title: Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings.
abstract: Hydrogen-bonding, intrastrand base-stacking, and interstrand base-stacking energies were calculated for RNA and DNA dimers at the MP2(full)/6-311G** level of theory. Standard A-form RNA and B-form DNA geometries from average fiber diffraction data were employed for all base monomer and dimer geometries, and all dimer binding energies were obtained via single-point calculations. The effects of water solvation were considered using the PCM model. The resulting dimer binding energies were used to calculate the 10 unique RNA and 10 unique DNA computational nearest-neighbor energies, and the ranking of these computational nearest neighbor energies are in excellent agreement with the ranking of the experimental nearest-neighbor free energies. These results dispel the notion that average fiber diffraction geometries are insufficient for calculating RNA and DNA stacking energies.
authors: Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, USA.
authors: Charles A
authors: CA
authors: Johnson
authors: Richard J
authors: RJ
authors: Bloomingdale
authors: Vikram E
authors: VE
authors: Ponnusamy
authors: Conor A
authors: CA
authors: Tillinghast
authors: Brent M
authors: BM
authors: Znosko
authors: Michael
authors: M
authors: Lewis
references: Phys Chem Chem Phys. 2008 May 21;10(19):2595-610
references: 18464974
references: Nucleic Acids Res. 2009 Aug;37(15):4898-918
references: 19528080
references: J Chem Phys. 2007 Aug 21;127(7):075104
references: 17718635
references: Biochemistry. 1998 Oct 20;37(42):14719-35
references: 9778347
references: Chem Rev. 1999 Nov 10;99(11):3247-76
references: 11749516
references: J Am Chem Soc. 2008 Jan 30;130(4):1304-8
references: 18163624
references: J Am Chem Soc. 2011 Mar 23;133(11):3854-62
references: 21361361
references: J Phys Chem B. 2008 Aug 7;112(31):9484-9
references: 18636761
references: Biochemistry. 1996 Mar 19;35(11):3555-62
references: 8639506
references: J Phys Chem B. 2006 Aug 17;110(32):15650-3
references: 16898705
references: J Am Chem Soc. 2008 Feb 13;130(6):1802-3
references: 18201088
references: J Chem Theory Comput. 2008 Dec 9;4(12):1996-2000
references: 26620472
references: Chemistry. 2005 Jul 18;11(15):4340-8
references: 15880545
references: Chemistry. 2006 Mar 20;12(10):2854-65
references: 16425171
references: Biochemistry. 2007 Apr 17;46(15):4625-34
references: 17378583
references: J Am Chem Soc. 2006 Sep 13;128(36):11730-1
references: 16953592
references: J Chem Inf Model. 2010 Dec 27;50(12):2151-61
references: 21090609
references: J Mol Biol. 2001 Oct 12;313(1):229-37
references: 11601858
references: Phys Chem Chem Phys. 2008 May 21;10(19):2665-72
references: 18464981
references: J Phys Chem B. 2010 Jan 21;114(2):1191-203
references: 20000584
references: J Phys Chem B. 2009 Apr 9;113(14):4907-14
references: 19284733
references: J Phys Chem A. 2010 Dec 30;114(51):13442-4
references: 21133342
references: Chem Rev. 1999 Aug 11;99(8):2161-2200
references: 11849023