Assembly of a highly DNA-duplex stabilizing salen-metallo-base pair

2005 ◽  
Author(s):  
Guido H. Clever ◽  
Thomas Carell
Keyword(s):  
Base Pair ◽  
Dna Duplex

Formation of Silver(I)-Mediated DNA Duplex and Triplex through an Alternative Base Pair of Pyridine Nucleobases

2002 ◽  
Vol 124 (30) ◽  
pp. 8802-8803 ◽  
Author(s):  
Kentaro Tanaka ◽  
Yasuyuki Yamada ◽  
Mitsuhiko Shionoya
Keyword(s):  
Base Pair ◽  
Dna Duplex

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.

Micromechanics of base pair unzipping in the DNA duplex

2011 ◽  
Vol 24 (3) ◽  
pp. 035104 ◽  
Author(s):  
Sergey N Volkov ◽  
Ekaterina V Paramonova ◽  
Alexander V Yakubovich ◽  
Andrey V Solov’yov
Keyword(s):  
Base Pair ◽  
Dna Duplex

Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair

Langmuir ◽  
2015 ◽  
Vol 31 (41) ◽  
pp. 11305-11310 ◽  
Author(s):  
Xinxin Tan ◽  
Stefanie Litau ◽  
Xi Zhang ◽  
Jens Müller
Keyword(s):  
Single Molecule ◽  
Base Pair ◽  
Force Spectroscopy ◽  
Dna Duplex ◽  
Single Molecule Force Spectroscopy ◽  
Artificial Dna

Relative Strand Orientation in a DNA Duplex Controls the Nuclearity of a Metal-Mediated Base Pair

2016 ◽  
Vol 23 (25) ◽  
pp. 5962-5965 ◽  
Author(s):  
Soham Mandal ◽  
Marian Hebenbrock ◽  
Jens Müller
Keyword(s):  
Base Pair ◽  
Dna Duplex ◽  
Strand Orientation

scholarly journals Free Energy Calculation for Base Pair Dissociation in a DNA Duplex

2016 ◽  
Vol 32 (5) ◽  
pp. 1282-1288
Author(s):  
Shao-Gui WU ◽  
◽  
Dan FENG ◽  
Keyword(s):  
Free Energy ◽  
Base Pair ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Dna Duplex
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