ... Full text Link to item Cite

HIV-1 leader RNA dimeric interface revealed by NMR.

Journal Article Proc Natl Acad Sci U S A · November 22, 2016 Full text Link to item Cite

Three RNA Microenvironments Detected in Fluxional Gene Delivery Polyplex Nanoassemblies.

Journal Article ACS Macro Lett · October 18, 2016 Prototropic and solvatochromatic properties of fluorescein (FL) were employed to detect the presence of microenvironments in polyplexes consisting of polycationic polymer (POCP) and a fluorescein-conjugated RNA, the HIV-1 transactivation response element ( ... Full text Link to item Cite

RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.

Journal Article J Mol Biol · October 9, 2016 Structured RNAs fold through multiple pathways, but we have little understanding of the molecular features that dictate folding pathways and determine rates along a given pathway. Here, we asked whether folding of a complex RNA can be understood from its s ... Full text Link to item Cite

m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.

Journal Article Nat Struct Mol Biol · September 2016 The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a r ... Full text Link to item Cite

Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.

Journal Article Biochemistry · August 16, 2016 Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the format ... Full text Link to item Cite

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.

Journal Article Nat Commun · June 13, 2016 Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining (15)N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k-1≈423 s(-1)) secondar ... Full text Link to item Cite

Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.

Journal Article Phys Chem Chem Phys · February 17, 2016 Detecting conformational heterogeneity in biological macromolecules is a key for the understanding of their biological function. We here provide a comparison between two independent approaches to assess conformational heterogeneity: molecular dynamics simu ... Full text Link to item Cite

Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release.

Journal Article Biomacromolecules · January 11, 2016 A combination of solution NMR, dynamic light scattering (DLS), and fluorescence quenching assays were employed to obtain insights into the dynamics and structural features of a polyplex system consisting of HIV-1 transactivation response element (TAR) and ... Full text Link to item Cite

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.

Journal Article Nucleic Acids Res · January 8, 2016 A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms con ... Full text Link to item Cite

Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.

Journal Article Cell Rep · December 1, 2015 Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational trans ... Full text Link to item Cite

Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity.

Journal Article Cell · October 22, 2015 A key effector route of the Sugar Code involves lectins that exert crucial regulatory controls by targeting distinct cellular glycans. We demonstrate that a single amino-acid substitution in a banana lectin, replacing histidine 84 with a threonine, signifi ... Full text Link to item Cite

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

Journal Article J Am Chem Soc · October 14, 2015 Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics in ... Full text Link to item Cite

Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.

Journal Article J Phys Chem B · July 30, 2015 A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well-known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, a ... Full text Link to item Cite

Slowdown of Interhelical Motions Induces a Glass Transition in RNA.

Journal Article Biophys J · June 16, 2015 RNA function depends crucially on the details of its dynamics. The simplest RNA dynamical unit is a two-way interhelical junction. Here, for such a unit--the transactivation response RNA element--we present evidence from molecular dynamics simulations, sup ... Full text Link to item Cite

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.

Journal Article Nucleic Acids Res · April 20, 2015 Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C ... Full text Open Access Link to item Cite

Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.

Journal Article Nature · March 19, 2015 Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that ar ... Full text Link to item Cite

Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

Journal Article J Am Chem Soc · March 18, 2015 Mammalian mitochondrial tRNA(Ser(UCN)) (mt-tRNA(Ser)) and pyrrolysine tRNA (tRNA(Pyl)) fold to near-canonical three-dimensional structures despite having noncanonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA te ... Full text Link to item Cite

Dynamic motions of the HIV-1 frameshift site RNA.

Journal Article Biophys J · February 3, 2015 The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulge ... Full text Link to item Cite

Characterizing RNA Excited States Using NMR Relaxation Dispersion.

Journal Article Methods Enzymol · 2015 Changes in RNA secondary structure play fundamental roles in the cellular functions of a growing number of noncoding RNAs. This chapter describes NMR-based approaches for characterizing microsecond-to-millisecond changes in RNA secondary structure that are ... Full text Link to item Cite

Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair.

