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Items: 1 to 50 of 116

1.

Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding.

Trachman RJ 3rd, Draper DE.

Nucleic Acids Res. 2017 May 5;45(8):4733-4742. doi: 10.1093/nar/gkw1327.

2.

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX.

Nature. 2017 Jan 12;541(7636):242-246. doi: 10.1038/nature20599. Epub 2016 Nov 14.

3.

Reflections on 20 years of RNA.

Draper DE.

RNA. 2015 Apr;21(4):601-2. doi: 10.1261/rna.050930.115. No abstract available.

4.
5.

Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water.

Draper DE.

Biopolymers. 2013 Dec;99(12):1105-13. doi: 10.1002/bip.22249. Review.

6.
7.

Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure.

Leipply D, Draper DE.

J Am Chem Soc. 2011 Aug 31;133(34):13397-405. doi: 10.1021/ja2020923. Epub 2011 Aug 4.

8.

Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA.

Leipply D, Draper DE.

Biochemistry. 2011 Apr 12;50(14):2790-9. doi: 10.1021/bi101948k. Epub 2011 Mar 21.

9.

The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration.

Lambert D, Leipply D, Draper DE.

J Mol Biol. 2010 Nov 19;404(1):138-57. doi: 10.1016/j.jmb.2010.09.043. Epub 2010 Sep 25.

10.
11.

Diagnostic usefulness of graded exercise testing in pediatric supraventricular tachycardia.

Draper DE, Giddins NG, McCort J, Gross GJ.

Can J Cardiol. 2009 Jul;25(7):407-10.

12.

Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

Chen AA, Draper DE, Pappu RV.

J Mol Biol. 2009 Jul 24;390(4):805-19. doi: 10.1016/j.jmb.2009.05.071. Epub 2009 May 29.

13.

The influence of monovalent cation size on the stability of RNA tertiary structures.

Lambert D, Leipply D, Shiman R, Draper DE.

J Mol Biol. 2009 Jul 24;390(4):791-804. doi: 10.1016/j.jmb.2009.04.083. Epub 2009 May 7.

14.

Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye.

Grilley D, Soto AM, Draper DE.

Methods Enzymol. 2009;455:71-94. doi: 10.1016/S0076-6879(08)04203-1.

15.

Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria.

Leipply D, Lambert D, Draper DE.

Methods Enzymol. 2009;469:433-63. doi: 10.1016/S0076-6879(09)69021-2. Epub 2009 Nov 17.

16.

RNA folding: thermodynamic and molecular descriptions of the roles of ions.

Draper DE.

Biophys J. 2008 Dec 15;95(12):5489-95. doi: 10.1529/biophysj.108.131813. Epub 2008 Oct 3. Review.

17.

Thermal methods for the analysis of RNA folding pathways.

Draper DE, Bukhman YV, Gluick TC.

Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 11:Unit 11.3. doi: 10.1002/0471142700.nc1103s02.

PMID:
18428829
18.

Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11.

Iben JR, Draper DE.

Biochemistry. 2008 Mar 4;47(9):2721-31. doi: 10.1021/bi701838y. Epub 2008 Feb 5.

PMID:
18247578
19.

Importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg2+ interactions.

Grilley D, Misra V, Caliskan G, Draper DE.

Biochemistry. 2007 Sep 11;46(36):10266-78. Epub 2007 Aug 18.

PMID:
17705557
20.

Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions.

Lambert D, Draper DE.

J Mol Biol. 2007 Jul 27;370(5):993-1005. Epub 2007 May 5.

21.

Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions.

Soto AM, Misra V, Draper DE.

Biochemistry. 2007 Mar 20;46(11):2973-83. Epub 2007 Feb 23.

PMID:
17315982
22.

The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.

Lee D, Walsh JD, Yu P, Markus MA, Choli-Papadopoulou T, Schwieters CD, Krueger S, Draper DE, Wang YX.

J Mol Biol. 2007 Apr 6;367(4):1007-22. Epub 2007 Jan 10.

23.

Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures.

Grilley D, Soto AM, Draper DE.

Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14003-8. Epub 2006 Sep 11.

24.

Optimization of a ribosomal structural domain by natural selection.

Maeder C, Conn GL, Draper DE.

Biochemistry. 2006 May 30;45(21):6635-43.

25.
26.

Interactions of the N-terminal domain of ribosomal protein L11 with thiostrepton and rRNA.

Bausch SL, Poliakova E, Draper DE.

