Literature DB >> 12823023

The structure and dynamics of DNA in the gas phase.

Manuel Rueda1, Susana G Kalko, F Javier Luque, Modesto Orozco.   

Abstract

The impact of the transfer from water to the vacuum in the duplex DNA has been explored by using long molecular dynamic simulations. In opposition to chemical intuition, it is found that vaporization of DNA, even at high temperatures, does not lead to a total disruption of the double helix. Rather, the DNA duplex preserves gross structural, energetic, and dynamic features of the conformation of the double helix in aqueous solution. Thus, the two strands remain bound, the global structure has a slight helicity, and the total number of DNA-DNA interactions is not dramatically different from that found in solution. The results provide detailed structural and dynamic information useful to complement current mass spectroscopy studies of DNA structures.

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Year:  2003        PMID: 12823023     DOI: 10.1021/ja0300564

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  17 in total

1.  Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

Authors:  Manuel Rueda; Elena Cubero; Charles A Laughton; Modesto Orozco
Journal:  Biophys J       Date:  2004-08       Impact factor: 4.033

2.  The relative flexibility of B-DNA and A-RNA duplexes: database analysis.

Authors:  Alberto Pérez; Agnes Noy; Filip Lankas; F Javier Luque; Modesto Orozco
Journal:  Nucleic Acids Res       Date:  2004-11-23       Impact factor: 16.971

3.  Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.

Authors:  Elena Cubero; F Javier Luque; Modesto Orozco
Journal:  Biophys J       Date:  2005-11-11       Impact factor: 4.033

4.  Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Authors:  Alberto Pérez; Iván Marchán; Daniel Svozil; Jiri Sponer; Thomas E Cheatham; Charles A Laughton; Modesto Orozco
Journal:  Biophys J       Date:  2007-03-09       Impact factor: 4.033

5.  Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations.

Authors:  Carolyn L Mazzitelli; Junmei Wang; Suncerae I Smith; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2007-07-17       Impact factor: 3.109

6.  Ion mobility spectrometry reveals duplex DNA dissociation intermediates.

Authors:  Anastasia Burmistrova; Valérie Gabelica; Anne-Sophie Duwez; Edwin De Pauw
Journal:  J Am Soc Mass Spectrom       Date:  2013-09-06       Impact factor: 3.109

7.  Asymmetric charge partitioning upon dissociation of DNA duplexes.

Authors:  James A Madsen; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2010-03-09       Impact factor: 3.109

8.  The 3D structures of G-quadruplexes of HIV-1 integrase inhibitors: molecular dynamics simulations in aqueous solution and in the gas phase.

Authors:  Ming-Hui Li; Yi-Han Zhou; Quan Luo; Ze-Sheng Li
Journal:  J Mol Model       Date:  2009-10-04       Impact factor: 1.810

9.  Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases.

Authors:  Henryk Wincel
Journal:  J Am Soc Mass Spectrom       Date:  2012-07-21       Impact factor: 3.109

10.  Chain and conformation stability of solid-state DNA: implications for room temperature storage.

Authors:  Jacques Bonnet; Marthe Colotte; Delphine Coudy; Vincent Couallier; Joseph Portier; Bénédicte Morin; Sophie Tuffet
Journal:  Nucleic Acids Res       Date:  2009-12-07       Impact factor: 16.971

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