cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA

Abstract The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.

[1]  Modesto Orozco,et al.  Multiscale simulation of DNA. , 2016, Current opinion in structural biology.

[2]  R. Dickerson,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, Journal of biomolecular structure & dynamics.

[3]  Alexey Savelyev,et al.  Chemically accurate coarse graining of double-stranded DNA , 2010, Proceedings of the National Academy of Sciences.

[4]  J. Maddocks,et al.  cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA , 2014, Nucleic acids research.

[5]  Christophe Blanchet,et al.  CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures , 2011, Nucleic Acids Res..

[6]  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.

[7]  O. Uhlenbeck,et al.  In vitro selection of DNAs with an increased propensity to form small circles , 2015, Biopolymers.

[8]  A. Joachimiak,et al.  Crystal structure of trp represser/operator complex at atomic resolution , 1988, Nature.

[9]  Rob Phillips,et al.  High flexibility of DNA on short length scales probed by atomic force microscopy , 2006, Nature nanotechnology.

[10]  A. Kabakçıoğlu,et al.  Twist-writhe partitioning in a coarse-grained DNA minicircle model. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[11]  Alexander Vologodskii,et al.  Strong bending of the DNA double helix , 2013, Nucleic acids research.

[12]  L. Dijkhuizen,et al.  Martini Coarse-Grained Force Field: Extension to DNA. , 2015, Journal of chemical theory and computation.

[13]  Lijiang Yang,et al.  Probing Allostery Through DNA , 2013, Science.

[14]  J. Widom,et al.  Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. , 1999, Journal of molecular biology.

[15]  H M Berman,et al.  A standard reference frame for the description of nucleic acid base-pair geometry. , 2001, Journal of molecular biology.

[16]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, The EMBO journal.

[17]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[18]  J. H. Maddocks,et al.  Conformational analysis of nucleic acids revisited: Curves+ , 2009, Nucleic acids research.

[19]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[20]  Carlos González,et al.  NAFlex: a web server for the study of nucleic acid flexibility , 2013, Nucleic Acids Res..

[21]  Oscar Gonzalez,et al.  Absolute versus Relative Entropy Parameter Estimation in a Coarse-Grain Model of DNA , 2017, Multiscale Model. Simul..

[22]  Alexander Vologodskii,et al.  Sequence dependence of DNA bending rigidity , 2010, Proceedings of the National Academy of Sciences.

[23]  J. Maddocks,et al.  Sequence-Dependent Persistence Lengths of DNA. , 2017, Journal of chemical theory and computation.

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

[25]  Ioan Andricioaei,et al.  Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. , 2012, Biochemistry.

[26]  A. Laaksonen,et al.  A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method. , 2014, Journal of chemical theory and computation.

[27]  David A. Case,et al.  μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA , 2014, Nucleic acids research.

[28]  Helgi I. Ingólfsson,et al.  Martini Coarse-Grained Force Field: Extension to RNA. , 2015, Biophysical journal.

[29]  J. Maddocks,et al.  A sequence-dependent rigid-base model of DNA. , 2013, The Journal of chemical physics.

[30]  A. Liwo,et al.  DNA Duplex Formation with a Coarse-Grained Model , 2014, Journal of chemical theory and computation.

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

[32]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Rottler,et al.  A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality. , 2009, The Journal of chemical physics.

[34]  J. Doye,et al.  Sequence-dependent thermodynamics of a coarse-grained DNA model. , 2012, The Journal of chemical physics.

[35]  Xiang-Jun Lu,et al.  Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures , 2009, Nucleic Acids Res..

[36]  Lin Yang,et al.  DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale , 2013, Nucleic Acids Res..

[37]  Juan J de Pablo,et al.  An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization. , 2013, The Journal of chemical physics.