Experts and Doctors on nucleic acid conformation in Baton Rouge, Louisiana, United States

Summary

Locale: Baton Rouge, Louisiana, United States
Topic: nucleic acid conformation

Top Publications

  1. Grove A, Saavedra T. The role of surface-exposed lysines in wrapping DNA about the bacterial histone-like protein HU. Biochemistry. 2002;41:7597-603 pubmed
    ..We propose that Lys3 forms an internal saltbridge to Asp26 in HU homologues characterized by shorter binding sites and that its surface exposure, and hence a longer binding site, may correlate with absence of this aspartate. ..
  2. Datta K, Wowor A, Richard A, LiCata V. Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA. Biophys J. 2006;90:1739-51 pubmed
    ..In the case of Klenow, surface area burial can account for only about half of the DeltaCp of binding. ..
  3. Nesterova I, Erdem S, Pakhomov S, Hammer R, Soper S. Phthalocyanine dimerization-based molecular beacons using near-IR fluorescence. J Am Chem Soc. 2009;131:2432-3 pubmed publisher
  4. Aboul ela F. Strategies for the design of RNA-binding small molecules. Future Med Chem. 2010;2:93-119 pubmed publisher
    ..While targeting of RNA for drug design is very challenging, continuing advances in our understanding of the principles of RNA-ligand interaction will be necessary to realize the full potential of this class of targets. ..
  5. Boyapati V, Huang W, Spedale J, Aboul ela F. Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch. RNA. 2012;18:1230-43 pubmed publisher
    ..Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding. ..
  6. Ghosh S, Grove A. Histone-like protein HU from Deinococcus radiodurans binds preferentially to four-way DNA junctions. J Mol Biol. 2004;337:561-71 pubmed
  7. Kamau E, Bauerle K, Grove A. The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains. J Biol Chem. 2004;279:55234-40 pubmed
    ..The unique DNA binding properties of HMO1 are consistent with global roles in the maintenance of chromatin structure. ..
  8. Wang J, Pettis G. The tra locus of streptomycete plasmid pIJ101 mediates efficient transfer of a circular but not a linear version of the same replicon. Microbiology. 2010;156:2723-33 pubmed publisher
    ..The results here suggest that the conjugation mechanisms of linear versus circular DNA in Streptomyces spp. are inherently different and/or that efficient transfer of linear DNA requires additional components. ..
  9. Frey W, Kim J. APeg3: regulation of Peg3 through an evolutionarily conserved ncRNA. Gene. 2014;540:251-7 pubmed publisher
    ..The observed down-regulation by APeg3 is also somewhat orientation-independent. Overall, these results suggest that APeg3 has evolved as a ncRNA gene and controls the function of its sense gene Peg3 within specific neuronal cells. ..

More Information

Publications16

  1. Kim D, Shih D, Cho D, Swenson D. Helix-stabilizing compounds CC-1065 and U-71,184 bind to RNA-DNA and DNA-DNA duplexes containing modified internucleotide linkages and stabilize duplexes against thermal melting. Antisense Res Dev. 1995;5:49-57 pubmed
    ..The results show that CC-1065 and U-71,184 are capable of binding and stabilizing a variety of nucleic acid duplexes. These agents or their analogs may become useful ligands for antisense oligonucleotide applications. ..
  2. Ghosh S, Grove A. The Deinococcus radiodurans-encoded HU protein has two DNA-binding domains. Biochemistry. 2006;45:1723-33 pubmed
  3. Bauerle K, Kamau E, Grove A. Interactions between N- and C-terminal domains of the Saccharomyces cerevisiae high-mobility group protein HMO1 are required for DNA bending. Biochemistry. 2006;45:3635-45 pubmed
    ..Taken together, our data suggest that interactions between box A and the C-terminal tail induce a conformation that is required for DNA bending. ..
  4. Foltz D. An ancient repeat sequence in the ATP synthase beta-subunit gene of forcipulate sea stars. J Mol Evol. 2007;65:564-73 pubmed
    ..In four species, the repeat in one or both introns has apparently experienced gene conversion. The two introns also show a correlated pattern of nucleotide substitutions, even after excluding the putative cases of gene conversion. ..
  5. Kim J, Kim J. In vivo YY1 knockdown effects on genomic imprinting. Hum Mol Genet. 2008;17:391-401 pubmed
    ..In sum, these results demonstrate that YY1 indeed functions as a trans factor for transcriptional regulation and DNA methylation of these imprinted domains in vivo. ..
  6. Mukherjee A, Sokunbi A, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res. 2008;36:3956-68 pubmed publisher
    ..We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA. ..
  7. Xiao L, Williams A, Grove A. The C-terminal domain of yeast high mobility group protein HMO1 mediates lateral protein accretion and in-phase DNA bending. Biochemistry. 2010;49:4051-9 pubmed publisher
    ..This mode of binding is reminiscent of that proposed for the mammalian RNA polymerase I transcription factor UBF. ..