Base Pairing at the Abasic Site in DNA Duplexes and Its Application in Adenosine Aptasensors

ChemBioChem ◽  
2012 ◽  
Vol 13 (3) ◽  
pp. 436-442 ◽  
Author(s):  
Yuanfeng Pang ◽  
Zhiai Xu ◽  
Yusuke Sato ◽  
Seiichi Nishizawa ◽  
Norio Teramae
Keyword(s):  
Dna Duplexes ◽  
Abasic Site ◽  
Base Pairing

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.

scholarly journals Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine

Molecules ◽  
2014 ◽  
Vol 19 (8) ◽  
pp. 11030-11044 ◽  
Author(s):  
Masayo Suzuki ◽  
Katsuhito Kino ◽  
Masayuki Morikawa ◽  
Takanobu Kobayashi ◽  
Hiroshi Miyazawa
Keyword(s):  
Dna Duplexes ◽  
Base Pairing

scholarly journals Electronic transitions and ESIPT kinetics of the thienyl-3-hydroxychromone nucleobase surrogate in DNA duplexes: a DFT/MD-TDDFT study

RSC Advances ◽  
2020 ◽  
Vol 10 (13) ◽  
pp. 7349-7359 ◽  
Author(s):  
Alain Sougnabé ◽  
Daniel Lissouck ◽  
Fabien Fontaine-Vive ◽  
Mama Nsangou ◽  
Yves Mély ◽  
...  
Keyword(s):  
Base Composition ◽  
Electronic Transitions ◽  
Dna Duplexes ◽  
Abasic Site ◽  
Environment Changes ◽  
Highly Sensitive ◽  
Kinetics Of

The fluorescent nucleobase surrogate M (2-thienyl-3-hydroxychromone fluorophore) when imbedded in DNA opposite an abasic site exhibits a two colour response highly sensitive to environment changes and base composition.

The effect of LNA nucleobases as enhancers for the binding of amiloride to an abasic site in DNA/DNA and DNA/RNA duplexes

2014 ◽  
Vol 12 (37) ◽  
pp. 7250-7256 ◽  
Author(s):  
Yusuke Sato ◽  
Tetsushi Sato ◽  
Takaya Sato ◽  
Seiichi Nishizawa ◽  
Norio Teramae
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Dna Duplexes ◽  
Abasic Site ◽  
Rna Duplexes

We report on a significant effect of locked nucleic acid (LNA) nucleobases on the binding of amiloride for abasic site (AP)-containing DNA duplexes.

Abasic site-binding ligands conjugated with cyanine dyes for “off–on” fluorescence sensing of orphan nucleobases in DNA duplexes and DNA–RNA hybrids

2014 ◽  
Vol 50 (5) ◽  
pp. 515-517 ◽  
Author(s):  
Yusuke Sato ◽  
Megumi Kudo ◽  
Yu Toriyabe ◽  
Shota Kuchitsu ◽  
Chun-xia Wang ◽  
...  
Keyword(s):  
Cyanine Dyes ◽  
Dna Duplexes ◽  
Abasic Site ◽  
Fluorescence Sensing ◽  
Site Binding

scholarly journals Preferential Incorporation of G Opposite Template T by the Low-Fidelity Human DNA Polymerase ι

2000 ◽  
Vol 20 (19) ◽  
pp. 7099-7108 ◽  
Author(s):  
Yanbin Zhang ◽  
Fenghua Yuan ◽  
Xiaohua Wu ◽  
Zhigang Wang
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Polymerase Activity ◽  
Abasic Site ◽  
Base Pairing ◽  
Base Pairs ◽  
Dna Lesion ◽  
Biological Source ◽  
Human Dna ◽  
Base Selection

ABSTRACT DNA polymerase activity is essential for replication, recombination, repair, and mutagenesis. All DNA polymerases studied so far from any biological source synthesize DNA by the Watson-Crick base-pairing rule, incorporating A, G, C, and T opposite the templates T, C, G, and A, respectively. Non-Watson-Crick base pairs would lead to mutations. In this report, we describe the ninth human DNA polymerase, Polι, encoded by the RAD30B gene. We show that human Polι violates the Watson-Crick base-pairing rule opposite template T. During base selection, human Polι preferred T-G base pairing, leading to G incorporation opposite template T. The resulting T-G base pair was less efficiently extended by human Polι compared to the Watson-Crick base pairs. Consequently, DNA synthesis frequently aborted opposite template T, a property we designated the T stop. This T stop restricted human Polι to a very short stretch of DNA synthesis. Furthermore, kinetic analyses show that human Polι copies template C with extraordinarily low fidelity, misincorporating T, A, and C with unprecedented frequencies of 1/9, 1/10, and 1/11, respectively. Human Polι incorporated one nucleotide opposite a template abasic site more efficiently than opposite a template T, suggesting a role for human Polι in DNA lesion bypass. The unique features of preferential G incorporation opposite template T and T stop suggest that DNA Polι may additionally play a specialized function in human biology.

Highly selective binding of naphthyridine with a trifluoromethyl group to cytosine opposite an abasic site in DNA duplexes

2012 ◽  
Vol 10 (20) ◽  
pp. 4003 ◽  
Author(s):  
Yusuke Sato ◽  
Yushuang Zhang ◽  
Takehiro Seino ◽  
Takashi Sugimoto ◽  
Seiichi Nishizawa ◽  
...  
Keyword(s):  
Trifluoromethyl Group ◽  
Dna Duplexes ◽  
Abasic Site ◽  
Selective Binding

scholarly journals New imidazopyridopyrimidine:naphthyridine base-pairing motif, ImNN:NaOO, consisting of a DAAD:ADDA hydrogen bonding pattern, markedly stabilize DNA duplexes

2011 ◽  
Vol 47 (38) ◽  
pp. 10818 ◽  
Author(s):  
Kazuyuki Kuramoto ◽  
Noriko Tarashima ◽  
Yasuyuki Hirama ◽  
Yusaku Kikuchi ◽  
Noriaki Minakawa ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Dna Duplexes ◽  
Base Pairing ◽  
Hydrogen Bonding Pattern

6,7-Dimethyllumazine as a potential ligand for selective recognition of adenine opposite an abasic site in DNA duplexes

2008 ◽  
pp. 6588 ◽  
Author(s):  
Zhiqiang Ye ◽  
Burki Rajendar ◽  
Dai Qing ◽  
Seiichi Nishizawa ◽  
Norio Teramae
Keyword(s):  
Selective Recognition ◽  
Dna Duplexes ◽  
Abasic Site ◽  
Potential Ligand

Structure and Dynamics of DNA Duplexes Containing a Cluster of Mutagenic 8-Oxoguanine and Abasic Site Lesions

2014 ◽  
Vol 426 (7) ◽  
pp. 1524-1538 ◽  
Author(s):  
Jan Zálešák ◽  
Morgane Lourdin ◽  
Lumίr Krejčί ◽  
Jean-François Constant ◽  
Muriel Jourdan
Keyword(s):  
Dna Duplexes ◽  
Abasic Site ◽  
Structure And Dynamics
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