Journal Article Biochemistry · November 25, 2014 We recently showed that Watson-Crick base pairs in canonical duplex DNA exist in dynamic equilibrium with G(syn)·C+ and A(syn)·T Hoogsteen base pairs that have minute populations of ∼1%. Here, using nuclear magnetic resonance R1ρ relaxation dispersion, we ... Full text Link to item Cite

Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids.

Journal Article J Biomol NMR · November 2014 Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation ... Full text Link to item Cite

Insights into domain-domain motions in proteins and RNA from solution NMR.

Journal Article Acc Chem Res · October 21, 2014 Many multidomain proteins and ribonucleic acids consist of domains that autonomously fold and that are linked together by flexible junctions. This architectural design allows domains to sample a wide range of positions with respect to one another, yet do s ... Full text Link to item Cite

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.

Journal Article Nucleic Acids Res · October 2014 Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in highe ... Full text Link to item Cite

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

Journal Article J Mol Biol · September 23, 2014 Ribosomes control the missense error rate of ~10(-4) during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRN ... Full text Link to item Cite

Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.

Journal Article Nat Commun · September 4, 2014 Hoogsteen (HG) base pairing involves a 180° rotation of the purine base relative to Watson-Crick (WC) base pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction and replication. Here, using ... Full text Link to item Cite

Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis.

Journal Article ACS Chem Biol · August 15, 2014 Recent studies have demonstrated that the active sites of S-adenosylmethionine (AdoMet)-dependent methyltransferases form strong carbon-oxygen (CH···O) hydrogen bonds with the substrate's sulfonium group that are important in AdoMet binding and catalysis. ... Full text Link to item Cite

An RNA tertiary switch by modifying how helices are tethered.

Journal Article Genome Biol · July 30, 2014 A viral tRNA-like structure has evolved a unique strategy to undergo a tertiary structure conformational switch that may help regulate viral regulation. ... Full text Link to item Cite

Invisible RNA state dynamically couples distant motifs.

Journal Article Proc Natl Acad Sci U S A · July 1, 2014 Using on- and off-resonance carbon and nitrogen R1ρ NMR relaxation dispersion in concert with mutagenesis and NMR chemical shift fingerprinting, we show that the transactivation response element RNA from the HIV-1 exists in dynamic equilibrium with a trans ... Full text Link to item Cite

Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange.

Journal Article J Magn Reson · July 2014 Spin relaxation in the rotating frame (R1ρ) is a powerful NMR technique for characterizing fast microsecond timescale exchange processes directed toward short-lived excited states in biomolecules. At the limit of fast exchange, only k(ex)=k(1)+k(-1) and Φe ... Full text Link to item Cite

Structural dynamics of a single-stranded RNA-helix junction using NMR.

Journal Article RNA · June 2014 Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3' e ... Full text Link to item Cite

Measuring similarity between dynamic ensembles of biomolecules.

Journal Article Nat Methods · May 2014 We present a simple and general approach termed REsemble for quantifying population overlap and structural similarity between ensembles. This approach captures improvements in the quality of ensembles determined using increasing input experimental data--im ... Full text Link to item Cite

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.

Journal Article J Phys Chem B · March 13, 2014 Recent studies have shown that simple stereochemical constraints encoded at the RNA secondary structure level significantly restrict the orientation of RNA helices across two-way junctions and yield physically reasonable distributions of RNA 3D conformatio ... Full text Link to item Cite

Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids.

Journal Article Curr Opin Struct Biol · February 2014 There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail the loss of energetically favorable interactions or require energetically costly base i ... Full text Link to item Cite

Hierarchy of RNA functional dynamics.

Journal Article Annu Rev Biochem · 2014 RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds ... Full text Link to item Cite

Advances in the determination of nucleic acid conformational ensembles.

Journal Article Annu Rev Phys Chem · 2014 Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical sh ... Full text Link to item Cite

NMR studies of nucleic acid dynamics.

Journal Article J Magn Reson · December 2013 Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to ... Full text Link to item Cite

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.

Journal Article Nucleic Acids Res · December 2013 Riboswitches are structural elements in the 5' untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 ... Full text Link to item Cite

A historical account of Hoogsteen base-pairs in duplex DNA.

