The conformational flexibility of nucleic acid bases paired in gas phase: A Car-Parrinello molecular dynamics study

2012 ◽  
Vol 136 (20) ◽  
pp. 205102 ◽  
Author(s):  
Shiyan Xiao ◽  
Haojun Liang
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Gas Phase ◽  
Conformational Flexibility ◽  
Nucleic Acid Bases

On the interaction between manganese cation (Mn2+) and the nucleic acid bases (T, U, C, A, G) in the gas phase

2002 ◽  
Vol 90 (2) ◽  
pp. 903-909 ◽  
Author(s):  
Nino Russo ◽  
Emilia Sicilia ◽  
Marirosa Toscano ◽  
Andr� Grand
Keyword(s):  
Nucleic Acid ◽  
Gas Phase ◽  
Nucleic Acid Bases ◽  
Manganese Cation

scholarly journals Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 532
Author(s):  
Jonathan H. Sheehan ◽  
Jarrod A. Smith ◽  
Pradeep S. Pallan ◽  
Terry P. Lybrand ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Base Pair ◽  
Crystal Packing ◽  
Md Simulations ◽  
Conformational Flexibility ◽  
Dynamics Simulation ◽  
Dna Duplex ◽  
Solution Studies

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution : Part 1. Cytosine

2002 ◽  
Vol 4 (17) ◽  
pp. 4192-4203 ◽  
Author(s):  
Semen A. Trygubenko ◽  
Tetyana V. Bogdan ◽  
Manuel Rueda ◽  
Modesto Orozco ◽  
F. Javier Luque ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Nucleic Acid ◽  
Ab Initio ◽  
Gas Phase ◽  
Ab Initio Study ◽  
Nucleic Acid Bases

Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment, and in Aqueous Solution. Part 3. Adenine

2004 ◽  
Vol 108 (6) ◽  
pp. 2087-2097 ◽  
Author(s):  
Michal Hanus ◽  
Martin Kabeláč ◽  
Jaroslav Rejnek ◽  
Filip Ryjáček ◽  
Pavel Hobza
Keyword(s):  
Aqueous Solution ◽  
Nucleic Acid ◽  
Ab Initio ◽  
Gas Phase ◽  
Ab Initio Study ◽  
Nucleic Acid Bases

New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics

2010 ◽  
Vol 12 (33) ◽  
pp. 9945 ◽  
Author(s):  
Al'ona Furmanchuk ◽  
Oleg V. Shishkin ◽  
Olexandr Isayev ◽  
Leonid Gorb ◽  
Jerzy Leszczynski
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Ab Initio ◽  
Structural Properties ◽  
Ab Initio Molecular Dynamics ◽  
Nucleic Acid Bases
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