Dramatic 5‘-Residue Effect on Conformer Distribution of Short Oligonucleotide Retro Models of the Cisplatin−DNA Cross-Link:  Implications for the Lippard and Cross-Link Distorted Base Pair Steps Present in Cisplatin−DNA Duplex Adducts

2002 ◽  
Vol 124 (8) ◽  
pp. 1558-1559 ◽  
Author(s):  
Sharon T. Sullivan ◽  
Jamil S. Saad ◽  
Francesco P. Fanizzi ◽  
Luigi G. Marzilli
Keyword(s):  
Base Pair ◽  
Cross Link ◽  
Dna Duplex ◽  
Short Oligonucleotide

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.

scholarly journals Solution Structures of a DNA Dodecamer Duplex with and without a Cisplatin 1,2-d(GG) Intrastrand Cross-Link:  Comparison with the Same DNA Duplex Containing an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (22) ◽  
pp. 6477-6487 ◽  
Author(s):  
Yibing Wu ◽  
Debadeep Bhattacharyya ◽  
Candice L. King ◽  
Irene Baskerville-Abraham ◽  
Sung-Ho Huh ◽  
...  
Keyword(s):  
Cross Link ◽  
Dna Duplex ◽  
Solution Structures ◽  
Dna Dodecamer

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

scholarly journals Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

2014 ◽  
Vol 10 ◽  
pp. 2293-2306 ◽  
Author(s):  
Christine Beuck ◽  
Elmar Weinhold
Keyword(s):  
Protein Binding ◽  
Base Pair ◽  
Dna Methyltransferase ◽  
Target Position ◽  
Sequence Specificity ◽  
Cross Link ◽  
Base Flipping ◽  
Base Pairs ◽  
Thermus Aquaticus ◽  
The Cross

Covalently interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function. The ideal DNA cross-link to study protein–DNA interactions should be specific and easy to synthesize, be stable during protein binding experiments, have a short covalent linker to avoid steric hindrance of protein binding, and should be available as a mimic for both A/T and G/C base pairs to cover all possible binding specificities. Several covalent interstrand cross-links have been described in the literature, but most of them fall short of at least one of the above criteria. We developed an efficient method to site-specifically and reversibly cross-link thionucleoside base pairs in synthetic duplex oligodeoxynucleotides by bisalkylation with 1,2-diiodoethane resulting in an ethylene-bridged base pair. Both linked A/T and G/C base pair analogs can conveniently be prepared which allows studying any base pair-opening enzyme regardless of its sequence specificity. The cross-link is stable in the absence of reducing agents but the linker can be quickly and tracelessly removed by the addition of thiol reagents like dithiothreitol. This property makes the cross-linking reaction fully reversible and allows for a switching of the linked base pair from locked to unlocked during biochemical experiments. Using the DNA methyltransferase from Thermus aquaticus (M.TaqI) as example, we demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI.

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