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

Publication ,  Journal Article
Nikolova, EN; Al-Hashimi, HM
Published in: 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 biologically relevant fluctuations occurring at nanosecond timescales is often inadequate. Here, we introduce a method for preparing residue-specific (13)C/(15)N-labeled elongated DNA along with a strategy for establishing resonance assignments and apply the approach to probe fast inter-helical bending motions induced by an adenine tract. Preliminary results suggest the presence of elevated A-tract independent end-fraying internal motions occurring at nanosecond timescales, which evade detection in short DNA constructs and that penetrate deep (7 bp) within the DNA helix and gradually fade away towards the helix interior.

Duke Scholars

Published In

J Biomol NMR

DOI

EISSN

1573-5001

Publication Date

September 2009

Volume

45

Issue

1-2

Start / End Page

9 / 16

Location

Netherlands

Related Subject Headings

  • Sequence Analysis, DNA
  • Polymerase Chain Reaction
  • Nuclear Magnetic Resonance, Biomolecular
  • Nitrogen Isotopes
  • Molecular Sequence Data
  • Models, Biological
  • DNA
  • Carbon Isotopes
  • Biophysics
  • Base Sequence
 

Citation

Journal cover image

Published In

J Biomol NMR

DOI

EISSN

1573-5001

Publication Date

September 2009

Volume

45

Issue

1-2

Start / End Page

9 / 16

Location

Netherlands

Related Subject Headings

  • Sequence Analysis, DNA
  • Polymerase Chain Reaction
  • Nuclear Magnetic Resonance, Biomolecular
  • Nitrogen Isotopes
  • Molecular Sequence Data
  • Models, Biological
  • DNA
  • Carbon Isotopes
  • Biophysics
  • Base Sequence