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

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.

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 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 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 Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction

2021 ◽  
Author(s):  
Cyong-Ru Jhan ◽  
Roshan Satange ◽  
Shun-Ching Wang ◽  
Jing-Yi Zeng ◽  
Yih-Chern Horng ◽  
...  
Keyword(s):  
Hot Spot ◽  
Hydration Shell ◽  
Repeat Motif ◽  
Dna Duplex ◽  
Base Pairs ◽  
Dna And Rna ◽  
Detailed Structural Analysis ◽  
Small Molecule Compound ◽  
Dna Backbone ◽  
Locomotor Deficits

Abstract The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.

scholarly journals Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs

1989 ◽  
Vol 17 (1) ◽  
pp. 55-72 ◽  
Author(s):  
W.B.T. Cruse ◽  
J. Aymani ◽  
Olga Kennard ◽  
Tom Brown ◽  
Audrey G.C. Jack ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Base Pairs

Molecular and Crystal Structure of d(CGCGmo4CG): N4−Methoxy-cytosineguanine Base Pairs in Z-DNA

1990 ◽  
Vol 9 (3) ◽  
pp. 467-469 ◽  
Author(s):  
L. Van Meervelt ◽  
M. H. Moore ◽  
P. Kong Thoo Lin ◽  
D. M. Brown ◽  
O. Kennard
Keyword(s):  
Crystal Structure ◽  
Molecular And Crystal Structure ◽  
Base Pairs ◽  
Z Dna

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

2015 ◽  
Vol 39 (11) ◽  
pp. 8752-8762 ◽  
Author(s):  
Gaofeng Liu ◽  
Zhiwen Li ◽  
Junfei Zhu ◽  
Yang Liu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Base Pairing ◽  
Dna Duplex ◽  
Base Pairs ◽  
Thermal Stabilities

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

Polyadenosine-based fluorescent probe for reversible pH sensing based on protonated adenine-adenine base pairs: Applications to sensing of enzyme-substrate system and enzymatic logic gates

2018 ◽  
Vol 273 ◽  
pp. 681-688 ◽  
Author(s):  
Kuan-Kun Yu ◽  
Wei-Bin Tseng ◽  
Man-Jyun Wu ◽  
A. Santhana Krishna Kumar Alagarsamy ◽  
Wei-Lung Tseng ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Logic Gates ◽  
Ph Sensing ◽  
Base Pairs ◽  
Enzyme Substrate ◽  
Adenine Base
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