Journal Article Biopolymers · December 2013 In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can associate with poly(rA)-poly(rU) duplexes to form triplexes. Two years later, Karst Hoogsteen visualized suc ... Full text Link to item Cite

Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

Journal Article J Am Chem Soc · October 16, 2013 S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental d ... Full text Link to item Cite

Influence of dimethylsulfoxide on RNA structure and ligand binding.

Journal Article Anal Chem · October 15, 2013 Dimethyl sulfoxide (DMSO) is widely used as a cosolvent to solubilize hydrophobic compounds in RNA-ligand binding assays. Although it is known that high concentrations of DMSO (>75%) can significantly affect RNA structure and folding energetics, a thorough ... Full text Link to item Cite

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

Journal Article J Am Chem Soc · May 8, 2013 G·C Hoogsteen base pairs can form transiently in duplex DNA and play important roles in DNA recognition, replication, and repair. G·C Hoogsteen base pairs are thought to be stabilized by protonation of cytosine N3, which affords a second key hydrogen bond, ... Full text Link to item Cite

A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

Journal Article J Am Chem Soc · April 10, 2013 The ability to modulate alignment and measure multiple independent sets of NMR residual dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at atomic resolution and with time scale sensitivity ranging from picoseconds ... Full text Link to item Cite

Utility of 1H NMR chemical shifts in determining RNA structure and dynamics.

Journal Article J Phys Chem B · February 21, 2013 The development of methods for predicting NMR chemical shifts with high accuracy and speed is increasingly allowing use of these abundant, readily accessible measurements in determining the structure and dynamics of proteins. For nucleic acids, however, de ... Full text Link to item Cite

Elucidating transient protonated GC+ Hoogstein base pairs in canonical DNA duplexes

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2013 Cite

Visualizing transient low-populated structures of RNA.

Journal Article Nature · November 29, 2012 The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captu ... Full text Link to item Cite

Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.

Journal Article Biochemistry · October 30, 2012 Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet few studies have experimentally explored the sequence dependence of DNA dynamics that occur on bi ... Full text Link to item Cite

Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release.

Journal Article Mol Pharm · September 4, 2012 The transfer of genetic material into cells using nonviral vectors offers unique potential for therapeutics; however, the efficacy of delivery depends upon a poorly understood, multistep pathway, limiting the prospects for successful gene delivery. Mechani ... Full text Link to item Cite

Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation.

Journal Article Biochemistry · August 28, 2012 The left-handed DNA structure, Z-DNA, is believed to play important roles in gene expression and regulation. Z-DNA forms sequence-specifically with a preference for sequences rich in pyrimidine/purine dinucleotide steps. In vivo, Z-DNA is generated in the ... Full text Link to item Cite

Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution.

Journal Article J Am Chem Soc · February 29, 2012 Nucleic acids transiently morph into alternative conformations that can be difficult to characterize at the atomic level by conventional methods because they exist for too little time and in too little abundance. We recently reported evidence for transient ... Full text Link to item Cite

Functional complexity and regulation through RNA dynamics.

Journal Article Nature · February 15, 2012 Changes to the conformation of coding and non-coding RNAs form the basis of elements of genetic regulation and provide an important source of complexity, which drives many of the fundamental processes of life. Although the structure of RNA is highly flexib ... Full text Link to item Cite

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.

Journal Article Nucleic Acids Res · February 2012 Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by ... Full text Link to item Cite

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.

Journal Article Nucleic Acids Res · January 2012 Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formu ... Full text Link to item Cite

RNA structure: Adding a second dimension.

Journal Article Nat Chem · November 23, 2011 Full text Link to item Cite

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.

Journal Article Nat Methods · October 28, 2011 Many recently discovered noncoding RNAs do not fold into a single native conformation but sample many different conformations along their free-energy landscape to carry out their biological function. Here we review solution-state NMR techniques that measur ... Full text Link to item Cite

3D maps of RNA interhelical junctions.

