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Items: 1 to 20 of 105

1.

The essential role of stacking adenines in a two-base-pair RNA kissing complex.

Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PT.

J Am Chem Soc. 2013 Apr 17;135(15):5602-11. doi: 10.1021/ja310820h.

2.
3.

Unusual mechanical stability of a minimal RNA kissing complex.

Li PT, Bustamante C, Tinoco I Jr.

Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15847-52.

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.

Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.

Chen AA, García AE.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):E1530-9. doi: 10.1073/pnas.1119552109.

6.
7.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

Di Palma F, Bottaro S, Bussi G.

BMC Bioinformatics. 2015;16 Suppl 9:S6. doi: 10.1186/1471-2105-16-S9-S6.

8.

Interactions of cations with RNA loop-loop complexes.

Singh A, Sethaphong L, Yingling YG.

Biophys J. 2011 Aug 3;101(3):727-35. doi: 10.1016/j.bpj.2011.06.033.

9.

NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA.

Mujeeb A, Parslow TG, Zarrinpar A, Das C, James TL.

FEBS Lett. 1999 Sep 24;458(3):387-92.

10.

Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics.

Sarzyńska J, Réblová K, Sponer J, Kuliński T.

Biopolymers. 2008 Sep;89(9):732-46. doi: 10.1002/bip.21001.

PMID:
18412127
11.

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J.

J Phys Chem B. 2015 Dec 10;119(49):15176-90. doi: 10.1021/acs.jpcb.5b08876.

PMID:
26548477
12.

A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.

Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J.

J Phys Chem B. 2011 Dec 1;115(47):13897-910. doi: 10.1021/jp2065584.

PMID:
21999672
13.

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex.

Van Melckebeke H, Devany M, Di Primo C, Beaurain F, Toulmé JJ, Bryce DL, Boisbouvier J.

Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9210-5. doi: 10.1073/pnas.0712121105.

14.
15.

Solution structure of a five-adenine bulge loop within a DNA duplex.

Dornberger U, Hillisch A, Gollmick FA, Fritzsche H, Diekmann S.

Biochemistry. 1999 Sep 28;38(39):12860-8.

PMID:
10504256
16.

The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues.

Shi K, Biswas R, Mitra SN, Sundaralingam M.

J Mol Biol. 2000 May 26;299(1):113-22.

PMID:
10860726
17.

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study.

Allnér O, Nilsson L, Villa A.

RNA. 2013 Jul;19(7):916-26. doi: 10.1261/rna.037549.112.

18.

A retroviral RNA kissing complex containing only two G.C base pairs.

Kim CH, Tinoco I Jr.

Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9396-401.

19.

The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA.

Liu JD, Zhao L, Xia T.

Biochemistry. 2008 Jun 3;47(22):5962-75. doi: 10.1021/bi800210t.

PMID:
18457418
20.

The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks.

Butcher SE, Pyle AM.

Acc Chem Res. 2011 Dec 20;44(12):1302-11. doi: 10.1021/ar200098t.

PMID:
21899297

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