Biblio
Found 49 results
Author Title [ Year] Filters: Author is Modesto Orozco and Keyword is Nucleic Acid Conformation [Clear All Filters]
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.,
, J Am Chem Soc, 2002 Mar 27, Volume 124, p.3133-42, (2002)
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines.,
, Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives.,
, J Am Chem Soc, 2003 Dec 24, Volume 125, p.16127-38, (2003)
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)
The structure and dynamics of DNA in the gas phase.,
, J Am Chem Soc, 2003 Jul 2, Volume 125, p.8007-14, (2003)
Theoretical methods for the simulation of nucleic acids.,
, Chem Soc Rev, 2003 Nov, Volume 32, p.350-64, (2003)
Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.,
, J Am Chem Soc, 2003 Nov 26, Volume 125, p.14603-12, (2003)
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)
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 relative flexibility of B-DNA and A-RNA duplexes: database analysis.,
, Nucleic Acids Res, 2004, Volume 32, p.6144-51, (2004)
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 the guanine –> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes.,
, J Am Chem Soc, 2004 Nov 10, Volume 126, p.14642-50, (2004)
Triplex-forming oligonucleotide target sequences in the human genome.,
, Nucleic Acids Res, 2004, Volume 32, p.354-60, (2004)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid.,
, J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)
Data mining of molecular dynamics trajectories of nucleic acids.,
, J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)
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)
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 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 Hoogsteen-Watson-Crick junctions in DNA.,
, Biophys J, 2006 Feb 1, Volume 90, p.1000-8, (2006)
Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.,
, Org Lett, 2007 Oct 25, Volume 9, p.4503-6, (2007)
Dynamics of B-DNA on the microsecond time scale.,
, J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)
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)
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)
Triplex formation using oligonucleotide clamps carrying 8-aminopurines.,
, Nucleosides Nucleotides Nucleic Acids, 2007, Volume 26, p.979-83, (2007)
Ab initio study of naphtho-homologated DNA bases.,
, J Phys Chem B, 2008 Feb 21, Volume 112, p.2179-86, (2008)
DNAlive: a tool for the physical analysis of DNA at the genomic scale.,
, Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.,
, J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility.,
, J Am Chem Soc, 2008 Mar 19, Volume 130, p.3486-96, (2008)
Towards a molecular dynamics consensus view of B-DNA flexibility.,
, Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)
Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer.,
, Nucleic Acids Res, 2009 Sep, Volume 37, p.5589-601, (2009)
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)
Nucleic acid simulations themed issue.,
, Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)
The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer.,
, Nucleic Acids Symp Ser (Oxf), 2009, p.109-10, (2009)
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)
Real-time atomistic description of DNA unfolding.,
, Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)
Toward a consensus view of duplex RNA flexibility.,
, Biophys J, 2010 Sep 22, Volume 99, p.1876-85, (2010)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.,
, J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)
Exploring polymorphisms in B-DNA helical conformations.,
, Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Impact of methylation on the physical properties of DNA.,
, Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)
Structure of triplex DNA in the gas phase.,
, J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)
Backbone FC-H···O hydrogen bonds in 2’F-substituted nucleic acids.,
, Angew Chem Int Ed Engl, 2013 Nov 11, Volume 52, p.12065-8, (2013)
NAFlex: a web server for the study of nucleic acid flexibility.,
, Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.,
, Nucleic Acids Res, 2013 Aug, Volume 41, p.7220-30, (2013)
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)
Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures.,
, FEBS J, 2014 Feb, Volume 281, p.1085-99, (2014)
Structure and properties of DNA in apolar solvents,
, J Phys Chem B, 2014 Jul 24, Volume 118, p.8540-8, (2014)
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)
The structural impact of DNA mismatches.,
, Nucleic Acids Res, 2015 Apr 30, Volume 43, p.4309-21, (2015)