Journal Article Nat Protoc · September 15, 2011 More than 50% of RNA secondary structure is estimated to be A-form helices, which are linked together by various junctions. Here we describe a protocol for computing three interhelical Euler angles describing the relative orientation of helices across RNA ... Full text Link to item Cite

Using fluorine nuclear magnetic resonance to probe changes in the structure and dynamics of membrane-active peptides interacting with lipid bilayers.

Journal Article Biochemistry · July 12, 2011 The antimicrobial peptide MSI-78 serves as a model system for studying interactions of bioactive peptides with membranes. Using a series of MSI-78 peptides that incorporate l-4,4,4-trifluoroethylglycine, a small and sensitive (19)F nuclear magnetic resonan ... Full text Link to item Cite

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble.

Journal Article Nat Chem Biol · June 26, 2011 Current approaches used to identify protein-binding small molecules are not suited for identifying small molecules that can bind emerging RNA drug targets. By docking small molecules onto an RNA dynamic ensemble constructed by combining NMR spectroscopy an ... Full text Link to item Cite

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.

Journal Article Curr Opin Struct Biol · June 2011 Accompanying recent advances in determining RNA secondary structure is the growing appreciation for the importance of relatively simple topological constraints, encoded at the secondary structure level, in defining the overall architecture, folding pathway ... Full text Link to item Cite

Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9.

Journal Article J Biol Chem · May 27, 2011 SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbo ... Full text Link to item Cite

Transient Hoogsteen base pairs in canonical duplex DNA.

Journal Article Nature · February 24, 2011 Sequence-directed variations in the canonical DNA double helix structure that retain Watson-Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectrosc ... Full text Link to item Cite

Sequence-specific B-DNA flexibility modulates Z-DNA formation.

Journal Article J Am Chem Soc · February 23, 2011 Conversion of right-handed B-DNA into left-handed Z-DNA is one of the largest structural transitions in biology that plays fundamental roles in gene expression and regulation. Z-DNA segments must form within genomes surrounded by a sea of B-DNA and require ... Full text Link to item Cite

A rare example of lock-and-key RNA recognition.

Journal Article J Mol Biol · December 10, 2010 Full text Link to item Cite

Biochemistry. Exciting structures.

Journal Article Science · September 10, 2010 Full text Link to item Cite

Thermodynamics of RNA melting, one base pair at a time.

Journal Article RNA · September 2010 The melting of base pairs is a ubiquitous feature of RNA structural transitions, which are widely used to sense and respond to cellular stimuli. A recent study employing solution nuclear magnetic resonance (NMR) imino proton exchange spectroscopy provides ... Full text Link to item Cite

Using fluorine nuclear magnetic resonance to probe the interaction of membrane-active peptides with the lipid bilayer.

Journal Article Biochemistry · July 13, 2010 A variety of biologically active peptides exert their function through direct interactions with the lipid membrane of the cell. These surface interactions are generally transient and highly dynamic, making them hard to study. Here we have examined the feas ... Full text Link to item Cite

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.

Journal Article Proc Natl Acad Sci U S A · February 9, 2010 Functionally critical metals interact with RNA through complex coordination schemes that are currently difficult to visualize at the atomic level under solution conditions. Here, we report a new approach that combines NMR and XAS to resolve and characteriz ... Full text Link to item Cite

Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.

Journal Article J Phys Chem B · January 21, 2010 Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations are both techniques that can be used to characterize the structural dynamics of biomolecules and their underlying time scales. Comparison of relaxation parameters obtaine ... Full text Link to item Cite

Topology links RNA secondary structure with global conformation, dynamics, and adaptation.

Journal Article Science · January 8, 2010 Thermodynamic rules that link RNA sequences to secondary structure are well established, but the link between secondary structure and three-dimensional global conformation remains poorly understood. We constructed comprehensive three-dimensional maps depic ... Full text Link to item Cite

Variable helix elongation as a tool to modulate RNA alignment and motional couplings.

Journal Article J Magn Reson · January 2010 The application of residual dipolar couplings (RDCs) in studies of RNA structure and dynamics can be complicated by the presence of couplings between collective helix motions and overall alignment and by the inability to modulate overall alignment of the m ... Full text Link to item Cite

NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F(1)F(0)-ATPase.

