Base Composition

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  Subject Areas on Research

  • A compensatory base change in human U2 snRNA can suppress a branch site mutation. 
  • A mutational analysis of the polypyrimidine tract of introns. Effects of sequence differences in pyrimidine tracts on splicing. 
  • A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes. 
  • A transcription factor affinity-based code for mammalian transcription initiation. 
  • Accelerated deamination of cytosine residues in UV-induced cyclobutane pyrimidine dimers leads to CC-->TT transitions. 
  • Base composition of mononucleotide runs affects DNA polymerase slippage and removal of frameshift intermediates by mismatch repair in Saccharomyces cerevisiae. 
  • Bidirectional excision in methyl-directed mismatch repair. 
  • Catechol dioxygenase is an insensitive reporter for transcription in Mycobacterium smegmatis. 
  • Characteristics of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People's Republic of China. 
  • Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans. 
  • Computational analysis of core promoters in the Drosophila genome. 
  • Conserved economics of transcription termination in eubacteria. 
  • Context dependence of meiotic recombination hotspots in yeast: the relationship between recombination activity of a reporter construct and base composition. 
  • Coordination of replication and transcription along a Drosophila chromosome. 
  • Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG). 
  • Cutting of M13mp7 phage DNA and excision of cloned single-stranded sequences by restriction endonucleases. 
  • Cytosine deamination in mismatched base pairs. 
  • DNA base modification: ionized base pairs and mutagenesis. 
  • DNA bending near the replication origin of IncFII plasmid NR1. 
  • DNA mismatch correction. 
  • DNA polymerase delta is required for human mismatch repair in vitro. 
  • DNA structural features that lead to strand breakage by eukaryotic type-I topoisomerase. 
  • Dynamic evolution of base composition: causes and consequences in avian phylogenomics. 
  • Effect of isopropyl-beta-D-thiogalactopyranosid induction of the lac operon on the specificity of spontaneous and doxorubicin-induced mutations in Escherichia coli. 
  • Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs. 
  • Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs. 
  • Escherichia coli mutY gene product is required for specific A-G----C.G mismatch correction. 
  • Euglena gracilis chloroplast small subunit rRNA. Sequence and base pairing potential of the 3' terminus, cleavage by colicin E3. 
  • Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. 
  • Exaggerated CpH methylation in the autism-affected brain. 
  • Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer. 
  • GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. 
  • GC sequence specific recognition by an N-formamido, C-terminus-modified and imidazole-containing analogue of netropsin. 
  • Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction. 
  • Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. 
  • Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content. 
  • Genetic bioaugmentation as an effective method for in situ bioremediation: functionality of catabolic plasmids following conjugal transfers. 
  • Genomic organization of rat rDNA. 
  • Hel-N1, an RNA-binding protein, is a ligand for an A + U rich region of the GLUT1 3' UTR. 
  • How many numbers are required to specify sequence-dependent properties of polynucleotides? 
  • Human MutSalpha recognizes damaged DNA base pairs containing O6-methylguanine, O4-methylthymine, or the cisplatin-d(GpG) adduct. 
  • Human colonic sulfomucin identified by a specific monoclonal antibody. 
  • Human strand-specific mismatch repair occurs by a bidirectional mechanism similar to that of the bacterial reaction. 
  • Immunostimulatory properties of genomic DNA from different bacterial species. 
  • Improvements to the differential display method for gene analysis. 
  • Increased transversions in a novel mutator colon cancer cell line. 
  • Initial sequencing and comparative analysis of the mouse genome. 
  • Isolation and characterization of a human pro alpha 2(I) collagen gene segment. 
  • Isolation of MutSbeta from human cells and comparison of the mismatch repair specificities of MutSbeta and MutSalpha. 
  • Isolation of an hMSH2-p160 heterodimer that restores DNA mismatch repair to tumor cells. 
  • Isolation of two E-box binding factors that interact with the rat tyrosine hydroxylase enhancer. 
  • Localisation of receptor interacting protein 140 (RIP140) within 100 kb of D21S13 on 21q11, a gene-poor region of the human genome. 
  • Methyl-directed DNA mismatch repair in Escherichia coli. 
  • Methyl-directed mismatch repair is bidirectional. 
  • Methyl-directed repair of DNA base-pair mismatches in vitro. 
  • Misincorporation and mispaired primer extension by human immunodeficiency virus reverse transcriptase. 
  • Mismatch repair, genetic stability, and cancer. 
  • Mismatch-, MutS-, MutL-, and helicase II-dependent unwinding from the single-strand break of an incised heteroduplex. 
  • Mispair specificity of methyl-directed DNA mismatch correction in vitro. 
  • Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions. 
  • Multifactorial determinants of protein expression in prokaryotic open reading frames. 
  • Multiple potential regulatory elements in the 5' flanking region of the human alpha 1a-adrenergic receptor. 
  • Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome. 
  • Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. 
  • Nucleotide bias observed with a short SELEX RNA aptamer library. 
  • OligoCalc: an online oligonucleotide properties calculator. 
  • Optimal self-cleavage activity of the hepatitis delta virus RNA is dependent on a homopurine base pair in the ribozyme core. 
  • Phage T3 DNA contains an exact copy of the 23 base-pair phage T7 RNA polymerase promoter sequence. 
  • Predicting cell-type-specific gene expression from regions of open chromatin. 
  • Properties of the genome of equine herpesvirus type 3. 
  • Protonated base pairs explain the ambiguous pairing properties of O6-methylguanine. 
  • Rapid DNA sequencing of more than 1000 bases per run by capillary electrophoresis using replaceable linear polyacrylamide solutions. 
  • Recombination hotspots flank the Cryptococcus mating-type locus: implications for the evolution of a fungal sex chromosome. 
  • Repair of specific base pair mismatches formed during meiotic recombination in the yeast Saccharomyces cerevisiae. 
  • Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. 
  • Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. 
  • Secondary structure of the self-cleaving RNA of hepatitis delta virus: applications to catalytic RNA design. 
  • Separation and sequence of the 3' termini of M double-stranded RNA from killer yeast. 
  • Sequence analysis of the cDNA encoding human liver glycogen phosphorylase reveals tissue-specific codon usage. 
  • Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. 
  • Sequencing of double-stranded polymerase chain reaction products for mutation analysis. 
  • Structural features of the trans-activation response RNA element of equine infectious anemia virus. 
  • Structural relationships in glycogen phosphorylases. 
  • Structure of a G.T.A triplet in an intramolecular DNA triplex. 
  • Structure of the genes encoding transcription factor IIB and TATA box-binding protein from Drosophila melanogaster. 
  • Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts. 
  • The 5'-untranslated region of the N-methyl-D-aspartate receptor NR2A subunit controls efficiency of translation. 
  • The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. 
  • The complete mitochondrial genome sequence of the Canada goose (Branta canadensis). 
  • The hydrogen bonding of cytosine with guanine: calorimetric and 1H-nmr analysis of the molecular interactions of nucleic acid bases. 
  • The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation. 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
  • Two mouse early embryonic beta-globin gene sequences. Evolution of the nonadult beta-globins. 
  • Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. 
  • Variable temperature infrared spectroscopy of cytosine-guanine base pairs: tautomerism versus polarization. 
  • Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications. 
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  Keywords of People

  • Sullivan, Daniel Carl, Professor Emeritus of Radiology, Radiology