J Biol Chem. 2005 Aug 19;280(33):29956-63. Epub 2005 Jun 22.

27.

Ions and RNA folding.

Draper DE, Grilley D, Soto AM.

Annu Rev Biophys Biomol Struct. 2005;34:221-43. Review.

PMID:
15869389
28.

Coevolution of protein and RNA structures within a highly conserved ribosomal domain.

Dunstan MS, Guhathakurta D, Draper DE, Conn GL.

Chem Biol. 2005 Feb;12(2):201-6.

29.

A guide to ions and RNA structure.

Draper DE.

RNA. 2004 Mar;10(3):335-43. Review.

30.

Electrostatic interactions in a peptide--RNA complex.

García-García C, Draper DE.

J Mol Biol. 2003 Aug 1;331(1):75-88.

PMID:
12875837
31.

A thermodynamic framework for the magnesium-dependent folding of RNA.

Misra VK, Shiman R, Draper DE.

Biopolymers. 2003 May;69(1):118-36.

32.

A compact RNA tertiary structure contains a buried backbone-K+ complex.

Conn GL, Gittis AG, Lattman EE, Misra VK, Draper DE.

J Mol Biol. 2002 May 10;318(4):963-73.

PMID:
12054794
33.

The linkage between magnesium binding and RNA folding.

Misra VK, Draper DE.

J Mol Biol. 2002 Apr 5;317(4):507-21.

PMID:
11955006
34.

Review of the sixth Annual Johns Hopkins Folding Meeting.

Lattman EE, Draper DE.

Proteins. 2002 Feb 15;46(3):237-42. No abstract available.

PMID:
11835498
35.

A thermodynamic framework for Mg2+ binding to RNA.

Misra VK, Draper DE.

Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12456-61.

36.

Translational repression of the Escherichia coli alpha operon mRNA: importance of an mRNA conformational switch and a ternary entrapment complex.

Schlax PJ, Xavier KA, Gluick TC, Draper DE.

J Biol Chem. 2001 Oct 19;276(42):38494-501. Epub 2001 Aug 14.

37.

Recognition of 16S rRNA by ribosomal protein S4 from Bacillus stearothermophilus.

Gerstner RB, Pak Y, Draper DE.

Biochemistry. 2001 Jun 19;40(24):7165-73.

PMID:
11401563
38.

Structural preordering in the N-terminal region of ribosomal protein S4 revealed by heteronuclear NMR spectroscopy.

Sayers EW, Gerstner RB, Draper DE, Torchia DA.

Biochemistry. 2000 Nov 7;39(44):13602-13.

PMID:
11063598
39.

Stabilization of RNA tertiary structure by monovalent cations.

Shiman R, Draper DE.

J Mol Biol. 2000 Sep 8;302(1):79-91.

PMID:
10964562
40.

Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.

Misra VK, Draper DE.

J Mol Biol. 2000 Jun 9;299(3):813-25.

PMID:
10835286
41.
42.

Contributions of basic residues to ribosomal protein L11 recognition of RNA.

GuhaThakurta D, Draper DE.

J Mol Biol. 2000 Jan 21;295(3):569-80.

PMID:
10623547
43.

The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory.

Misra VK, Draper DE.

J Mol Biol. 1999 Dec 17;294(5):1135-47.

PMID:
10600372
44.

Themes in RNA-protein recognition.

Draper DE.

J Mol Biol. 1999 Oct 22;293(2):255-70. Review.

PMID:
10550207
45.
46.

A complete conformational map for RNA.

Murthy VL, Srinivasan R, Draper DE, Rose GD.

J Mol Biol. 1999 Aug 13;291(2):313-27.

PMID:
10438623
47.

On the role of magnesium ions in RNA stability.

Misra VK, Draper DE.

Biopolymers. 1998;48(2-3):113-35. Review.

PMID:
10333741
48.

Crystal structure of a conserved ribosomal protein-RNA complex.

Conn GL, Draper DE, Lattman EE, Gittis AG.

Science. 1999 May 14;284(5417):1171-4.

49.

Protein-RNA sequence covariation in a ribosomal protein-rRNA complex.

GuhaThakurta D, Draper DE.

Biochemistry. 1999 Mar 23;38(12):3633-40.

PMID:
10090750
50.

RNA binding strategies of ribosomal proteins.

Draper DE, Reynaldo LP.

Nucleic Acids Res. 1999 Jan 15;27(2):381-8. Review.

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