Journal Article Biopolymers · January 2010 Bz-423 is an inhibitor of the mitochondrial F(1)F(0)-ATPase, with therapeutic properties in murine models of immune diseases. Here, we study the binding of a water-soluble Bz-423 analog (5-(3-(aminomethyl)phenyl)-7-chloro- 1-methyl-3-(naphthalen-2-ylmethyl ... Full text Link to item Cite

Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects.

Journal Article Biochemistry · November 17, 2009 The incorporation of extensively fluorinated, or fluorous, analogues of hydrophobic amino acids into proteins potentially provides the opportunity to modulate the physicochemical properties of proteins in a predictable manner. On the basis of the propertie ... Full text Link to item Cite

Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.

Journal Article RNA · November 2009 By simplifying the interpretation of nuclear magnetic resonance spin relaxation and residual dipolar couplings data, recent developments involving the elongation of RNA helices are providing new atomic insights into the dynamical properties that allow RNA ... Full text Link to item Cite

Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.

Journal Article Methods · October 2009 A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-res ... Full text Link to item Cite

Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR.

Journal Article J Biomol NMR · September 2009 DNA is a highly flexible molecule that undergoes functionally important structural transitions in response to external cellular stimuli. Atomic level spin relaxation NMR studies of DNA dynamics have been limited to short duplexes in which sensitivity to bi ... Full text Link to item Cite

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.

Journal Article Nucleic Acids Res · June 2009 We describe a strategy for constructing atomic resolution dynamical ensembles of RNA molecules, spanning up to millisecond timescales, that combines molecular dynamics (MD) simulations with NMR residual dipolar couplings (RDC) measured in elongated RNA. Th ... Full text Link to item Cite

Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors.

Journal Article ACS Chem Biol · May 15, 2009 Small molecules that reconstitute the binding mode(s) of a protein and in doing so elicit a programmed functional response offer considerable advantages in the control of complex biological processes. The development challenges of such molecules are signif ... Full text Link to item Cite

Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.

Journal Article J Phys Chem B · May 7, 2009 NMR spectroscopy is one of the most powerful techniques for studying the internal dynamics of biomolecules. Current formalisms approximate the dynamics using simple continuous motional models or models involving discrete jumps between a small number of sta ... Full text Link to item Cite

Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy.

Journal Article J Am Chem Soc · March 25, 2009 We present an off-resonance carbon R(1rho) NMR experiment utilizing weak radiofrequency fields and selective polarization transfers for quantifying chemical-exchange processes in nucleic acids. The experiment extends the range of accessible time scales to ... Full text Link to item Cite

Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR.

Journal Article J Phys Chem B · December 25, 2008 Nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) provide a unique opportunity for spatially characterizing complex motions in biomolecules with time scale sensitivity extending up to milliseconds. Up to five motionally averaged Wigner rot ... Full text Link to item Cite

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

Journal Article Biophys J · October 2008 The HIV-1 transactivation response element (TAR) RNA binds a variety of proteins and is a target for developing anti-HIV therapies. TAR has two primary binding sites: a UCU bulge and a CUGGGA apical loop. We used NMR residual dipolar couplings, carbon spin ... Full text Link to item Cite

RNA dynamics: it is about time.

Journal Article Curr Opin Struct Biol · June 2008 Many recently discovered RNA functions rely on highly complex multistep conformational transitions that occur in response to an array of cellular signals. These dynamics accompany and guide, for example, RNA cotranscriptional folding, ligand sensing and si ... Full text Link to item Cite

Extending the NMR spatial resolution limit for RNA by motional couplings.

Journal Article Nat Methods · March 2008 Experimental resolution of distinct dynamical processes in molecules can prove impossible when they are correlated to one another. In nuclear magnetic resonance (NMR) spectroscopy, couplings between internal and overall motions lead to intractable complexi ... Full text Link to item Cite

Dynamics of large elongated RNA by NMR carbon relaxation.

