Biblio
] Ab initio study of naphtho-homologated DNA bases.,
, J Phys Chem B, 2008 Feb 21, Volume 112, p.2179-86, (2008)
Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides.,
, Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)
The (in)dependence of alternative splicing and gene duplication.,
, PLoS Comput Biol, 2007 Mar 2, Volume 3, p.e33, (2007)
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.,
, Chemistry, 2006 Mar 20, Volume 12, p.2854-65, (2006)
Theoretical study of the guanine –> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes.,
, J Am Chem Soc, 2004 Nov 10, Volume 126, p.14642-50, (2004)
The structure and dynamics of DNA in the gas phase.,
, J Am Chem Soc, 2003 Jul 2, Volume 125, p.8007-14, (2003)
G-quadruplexes can maintain their structure in the gas phase.,
, J Am Chem Soc, 2006 Mar 22, Volume 128, p.3608-19, (2006)
Nature of minor-groove binders-DNA complexes in the gas phase.,
, J Am Chem Soc, 2005 Aug 24, Volume 127, p.11690-8, (2005)
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?,
, Biophys J, 2004 Aug, Volume 87, p.800-11, (2004)
The structural impact of DNA mismatches.,
, Nucleic Acids Res, 2015 Apr 30, Volume 43, p.4309-21, (2015)
Non-coding recurrent mutations in chronic lymphocytic leukaemia.,
, Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)
Multiple routes to characterize the folding of a small DNA hairpin.,
, Angew Chem Int Ed Engl, 2010 Oct 11, Volume 49, p.7673-6, (2010)
MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents.,
, J Am Chem Soc, 2014 Feb 26, Volume 136, p.3075-86, (2014)
Impact of methylation on the physical properties of DNA.,
, Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)
Dynamics of B-DNA on the microsecond time scale.,
, J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)
The relative flexibility of B-DNA and A-RNA duplexes: database analysis.,
, Nucleic Acids Res, 2004, Volume 32, p.6144-51, (2004)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.,
, Chemistry, 2005 Aug 19, Volume 11, p.5062-6, (2005)
Real-time atomistic description of DNA unfolding.,
, Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)
Towards a molecular dynamics consensus view of B-DNA flexibility.,
, Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.,
, Biophys J, 2007 Jun 1, Volume 92, p.3817-29, (2007)
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.,
, Nucleic Acids Res, 2014 Oct 29, Volume 42, p.12272-83, (2014)
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility.,
, J Am Chem Soc, 2008 Mar 19, Volume 130, p.3486-96, (2008)
Data mining of molecular dynamics trajectories of nucleic acids.,
, J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)
The impact of monovalent ion force field model in nucleic acids simulations.,
, Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (2009)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid.,
, J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)
Relative flexibility of DNA and RNA: a molecular dynamics study.,
, J Mol Biol, 2004 Oct 22, Volume 343, p.627-38, (2004)
Theoretical study of large conformational transitions in DNA: the B<–>A conformational change in water and ethanol/water.,
, Nucleic Acids Res, 2007, Volume 35, p.3330-8, (2007)
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.,
, Genome Biol, 2012, Volume 13, p.R106, (2012)
Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index.,
, J Comput Chem, 2002 Apr 15, Volume 23, p.554-63, (2002)
Visualizing phosphodiester-bond hydrolysis by an endonuclease.,
, Nat Struct Mol Biol, 2015 Jan, Volume 22, p.65-72, (2015)
Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.,
, J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.,
, Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)
Nucleic acid simulations themed issue.,
, Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.,
, Hum Mol Genet, 2014 Dec 20, Volume 23, p.6927-34, (2014)
A genome-wide association study on a southern European population identifies a new Crohn’s disease susceptibility locus at RBX1-EP300.,
, Gut, 2013 Oct, Volume 62, p.1440-5, (2013)
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.,
, Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)
NAFlex: a web server for the study of nucleic acid flexibility.,
, Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
Triplex-forming oligonucleotide target sequences in the human genome.,
, Nucleic Acids Res, 2004, Volume 32, p.354-60, (2004)
DNAlive: a tool for the physical analysis of DNA at the genomic scale.,
, Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)
Determining promoter location based on DNA structure first-principles calculations.,
, Genome Biol, 2007, Volume 8, p.R263, (2007)
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.,
, BMC Genomics, 2006, Volume 7, p.63, (2006)
Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct.,
, J Biol Chem, 2004 Jun 4, Volume 279, p.24552-60, (2004)
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.,
, J Biol Chem, 2007 Oct 26, Volume 282, p.31444-52, (2007)
Fuzziness and noise in nucleosomal architecture.,
, Nucleic Acids Res, 2014 Apr, Volume 42, p.4934-46, (2014)
Unique tautomeric and recognition properties of thioketothymines?,
, J Am Chem Soc, 2009 Sep 9, Volume 131, p.12845-53, (2009)
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.,
, J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)
On the nature of DNA hyperchromic effect.,
, J Phys Chem B, 2013 Jul 25, Volume 117, p.8697-704, (2013)
Effects of local electric fields on the redox free energy of single stranded DNA.,
, Chem Commun (Camb), 2011 Mar 7, Volume 47, p.2646-8, (2011)