title: B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics.
abstract: The forced extension of a DNA segment is studied in a series of steered molecular dynamics simulations, employing a broad range of pulling forces. Throughout the entire force range, the formation of a zipper-like (zip-) DNA structure is observed. In that structure, first predicted by Lohikoski et al., the bases of the DNA strands interdigitate with each other and form a single-base aromatic stack. Similar motifs, albeit only a few base pairs in extent, have been observed in experimental crystal structures. Analysis of the dynamics of structural changes in pulled DNA shows that S-form DNA, thought to be adopted by DNA under applied force, serves as an intermediate between B-DNA and zip-DNA. Therefore, the phase transition plateau observed in force-extension curves of DNA is suggested to reflect the B-DNA to zip-DNA structural transition. Electronic structure analysis of purine bases in zip-DNA indicates a several-fold to order of magnitude increase in the π-π electronic coupling among nearest-neighbor nucleobases, compared to B-DNA. We further observe that zip-DNA does not require base pair complementarity between DNA strands, and we predict that the increased electronic coupling in zip-DNA will result in a much higher rate of charge transfer through an all-purine zip-DNA compared to B-DNA of equal length.
authors: Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. abalaeff@duke.edu
authors: Alexander
authors: A
authors: Balaeff
authors: Stephen L
authors: SL
authors: Craig
authors: David N
authors: DN
authors: Beratan
references: Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):422-31
references: 14993665
references: Phys Rev Lett. 2005 Oct 7;95(15):158102
references: 16241765
references: Science. 1996 Feb 9;271(5250):795-9
references: 8628994
references: J Biomol Struct Dyn. 1998 Dec;16(3):593-604
references: 10052616
references: J Comput Chem. 2005 Dec;26(16):1781-802
references: 16222654
references: J Phys Condens Matter. 2009 Jan 21;21(3):34114
references: 20046972
references: J Am Chem Soc. 2008 Sep 3;130(35):11752-61
references: 18693722
references: Biophys J. 2005 Mar;88(3):1684-91
references: 15626714
references: Nat Chem. 2011 Mar;3(3):228-33
references: 21336329
references: Biophys J. 2001 Feb;80(2):894-900
references: 11159456
references: Annu Rev Biochem. 2008;77:51-76
references: 18412538
references: Structure. 1998 Jul 15;6(7):849-61
references: 9687367
references: Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13196-201
references: 19666582
references: J Mol Biol. 1999 Jun 25;289(5):1301-26
references: 10373369
references: Chem Soc Rev. 2009 Jun;38(6):1714-25
references: 19587964
references: J Am Chem Soc. 2009 May 13;131(18):6498-507
references: 19382798
references: Acc Chem Res. 2009 Oct 20;42(10):1669-78
references: 19645446
references: Biophys J. 2001 Feb;80(2):874-81
references: 11159454
references: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references: 8744570
references: Curr Opin Chem Biol. 2010 Oct;14(5):597-607
references: 20869905
references: Nano Lett. 2008 Oct;8(10):3217-20
references: 18759487
references: Phys Rev Lett. 2006 May 5;96(17):178102
references: 16712339
references: Acc Chem Res. 2002 Mar;35(3):159-66
references: 11900519
references: J Am Chem Soc. 2008 Mar 26;130(12):3752-3
references: 18311981
references: Curr Opin Struct Biol. 2001 Apr;11(2):224-30
references: 11297932
references: Biochemistry. 1994 Nov 22;33(46):13540-6
references: 7947764
references: Trends Biochem Sci. 1998 Sep;23(9):341-7
references: 9787640
references: J Am Chem Soc. 2005 Oct 26;127(42):14894-903
references: 16231945
references: Biophys J. 2002 Jun;82(6):3160-9
references: 12023240
references: Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18231-6
references: 19841258
references: Phys Life Rev. 2010 Sep;7(3):299-341
references: 20576476
references: Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2010 Nov-Dec;2(6):648-69
references: 20730873
references: Science. 1994 Sep 9;265(5178):1599-600
references: 8079175
references: J Am Chem Soc. 2004 Mar 17;126(10):3038-9
references: 15012119
references: J Phys Condens Matter. 2009 Jan 21;21(3):034113
references: 21817258
references: J Am Chem Soc. 2011 Mar 16;133(10):3219-21
references: 21207940
references: Curr Opin Struct Biol. 2002 Jun;12(3):330-6
references: 12127451
references: Philos Trans A Math Phys Eng Sci. 2006 Dec 15;364(1849):3319-34
references: 17090462
references: Biophys J. 2001 Feb;80(2):882-93
references: 11159455
references: Nucleic Acids Res. 2005 Dec 14;33(22):7029-38
references: 16356925
references: Biophys J. 2000 Apr;78(4):1997-2007
references: 10733978
references: J Am Chem Soc. 2008 Apr 16;130(15):5157-66
references: 18324767
references: Science. 2007 May 25;316(5828):1144-8
references: 17525328
references: Phys Rev Lett. 2008 Sep 12;101(11):118101
references: 18851334
references: Biophys J. 2002 Mar;82(3):1537-53
references: 11867467
references: Nucleic Acids Res. 2010 Sep;38(16):5594-600
references: 20435680
references: Nucleic Acids Res. 1992 Jun 11;20(11):2803-12
references: 1614866
references: Annu Rev Biochem. 2004;73:705-48
references: 15189157
references: Annu Rev Phys Chem. 2007;58:535-64
references: 17134372
references: Nature. 1997 Jan 9;385(6612):176-81
references: 8990123
references: Science. 2000 Mar 31;287(5462):2497-500
references: 10741971
references: J Am Chem Soc. 2002 Dec 25;124(51):15174-5
references: 12487583
references: Biophys J. 2001 Apr;80(4):1932-9
references: 11259306
references: Annu Rev Phys Chem. 2010;61:461-85
references: 20192814
references: Science. 1996 Feb 9;271(5250):792-4
references: 8628993
references: Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11589-93
references: 16087871
references: Curr Opin Chem Biol. 2000 Oct;4(5):524-30
references: 11006539
references: Chem Biol. 1997 Jan;4(1):3-8
references: 9070421
references: Coord Chem Rev. 2011 Apr 1;255(7-8):635-648
references: 21528017
references: Annu Rev Biophys Biomol Struct. 2000;29:523-43
references: 10940258
references: Nat Struct Biol. 1999 Apr;6(4):346-9
references: 10201403
references: Science. 1992 Nov 13;258(5085):1122-6
references: 1439819
references: Phys Rev Lett. 2007 Jul 6;99(1):018302
references: 17678193
references: Nucleic Acids Res. 1996 Jun 15;24(12):2260-7
references: 8710494
references: Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13954-9
references: 17709749
references: J Am Chem Soc. 2001 Apr 11;123(14):3295-307
references: 11457065