Journal Article J Am Chem Soc · December 26, 2007 We present an NMR strategy for characterizing picosecond-to-nanosecond internal motions in uniformly 13C/15N-labeled RNAs that combines measurements of R1, R1rho, and heteronuclear 13C{1H} NOEs for protonated base (C2, C5, C6, and C8) and sugar (C1') carbo ... Full text Link to item Cite

Visualizing spatially correlated dynamics that directs RNA conformational transitions.

Journal Article Nature · December 20, 2007 RNAs fold into three-dimensional (3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals. RNA structures are believed to encode spatially tuned flexibility that can di ... Full text Link to item Cite

NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.

Journal Article Biopolymers · August 5, 2007 An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, ... Full text Link to item Cite

iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.

Journal Article Biophys J · July 15, 2007 The HIV-1 transactivation response RNA element (TAR), which is essential to the lifecycle of the virus, has been suggested, based on NMR and hydrodynamic measurements, to undergo substantial, collective, structural dynamics that are important for its funct ... Full text Link to item Cite

Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition.

Journal Article Biochemistry · June 5, 2007 Many regulatory RNAs undergo large changes in structure upon recognition of proteins and ligands, but the mechanism by which this occurs remains poorly understood. Using NMR residual dipolar coupling (RDCs), we characterized Na+-induced changes in the stru ... Full text Link to item Cite

Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation.

Journal Article RNA · February 2007 The P4 helix is an essential element of ribonuclease P (RNase P) that is believed to bind catalytically important metals. Here, we applied a combination of NMR residual dipolar couplings (RDCs) and a recently introduced domain-elongation strategy for measu ... Full text Link to item Cite

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.

Journal Article Nat Protoc · 2007 We present a protocol for determining the relative orientation and dynamics of A-form helices in 13C/15N isotopically enriched RNA samples using NMR residual dipolar couplings (RDCs). Non-terminal Watson-Crick base pairs in helical stems are experimentally ... Full text Link to item Cite

Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition.

Journal Article Nucleic Acids Res · 2007 Stem loop 1 (SL1) is a highly conserved hairpin in the 5'-leader of the human immunodeficiency virus type I that forms a metastable kissing dimer that is converted during viral maturation into a stable duplex with the aid of the nucleocapsid (NC) protein. ... Full text Link to item Cite

Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings.

Journal Article J Biomol NMR · December 2006 We examined how static and dynamic deviations from the idealized A-form helix propagate into errors in the principal order tensor parameters determined using residual dipolar couplings (rdcs). A 20-ns molecular dynamics (MD) simulation of the HIV-1 transac ... Full text Link to item Cite

Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints.

Journal Article J Magn Reson · April 2006 Using residual chemical shift anisotropies (RCSAs) measured in a weakly aligned stem-loop RNA, we examined the carbon chemical shift anisotropy (CSA) tensors of nucleobase adenine C2, pyrimidine C5 and C6, and purine C8. The differences between the measure ... Full text Link to item Cite

Resolving the motional modes that code for RNA adaptation.

Journal Article Science · February 3, 2006 Using a domain elongation strategy, we decoupled internal motions in RNA from overall rotational diffusion. This allowed us to site-specifically resolve a manifold of motional modes in two regulatory RNAs from HIV-1 with the use of nuclear magnetic resonan ... Full text Link to item Cite

Modulating protein structure with fluorous amino acids: increased stability and native-like structure conferred on a 4-helix bundle protein by hexafluoroleucine.

Journal Article J Am Chem Soc · January 11, 2006 There has recently been much interest in exploiting the unusual properties associated with fluorocarbons to modulate the physicochemical properties of proteins. Here we present a detailed investigation into the effect on structure and stability of systemat ... Full text Link to item Cite

Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy.

Journal Article Chembiochem · September 2005 The ever-increasing cellular roles ascribed to RNA raise fundamental questions regarding how a biopolymer composed of only four chemically similar building-block nucleotides achieves such functional diversity. Here, I discuss how RNA achieves added mechani ... Full text Link to item Cite

Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization.

Journal Article J Mol Biol · April 16, 2004 The structure and dynamics of the stem-loop transactivation response element (TAR) RNA from the human immunodeficiency virus type-1 (HIV-1) bound to the ligand argininamide (ARG) has been characterized using a combination of a large number of residual dipo ... Full text Link to item Cite

Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment.

