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Items: 1 to 20 of 114

1.

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study.

Mukherjee S, Kailasam S, Bansal M, Bhattacharyya D.

Biopolymers. 2014 Jan;101(1):107-20. doi: 10.1002/bip.22289.

PMID:
23722519
2.

Stacking interactions in RNA and DNA: Roll-slide energy hyperspace for ten unique dinucleotide steps.

Mukherjee S, Kailasam S, Bansal M, Bhattacharyya D.

Biopolymers. 2015 Mar;103(3):134-47. doi: 10.1002/bip.22566.

PMID:
25257334
3.

Sequence-dependent DNA structure: the role of the sugar-phosphate backbone.

Packer MJ, Hunter CA.

J Mol Biol. 1998 Jul 17;280(3):407-20.

PMID:
9665845
4.

Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

Svozil D, Hobza P, Sponer J.

J Phys Chem B. 2010 Jan 21;114(2):1191-203. doi: 10.1021/jp910788e. Erratum in: J Phys Chem B. 2010 Feb 25;114(7):2547.

PMID:
20000584
5.

Stacking geometry for non-canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion-corrected DFT-D study.

Mondal M, Mukherjee S, Halder S, Bhattacharyya D.

Biopolymers. 2015 Jun;103(6):328-38. doi: 10.1002/bip.22616.

PMID:
25652776
6.

Sequence-dependent DNA structure. The role of base stacking interactions.

Hunter CA.

J Mol Biol. 1993 Apr 5;230(3):1025-54.

PMID:
8478917
7.

Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs.

Mondal M, Halder S, Chakrabarti J, Bhattacharyya D.

Biopolymers. 2016 Apr;105(4):212-26. doi: 10.1002/bip.22787.

PMID:
26600167
8.

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale.

Mohanty D, Bansal M.

J Biomol Struct Dyn. 1991 Aug;9(1):127-42.

PMID:
1781943
9.

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers.

Yanagi K, Privé GG, Dickerson RE.

J Mol Biol. 1991 Jan 5;217(1):201-14.

PMID:
1988678
10.

Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.

Kailasam S, Bhattacharyya D, Bansal M.

BMC Res Notes. 2014 Feb 7;7:83. doi: 10.1186/1756-0500-7-83.

12.

Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids.

Kimsey I, Al-Hashimi HM.

Curr Opin Struct Biol. 2014 Feb;24:72-80. doi: 10.1016/j.sbi.2013.12.003. Epub 2014 Jan 9. Review.

14.

Sequence-dependent DNA structure: tetranucleotide conformational maps.

Packer MJ, Dauncey MP, Hunter CA.

J Mol Biol. 2000 Jan 7;295(1):85-103.

PMID:
10623510
15.

Solution structure of [d(GCGTATACGC)]2.

Cheng JW, Chou SH, Salazar M, Reid BR.

J Mol Biol. 1992 Nov 5;228(1):118-37.

PMID:
1447776
16.

Analysis of stacking overlap in nucleic acid structures: algorithm and application.

Pingali PK, Halder S, Mukherjee D, Basu S, Banerjee R, Choudhury D, Bhattacharyya D.

J Comput Aided Mol Des. 2014 Aug;28(8):851-67. doi: 10.1007/s10822-014-9767-6. Epub 2014 Jul 3.

PMID:
24990628
17.
18.

DNA basepair step deformability inferred from molecular dynamics simulations.

Lankas F, Sponer J, Langowski J, Cheatham TE 3rd.

Biophys J. 2003 Nov;85(5):2872-83.

19.

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures.

Bansal M, Bhattacharyya D, Ravi B.

Comput Appl Biosci. 1995 Jun;11(3):281-7.

PMID:
7583696
20.

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study.

Reha D, Kabelác M, Ryjácek F, Sponer J, Sponer JE, Elstner M, Suhai S, Hobza P.

J Am Chem Soc. 2002 Apr 3;124(13):3366-76. Erratum in: J Am Chem Soc. 2003 May 7;125(18):folllowing 5580.

PMID:
11916422
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