Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 101

1.

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T 3rd, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, Singh T, Spackova N, Sponer J.

Nucleic Acids Res. 2010 Jan;38(1):299-313. doi: 10.1093/nar/gkp834. Epub 2009 Oct 22.

2.

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
3.

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.

Dixit SB, Beveridge DL, Case DA, Cheatham TE 3rd, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P.

Biophys J. 2005 Dec;89(6):3721-40. Epub 2005 Sep 16.

4.

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
5.

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.

Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T 3rd, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevičiūtė D, Spackova N, Sponer J, Zakrzewska K, Lavery R.

Nucleic Acids Res. 2014 Oct 29;42(19):12272-83. doi: 10.1093/nar/gku855. Epub 2014 Sep 26.

7.

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair.

Wang Y, Wang Z, Wang Y, Liu T, Zhang W.

J Chem Phys. 2018 Jan 28;148(4):045101. doi: 10.1063/1.5013282.

PMID:
29390847
8.

A sequence-dependent rigid-base model of DNA.

Gonzalez O, Petkevičiūtė D, Maddocks JH.

J Chem Phys. 2013 Feb 7;138(5):055102. doi: 10.1063/1.4789411.

PMID:
23406150
9.

Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability.

Doktycz MJ, Morris MD, Dormady SJ, Beattie KL, Jacobson KB.

J Biol Chem. 1995 Apr 14;270(15):8439-45.

11.

Effect of structural dynamics and base pair sequence on the nature of excited states in DNA hairpins.

Patwardhan S, Tonzani S, Lewis FD, Siebbeles LD, Schatz GC, Grozema FC.

J Phys Chem B. 2012 Sep 20;116(37):11447-58. Epub 2012 Sep 10.

PMID:
22889328
12.

DNA deformability at the base pair level.

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

J Am Chem Soc. 2004 Apr 7;126(13):4124-5.

PMID:
15053599
13.

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.

Blose JM, Manni ML, Klapec KA, Stranger-Jones Y, Zyra AC, Sim V, Griffith CA, Long JD, Serra MJ.

Biochemistry. 2007 Dec 25;46(51):15123-35. Epub 2007 Nov 30.

14.

On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics.

Fadda E, Pomès R.

Nucleic Acids Res. 2011 Jan;39(2):767-80. doi: 10.1093/nar/gkq812. Epub 2010 Sep 28.

15.

Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility.

McConnell KJ, Beveridge DL.

J Mol Biol. 2001 Nov 16;314(1):23-40.

PMID:
11724529
16.
17.

Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data.

Gray DM, Gray CW, Yoo BH, Lou TF.

BMC Bioinformatics. 2010 May 14;11:252. doi: 10.1186/1471-2105-11-252.

18.
19.

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.

Zgarbová M, Jurečka P, Lankaš F, Cheatham TE 3rd, Šponer J, Otyepka M.

J Chem Inf Model. 2017 Feb 27;57(2):275-287. doi: 10.1021/acs.jcim.6b00621. Epub 2017 Jan 20.

PMID:
28059516
20.

Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability.

Vallone PM, Paner TM, Hilario J, Lane MJ, Faldasz BD, Benight AS.

Biopolymers. 1999 Oct 5;50(4):425-42.

PMID:
10423551

Supplemental Content

Support Center