Journal Article J Am Chem Soc · September 3, 2003 Approaches developed thus for extracting structural and dynamical information from RDCs have rested on the assumption that motions do not affect molecular alignment. However, it is well established that molecular alignment in ordered media is dependent on ... Full text Link to item Cite

Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings.

Journal Article J Mol Biol · June 20, 2003 The effects of divalent Mg(2+) on the conformation and dynamics of the stem-loop transactivation response element (TAR) RNA from HIV-1 have been characterized using NMR residual dipolar couplings (RDCs). Order matrix analysis of one bond 13C-1H RDCs measur ... Full text Link to item Cite

NMR Studies of Biomolecular Dynamics and Structural Plasticity Using Residual Dipolar Couplings

Journal Article Annual Reports on NMR Spectroscopy · 2003 Due to their exquisite sensitivity to bond vector orientations and distances, residual dipolar couplings are emerging as a powerful NMR methodology for probing the conformational dynamics of biomolecules. The global organization of multi-domain proteins an ... Full text Link to item Cite

Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings.

Journal Article J Mol Biol · May 3, 2002 We report a new residual dipolar couplings (RDCs) based NMR procedure for rapidly determining RNA tertiary structure demonstrated on a uniformly (15)N/(13)C-labeled 27 nt variant of the trans-activation response element (TAR) RNA from HIV-I. In this proced ... Full text Link to item Cite

Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

Journal Article J Mol Biol · January 11, 2002 Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human ... Full text Link to item Cite

Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.

Journal Article OMICS · 2002 The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding ... Full text Link to item Cite

Residual dipolar couplings: synergy between NMR and structural genomics.

Journal Article J Biomol NMR · January 2002 Structural genomics is on a quest for the structure and function of a significant fraction of gene products. Current efforts are focusing on structure determination of single-domain proteins, which can readily be targeted by X-ray crystallography, NMR spec ... Full text Link to item Cite

Structural and dynamic analysis of residual dipolar coupling data for proteins.

Journal Article J Am Chem Soc · February 21, 2001 The measurement of residual dipolar couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which ... Full text Link to item Cite

Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.

Journal Article J Am Chem Soc · January 31, 2001 We present a new NMR procedure for determining the three-dimensional fold of C2-symmetric nucleic acid homodimers that relies on long-range orientational constraints derived from the measurement of two independent sets of residual dipolar couplings under t ... Full text Link to item Cite

Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.

Journal Article J Am Chem Soc · January 24, 2001 We present a new approach to the analysis of the conformational and the motional properties of an oligosaccharide, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside. The approach relies on an order matrix analysis of residual dipolar couplin ... Full text Link to item Cite

Rapid determination of protein folds using residual dipolar couplings.

Journal Article J Mol Biol · December 1, 2000 Over the next few years, various genome projects will sequence many new genes and yield many new gene products. Many of these products will have no known function and little, if any, sequence homology to existing proteins. There is reason to believe that a ... Full text Link to item Cite

Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.

Journal Article J Magn Reson · April 2000 Residual dipolar couplings for pairs of proximate magnetic nuclei in macromolecules can easily be measured using high-resolution NMR methods when the molecules are dissolved in dilute liquid crystalline media. The resulting couplings can in principle be us ... Full text Link to item Cite

Molecular symmetry as an aid to geometry determination in ligand protein complexes.

Journal Article J Magn Reson · January 2000 Dipole-dipole couplings between pairs of spin 12 nuclei, which can be measured from NMR spectra in field-ordered media, offer useful constraints on the orientation of various fragments in molecular systems. However, the orientation of fragments relative to ... Full text Link to item Cite

Residual dipolar coupling derived orientational constraints on ligand geometry in a 53 kDa protein-ligand complex.

Journal Article J Mol Biol · October 15, 1999 The geometric relationships between ligands and the functional groups that bind ligands in soluble ligand-protein complexes have traditionally been deduced from distance constraints between pairs of NMR active nuclei spanning the ligand-protein interface. ... Full text Link to item Cite