title: The contribution of phosphate-phosphate repulsions to the free energy of DNA bending.
abstract: DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate-phosphate repulsions. In the present work, the electrostatic contribution of phosphate-phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate-phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate-phosphate repulsions account for approximately 30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.
authors.affiliation: Department of Chemistry, University of Minnesota 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Range
authors.forename: Evelyn
authors.initials: E
authors.lastname: Mayaan
authors.forename: L J
authors.initials: LJ
authors.lastname: Maher
authors.forename: Darrin M
authors.initials: DM
authors.lastname: York
mesh_terms: D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D007477:Ions; D010710:Phosphates; D012997:Solvents; D004247:DNA
references.citation: Biophys J. 1995 Mar;68(3):1063-72
references.pmid: 7756526
references.citation: Science. 1995 May 26;268(5214):1144-9
references.pmid: 7761829
references.citation: Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):7060-4
references.pmid: 7624369
references.citation: Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2511-6
references.pmid: 8637905
references.citation: Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6185-90
references.pmid: 9177192
references.citation: Nature. 2003 Jan 23;421(6921):427-31
references.pmid: 12540916
references.citation: Nucleic Acids Res. 2003 Feb 1;31(3):1059-66
references.pmid: 12560504
references.citation: Nature. 2003 May 8;423(6936):145-50
references.pmid: 12736678
references.citation: J Mol Biol. 2003 Jul 25;330(5):993-1004
references.pmid: 12860122
references.citation: Nucleic Acids Res. 2003 Sep 1;31(17):5108-21
references.pmid: 12930962
references.citation: Biochemistry. 1998 Jan 27;37(4):1060-6
references.pmid: 9454597
references.citation: Nucleic Acids Res. 1998 May 15;26(10):2298-305
references.pmid: 9580678
references.citation: Biochemistry. 1998 Jun 9;37(23):8341-55
references.pmid: 9622486
references.citation: Biophys J. 1998 Jun;74(6):3152-64
references.pmid: 9635768
references.citation: Biophys J. 1998 Jul;75(1):372-81
references.pmid: 9649394
references.citation: Biophys Chem. 1998 Jun 9;72(3):297-306
references.pmid: 9691271
references.citation: J Mol Biol. 1998 Aug 28;281(4):675-87
references.pmid: 9710539
references.citation: Biochemistry. 1997 Jul 22;36(29):8692-8
references.pmid: 9220955
references.citation: Annu Rev Biophys Biomol Struct. 1997;26:139-56
references.pmid: 9241416
references.citation: Biochemistry. 1997 Aug 19;36(33):10026-32
references.pmid: 9254597
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: J Biol Chem. 1997 Dec 12;272(50):31570-5
references.pmid: 9395494
references.citation: Nucleic Acids Res. 2002 Aug 15;30(16):3615-23
references.pmid: 12177304
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Jul;66(1 Pt 1):011918
references.pmid: 12241395
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
references.pmid: 9736707
references.citation: Biochemistry. 1998 Dec 1;37(48):16877-87
references.pmid: 9836580
references.citation: Biochemistry. 1998 Dec 22;37(51):18094-101
references.pmid: 9922178
references.citation: Curr Opin Struct Biol. 1999 Jun;9(3):298-304
references.pmid: 10361089
references.citation: Trends Biotechnol. 1999 Nov;17(11):437-43
references.pmid: 10511701
references.citation: Biophys J. 1999 Oct;77(4):1769-81
references.pmid: 10512802
references.citation: Curr Opin Struct Biol. 2000 Apr;10(2):182-96
references.pmid: 10753816
references.citation: Curr Opin Struct Biol. 2000 Jun;10(3):286-97
references.pmid: 10851199
references.citation: Annu Rev Biophys Biomol Struct. 2000;29:497-521
references.pmid: 10940257
references.citation: Trends Biochem Sci. 2000 Sep;25(9):453-5
references.pmid: 10973060
references.citation: Phys Rev Lett. 2000 Nov 13;85(20):4389-92
references.pmid: 11060645
references.citation: J Mol Biol. 2000 Dec 15;304(5):803-20
references.pmid: 11124028
references.citation: Biopolymers. 2000-2001;56(4):232-56
references.pmid: 11754338
references.citation: J Am Chem Soc. 2002 May 1;124(17):4838-47
references.pmid: 11971734
references.citation: Nucleic Acids Res. 2002 May 1;30(9):1879-85
references.pmid: 11972323
references.citation: Nucleic Acids Res. 2003 Oct 15;31(20):5971-81
references.pmid: 14530445
references.citation: Biophys J. 2003 Nov;85(5):2872-83
references.pmid: 14581192
references.citation: J Am Chem Soc. 2003 Dec 10;125(49):15087-92
references.pmid: 14653743
references.citation: Structure. 2004 Jan;12(1):113-22
references.pmid: 14725771
references.citation: Biopolymers. 2004 Feb 15;73(3):369-79
references.pmid: 14755573
references.citation: Biopolymers. 2004 Feb 15;73(3):380-403
references.pmid: 14755574
references.citation: Nucleic Acids Res. 2004;32(8):2298-305
references.pmid: 15118075
references.citation: Biochemistry. 2004 Jun 8;43(22):6841-57
references.pmid: 15170321
references.citation: Biochemistry. 2004 Jun 8;43(22):7090-101
references.pmid: 15170346
references.citation: Proteins. 2004 Sep 1;56(4):724-37
references.pmid: 15281126
references.citation: Nucleic Acids Res. 2004;32(13):4055-9
references.pmid: 15289578
references.citation: Biophys J. 2004 Aug;87(2):764-7
references.pmid: 15298885
references.citation: Biophys J. 2004 Aug;87(2):800-11
references.pmid: 15298889
references.citation: Nucleic Acids Res. 2004;32(14):4269-80
references.pmid: 15304564
references.citation: Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9
references.pmid: 5040245
references.citation: J Mol Biol. 1985 Aug 5;184(3):503-16
references.pmid: 4046024
references.citation: Proteins. 1986 Sep;1(1):47-59
references.pmid: 3449851
references.citation: Proteins. 1988;4(2):148-56
references.pmid: 3227015
references.citation: Proc Natl Acad Sci U S A. 1989 Oct;86(20):7766-70
references.pmid: 2813356
references.citation: J Biomol Struct Dyn. 1989 Apr;6(5):877-89
references.pmid: 2590506
references.citation: Annu Rev Biophys Biophys Chem. 1990;19:423-65
references.pmid: 2194482
references.citation: Biopolymers. 1991 Nov;31(13):1471-81
references.pmid: 1814499
references.citation: Biopolymers. 1991 Nov;31(13):1559-64
references.pmid: 1814504
references.citation: Biopolymers. 1991 Nov;31(13):1593-604
references.pmid: 1814506
references.citation: Biophys J. 1993 Oct;65(4):1363-70
references.pmid: 8274630
references.citation: Biochemistry. 1994 Mar 15;33(10):2997-3006
references.pmid: 8130213
references.citation: Cold Spring Harb Symp Quant Biol. 1993;58:115-22
references.pmid: 7956021
references.citation: Science. 1994 Dec 16;266(5192):1829-34
references.pmid: 7997878
references.citation: Nature. 1995 Feb 23;373(6516):724-7
references.pmid: 7854460
references.citation: Biophys J. 1995 Feb;68(2):634-47
references.pmid: 7696515