IBBR Publications

Found 40 results
Filters: Keyword is RNA  [Clear All Filters]
2016
Xu Y, Vanommeslaeghe K, Aleksandrov A, Mackerell AD, Nilsson L. Additive CHARMM force field for naturally occurring modified ribonucleotides. J Comput Chem. 2016 ;37(10):896-912.
2015
Kasavajhala K, Bikkina S, Patil I, Mackerell AD, U Priyakumar D. Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution. J Phys Chem B. 2015 ;119(9):3755-61.
2013
Denning EJ, Thirumalai D, Mackerell AD. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophys Chem. 2013 ;184:8-16.
2012
Stagno JR, Ma B, Li J, Altieri AS, R Byrd A, Ji X. Crystal structure of a plectonemic RNA supercoil. Nat Commun. 2012 ;3:901.
Denning EJ, Mackerell AD. Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. J Am Chem Soc. 2012 ;134(5):2800-6.
2011
Denning EJ, U Priyakumar D, Nilsson L, Mackerell AD. Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem. 2011 ;32(9):1929-43.
Nuss DL. Mycoviruses, RNA silencing, and viral RNA recombination. Adv Virus Res. 2011 ;80:25-48.
Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, R Byrd A, Ji X. Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic Acids Res. 2011 ;39(17):7803-15.
2010
Zucconi BE, Ballin JD, Brewer BY, Ross CR, Huang J, Toth EA, Wilson GM. Alternatively expressed domains of AU-rich element RNA-binding protein 1 (AUF1) regulate RNA-binding affinity, RNA-induced protein oligomerization, and the local conformation of bound RNA ligands. J Biol Chem. 2010 ;285(50):39127-39.
Ballin JD, Prevas JP, Ross CR, Toth EA, Wilson GM, M Record T. Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH. Biochemistry. 2010 ;49(9):2018-30.
2009
Grishaev A, Yao L, Ying J, Pardi A, Bax A. Chemical shift anisotropy of imino 15N nuclei in Watson-Crick base pairs from magic angle spinning liquid crystal NMR and nuclear spin relaxation. J Am Chem Soc. 2009 ;131(27):9490-1.
Brinson RG, Turner KB, Yi-Brunozzi HYoung, Le Grice SFJ, Fabris D, Marino JP. Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B. Biochemistry. 2009 ;48(29):6988-97.
Turner KB, Yi-Brunozzi HYoung, Brinson RG, Marino JP, Fabris D, Le Grice SFJ. SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA. 2009 ;15(8):1605-13.
U Priyakumar D, Hyeon C, Thirumalai D, Mackerell AD. Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. J Am Chem Soc. 2009 ;131(49):17759-61.
2008
U Priyakumar D, Mackerell AD. Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study. J Phys Chem B. 2008 ;112(5):1515-24.
Zhang X, Nuss DL. A host dicer is required for defective viral RNA production and recombinant virus vector RNA instability for a positive sense RNA virus. Proc Natl Acad Sci U S A. 2008 ;105(43):16749-54.
Struble EB, Ladner JE, Brabazon DM. New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition. Proteins. 2008 ;72(2):761-8.
2006
Ying J, Grishaev A, Bryce DL, Bax A. Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements. J Am Chem Soc. 2006 ;128(35):11443-54.
U Priyakumar D, Mackerell AD. Computational approaches for investigating base flipping in oligonucleotides. Chem Rev. 2006 ;106(2):489-505.
Shin J-H, Kelman Z. The replicative helicases of bacteria, archaea, and eukarya can unwind RNA-DNA hybrid substrates. J Biol Chem. 2006 ;281(37):26914-21.
2005
Pan Y, U Priyakumar D, Mackerell AD. Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations. Biochemistry. 2005 ;44(5):1433-43.
Bryce DL, Grishaev A, Bax A. Measurement of ribose carbon chemical shift tensors for A-form RNA by liquid crystal NMR spectroscopy. J Am Chem Soc. 2005 ;127(20):7387-96.
Yi-Brunozzi HYoung, Brabazon DM, Lener D, Le Grice SFJ, Marino JP. A ribose sugar conformational switch in the LTR-retrotransposon Ty3 polypurine tract-containing RNA/DNA hybrid. J Am Chem Soc. 2005 ;127(47):16344-5.
2004
Segers GC, Regier JC, Nuss DL. Evidence for a role of the regulator of G-protein signaling protein CPRGS-1 in Galpha subunit CPG-1-mediated regulation of fungal virulence, conidiation, and hydrophobin synthesis in the chestnut blight fungus Cryphonectria parasitica. Eukaryot Cell. 2004 ;3(6):1454-63.
Yi H, Wu L-Q, Ghodssi R, Rubloff GW, Payne GF, Bentley WE. A robust technique for assembly of nucleic acid hybridization chips based on electrochemically templated chitosan. Anal Chem. 2004 ;76(2):365-72.