scholarly journals Crystal structure of metallo-DNA duplex containing T-Hg(II)-T base pairs

2014 ◽  
Vol 70 (a1) ◽  
pp. C1375-C1375
Author(s):  
Jiro Kondo ◽  
Tom Yamada ◽  
Chika Hirose ◽  
Itaru Okamoto ◽  
Yoshiyuki Tanaka ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Nucleic Acid ◽  
Helical Conformation ◽  
Helical Axis ◽  
Dna Duplex ◽  
Base Pairs ◽  
Imino Proton ◽  
Sensing System ◽  
Hybrid Duplex

The DNA duplex containing mercury-mediated base pairs (T-Hg(II)-T) is an attractive biomacromolecular nanomaterials. In a recent study, it was confirmed that the Hg(II) ion significantly stabilizes a DNA duplex by binding selectively to a T-T mispair [1]. Based on the phenomenon observed, a DNA-based sensing system that selectively and sensitively detects Hg(II) ions in aqueous solution was developed [2]. In the present study, we have solved the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs [3]. The Hg(II) ion occupies the center between two T residues. The geometry of the T-Hg(II)-T base pair is very similar to that of the canonical Watson-Crick base pairs. The distance of N3-Hg(II) bond is 2.0 Å, suggesting that the N3 nitrogen releases an imino-proton even at neutral pH (pKa of N3 position of T is 9.8) and directly bonds to Hg(II). In the B-form DNA, the helical axis runs through the center of base pairs, and the Hg(II) ions are therefore aligned along the helical axis. The distance between the two neighboring Hg(II) ions is 3.3 Å. The relatively short Hg(II)-Hg(II) distance indicates that the metallophilic attraction could exit between them and may stabilize the B-form duplex. To support this, the DNA duplex is largely distorted and adopts an unusual non-helical conformation in the absence of Hg(II). In conclusion, the Hg(II) ion is essential for maintaining the B-form conformation of the DNA duplex containing T-T mispairs. The structure of the Hg(II)-DNA hybrid duplex itself and the Hg(II)-induced structural switching from the non-helical form to the B-form provide the basis for the structure-based design of metal-conjugated nucleic acid nanomaterials.

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 Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine–2Ag(i)–4-thiothymine

2017 ◽  
Vol 53 (86) ◽  
pp. 11747-11750 ◽  
Author(s):  
Jiro Kondo ◽  
Toru Sugawara ◽  
Hisao Saneyoshi ◽  
Akira Ono
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Base Pairs

The crystal structures of 4-thiothymine–2AgI–4-thiothymine base pairs in B-form DNA duplexes have been solved.

High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs

2015 ◽  
Vol 127 (45) ◽  
pp. 13521-13524 ◽  
Author(s):  
Jiro Kondo ◽  
Yoshinari Tada ◽  
Takenori Dairaku ◽  
Hisao Saneyoshi ◽  
Itaru Okamoto ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Base Pairs ◽  
Hybrid Duplex

High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs

2015 ◽  
Vol 54 (45) ◽  
pp. 13323-13326 ◽  
Author(s):  
Jiro Kondo ◽  
Yoshinari Tada ◽  
Takenori Dairaku ◽  
Hisao Saneyoshi ◽  
Itaru Okamoto ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Base Pairs ◽  
Hybrid Duplex

Crystal structure and stability of a DNA duplex containing A(anti) · G(syn) base-pairs

1989 ◽  
Vol 207 (2) ◽  
pp. 455-457 ◽  
Author(s):  
Tom Brown ◽  
Gordon A. Leonard ◽  
Ewan D. Booth ◽  
Jenny Chambers
Keyword(s):  
Crystal Structure ◽  
Dna Duplex ◽  
Base Pairs ◽  
Structure And Stability

Crystal Structure of a DNA Duplex Containing 8-Hydroxydeoxyguanine-Adenine Base Pairs

Biochemistry ◽  
1994 ◽  
Vol 33 (34) ◽  
pp. 10266-10270 ◽  
Author(s):  
Katherine E. McAuley-Hecht ◽  
Gordon A. Leonard ◽  
Neil J. Gibson ◽  
James B. Thomson ◽  
William P. Watson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Duplex ◽  
Base Pairs ◽  
Adenine Base

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-HgII-T Base Pairs

2014 ◽  
Vol 53 (9) ◽  
pp. 2385-2388 ◽  
Author(s):  
Jiro Kondo ◽  
Tom Yamada ◽  
Chika Hirose ◽  
Itaru Okamoto ◽  
Yoshiyuki Tanaka ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Duplex ◽  
Base Pairs

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-HgII-T Base Pairs

2014 ◽  
Vol 126 (9) ◽  
pp. 2417-2420 ◽  
Author(s):  
Jiro Kondo ◽  
Tom Yamada ◽  
Chika Hirose ◽  
Itaru Okamoto ◽  
Yoshiyuki Tanaka ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Duplex ◽  
Base Pairs

scholarly journals Insights into peptide nucleic acid (PNA) structural features: The crystal structure of a D-lysine-based chiral PNA-DNA duplex

2003 ◽  
Vol 100 (21) ◽  
pp. 12021-12026 ◽  
Author(s):  
V. Menchise ◽  
G. De Simone ◽  
T. Tedeschi ◽  
R. Corradini ◽  
S. Sforza ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Structural Features ◽  
Dna Duplex

scholarly journals Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson–Crick selectivity

2018 ◽  
Vol 115 (33) ◽  
pp. E7658-E7664 ◽  
Author(s):  
Gregory P. Smith ◽  
Tommaso P. Fraccia ◽  
Marco Todisco ◽  
Giuliano Zanchetta ◽  
Chenhui Zhu ◽  
...  
Keyword(s):  
Phase Transition ◽  
Aqueous Solution ◽  
Liquid Crystal ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Self Assembly ◽  
Structural Elements ◽  
High Concentration ◽  
Base Pairs ◽  
All Solutions

We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson–Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.

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