Probing persistence in DNA curvature properties with atomic force microscopy.

We elaborate on a mean-field extension of the wormlike chain model that accounts for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of genomic DNA, the stronger the LRC, the smaller the persistence length. The comparison of atomic force microscopy imaging of straight, uncorrelated virus and correlated human DNA fragments with DNA simulations confirms that the observed decrease in persistence length for human DNA more likely results from a sequence-induced large-scale intrinsic curvature than from some increased flexibility.

[1]  A. Arneodo,et al.  Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder , 2006, The European physical journal. E, Soft matter.

[2]  Jacques Barbet,et al.  Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer. , 2002, Ultramicroscopy.

[3]  M. Borodovsky,et al.  Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. , 1996, Journal of molecular biology.

[4]  C. Bustamante,et al.  Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. , 1996, Journal of molecular biology.

[5]  S. Harvey,et al.  Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. , 1995, Biophysical chemistry.

[6]  R. Cortese,et al.  Cell Entry of Hepatitis C Virus Requires a Set of Co-receptors That Include the CD81 Tetraspanin and the SR-B1 Scavenger Receptor* , 2003, Journal of Biological Chemistry.

[7]  A. Arneodo,et al.  Thermodynamics of DNA loops with long-range correlated structural disorder. , 2005, Physical review letters.

[8]  M. Marilley,et al.  Fine mapping of inherent flexibility variation along DNA molecules. Validation by atomic force microscopy (AFM) in buffer , 2005, Molecular Genetics and Genomics.

[9]  Stéphane Fusil,et al.  Adsorption of DNA to mica mediated by divalent counterions: a theoretical and experimental study. , 2003, Biophysical journal.

[10]  Giampaolo Zuccheri,et al.  Sequence-dependent DNA curvature and flexibility from scanning force microscopy images. , 2002, Biophysical journal.

[11]  D M Crothers,et al.  Intrinsically bent DNA. , 1990, The Journal of biological chemistry.

[12]  A. Fire,et al.  Structural analysis of hyperperiodic DNA from Caenorhabditis elegans , 2006, Nucleic acids research.

[13]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[14]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[15]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[16]  J. Dubochet,et al.  Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. , 1995, Journal of molecular biology.

[17]  H. Hansma,et al.  Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. , 1996, Nucleic acids research.

[18]  A. Mazur.  Evaluation of elastic properties of atomistic DNA models. , 2006, Biophysical journal.

[19]  Alain Arneodo,et al.  Long-Range Correlations in Genomic DNA , 2001 .

[20]  S. Codeluppi,et al.  Accurate length determination of DNA molecules visualized by atomic force microscopy: evidence for a partial B- to A-form transition on mica. , 2001, Ultramicroscopy.

[21]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[22]  J. Widom.  Short-range order in two eukaryotic genomes: relation to chromosome structure. , 1996, Journal of molecular biology.

[23]  J A Cognet,et al.  Static curvature and flexibility measurements of DNA with microscopy. A simple renormalization method, its assessment by experiment and simulation. , 1999, Journal of molecular biology.

[24]  P. Hagerman.  Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[25]  M. Vologodskaia,et al.  Contribution of the intrinsic curvature to measured DNA persistence length. , 2002, Journal of molecular biology.

[26]  H. Berg.  Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00. , 1989 .

[27]  D. Crothers,et al.  A bent helix in kinetoplast DNA. , 1983, Cold Spring Harbor symposia on quantitative biology.

[28]  Alain Arneodo,et al.  Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes. , 2002, Journal of molecular biology.

[29]  C. Anselmi,et al.  Nanoscale mechanical and dynamical properties of DNA single molecules. , 2005, Biophysical chemistry.

[30]  J. Muzy,et al.  Long-range correlations in genomic DNA: a signature of the nucleosomal structure. , 2001, Physical review letters.

[31]  I. Albert,et al.  Nucleosome positions predicted through comparative genomics , 2006, Nature Genetics.

[32]  C. Bustamante,et al.  Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. , 1998, Journal of molecular biology.

[33]  A. Shluger,et al.  Simple model for DNA adsorption onto a mica surface in 1:1 and 2:1 electrolyte solutions. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[34]  J. Schellman,et al.  Flexibility of DNA , 1974, Biopolymers.