IBBR Publications

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.

Jain V, Hilton B, Lin B, Jain A, Mackerell AD, Zou Y, Cho BP. Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence. Chem Res Toxicol. 2013 ;26(8):1251-62.

Wang X, Culver JN. DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus. BMC Plant Biol. 2012 ;12:157.

Esnault C, Palavesam A, Pilitt K, O'Brochta DA. Intrinsic characteristics of neighboring DNA modulate transposable element activity in Drosophila melanogaster. Genetics. 2011 ;187(1):319-31.

Brinson RG, Szakal AL. Structural characterization of the viral and cRNA panhandle motifs from the infectious salmon anemia virus. J Virol. 2011 ;85(24):13398-408.

Banavali NK, Mackerell AD. Characterizing structural transitions using localized free energy landscape analysis. PLoS One. 2009 ;4(5):e5525.

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.

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.

Macias AT, Banavali NK, Mackerell AD. DNA bending induced by carbocyclic sugar analogs constrained to the north conformation. Biopolymers. 2007 ;85(5-6):438-49.

U Priyakumar D, Mackerell AD. NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J Am Chem Soc. 2006 ;128(3):678-9.

Huang N, Mackerell AD. Atomistic view of base flipping in DNA. Philos Trans A Math Phys Eng Sci. 2004 ;362(1820):1439-60.

Pan Y, Mackerell AD. Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res. 2003 ;31(24):7131-40.

Huang N, Banavali NK, Mackerell AD. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A. 2003 ;100(1):68-73.

Banavali NK, Mackerell AD. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol. 2002 ;319(1):141-60.

Luy B, Richter U, DeJong ES, Sørensen OW, Marino JP. Observation of H-bond mediated 3hJH2H3 coupling constants across Watson-Crick AU base pairs in RNA. J Biomol NMR. 2002 ;24(2):133-42.

Barsky D, Foloppe N, Ahmadia S, Wilson DM, Mackerell AD. New insights into the structure of abasic DNA from molecular dynamics simulations. Nucleic Acids Res. 2000 ;28(13):2613-26.