title: Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns.
abstract: The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical X-ray diffraction patterns of DNA contain information about the flexibility, interactions and sequence-related variations encoded within the helical structure. To extract this information, we have developed a new diffraction theory that accounts for these effects. We show how double helix non-ideality and fluctuations broaden the diffraction peaks. Meridional intensity profiles of the peaks at the first three helical layer lines reveal information about structural adaptation and intermolecular interactions. The meridional width of the fifth layer line peaks is inversely proportional to the helical coherence length that characterizes sequence-related and thermal variations in the double helix structure. Analysis of measured fiber diffraction patterns based on this theory yields important parameters that control DNA structure, packing and function.
authors: Department of Chemistry, Faculty of Natural Sciences, Imperial College London, SW7 2AZ, London, UK. a.kornyshev@imperial.ac.uk
authors: A A
authors: AA
authors: Kornyshev
authors: D J
authors: DJ
authors: Lee
authors: A
authors: A
authors: Wynveen
authors: S
authors: S
authors: Leikin
references: Nature. 1953 Apr 25;171(4356):738-40
references: 13054693
references: Acta Crystallogr A. 1994 Sep 1;50 ( Pt 5):644-6
references: 7946155
references: Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19824-9
references: 19903884
references: Biophys J. 1992 Jan;61(1):246-59
references: 1540693
references: J Phys Chem B. 2008 Jan 31;112(4):1060-4
references: 18181611
references: Biopolymers. 1997;44(3):269-82
references: 9591479
references: Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20274-9
references: 19074292
references: Proc Natl Acad Sci U S A. 1984 May;81(9):2621-5
references: 6585818
references: Nature. 1953 Apr 25;171(4356):737-8
references: 13054692
references: Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6492-6
references: 1631148
references: Annu Rev Genet. 1999;33:603-754
references: 10690419
references: Phys Rev Lett. 2005 Sep 30;95(14):148102
references: 16241694
references: Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4683-8
references: 19273848
references: Biophys J. 2008 Jun;94(12):4775-82
references: 18326632
references: Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2312-6
references: 2006170
references: Proc Natl Acad Sci U S A. 1978 Feb;75(2):640-4
references: 273227
references: Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15194-9
references: 9860945
references: J Phys Condens Matter. 2010 Feb 24;22(7):72202
references: 20352061
references: Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:67-76
references: 6190610
references: Genetics. 1986 Mar;112(3):441-57
references: 3007275
references: Phys Chem Chem Phys. 2010 Oct 21;12(39):12352-78
references: 20945523
references: Proc Natl Acad Sci U S A. 1979 Jun;76(6):2703-7
references: 288058
references: J Phys Chem B. 2010 Sep 9;114(35):11668-80
references: 20718454
references: Curr Opin Struct Biol. 2000 Jun;10(3):286-97
references: 10851199
references: Nucleic Acids Res. 2008 Oct;36(17):5540-51
references: 18755709
references: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9157-62
references: 19470490
references: Proc Natl Acad Sci U S A. 1985 Jul;82(14):4768-72
references: 3161076
references: Cell. 1982 Nov;31(1):25-33
references: 6297750
references: J Phys Chem B. 2004 May 20;108(20):6508-18
references: 18950140
references: Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4261-6
references: 8633052
references: Science. 1978 Aug 11;201(4355):525-7
references: 663672
references: Methods Enzymol. 1992;211:67-111
references: 1406328
references: Biochemistry. 2007 Jan 9;46(1):164-71
references: 17198386
references: Phys Rev Lett. 2001 Apr 16;86(16):3666-9
references: 11328049
references: J Cell Biol. 1987 Apr;104(4):1005-17
references: 3558475
references: Nat Cell Biol. 2000 Nov;2(11):812-8
references: 11056536
references: Biophys J. 2010 Oct 20;99(8):2608-15
references: 20959102
references: Proc Natl Acad Sci U S A. 1979 Jan;76(1):200-3
references: 284332
references: Nat Rev Genet. 2008 Jan;9(1):27-37
references: 18040271
references: Nature. 1953 Apr 25;171(4356):740-1
references: 13054694
references: Mol Cell Biol. 1984 Nov;4(11):2253-8
references: 6096689
references: J Mol Biol. 1981 Jul 15;149(4):761-86
references: 6273591
references: Genetics. 2008 Jan;178(1):99-112
references: 18202361
references: J Mol Biol. 1995 Mar 17;247(1):34-48
references: 7897660
references: Nature. 1980 Aug 7;286(5773):573-8
references: 7402337