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 Competitive Binding of Abasic Site-Binding Ligands and Masking Ligands to DNA Duplexes for the Analysis of Single-Base Mutation

2013 ◽  
Vol 29 (1) ◽  
pp. 15-19 ◽  
Author(s):  
Yusuke SATO ◽  
Tomoe KAGEYAMA ◽  
Seiichi NISHIZAWA ◽  
Norio TERAMAE
Keyword(s):  
Competitive Binding ◽  
Dna Duplexes ◽  
Abasic Site ◽  
Single Base ◽  
Site Binding

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.

scholarly journals Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes

2020 ◽  
Vol 10 (12) ◽  
pp. 4133
Author(s):  
Chun-xia Wang ◽  
Yusuke Sato ◽  
Takashi Sugimoto ◽  
Norio Teramae ◽  
Seiichi Nishizawa
Keyword(s):  
Nucleic Acid ◽  
Sequence Analysis ◽  
Fluorescent Probes ◽  
Dna Duplexes ◽  
Thiazole Orange ◽  
Fluorescence Sensing ◽  
Binding Selectivity ◽  
Target Dna ◽  
Fluorescence Signaling ◽  
Ap Site

Fluorescent probes with the binding selectivity to specific structures in DNAs or RNAs have gained much attention as useful tools for the study of nucleic acid functions. Here, chloro-substituted 2-amino-5,7-dimethyl-1,8-naphthyridine (ClNaph) was developed as a strong and highly selective binder for target orphan cytosine opposite an abasic (AP) site in the DNA duplexes. ClNaph was then conjugated with thiazole orange (TO) via an alkyl spacer (ClNaph–TO) to design a light-up probe for the detection of cytosine-related mutations in target DNA. In addition, we found the useful binding and fluorescence signaling of the ClNaph–TO conjugate to target C in AP site-containing DNA/RNA hybrid duplexes with a view toward sequence analysis of microRNAs.

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

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

Efficient inhibition of human AP endonuclease 1 (APE1) via substrate masking by abasic site-binding macrocyclic ligands

2015 ◽  
Vol 51 (88) ◽  
pp. 15948-15951 ◽  
Author(s):  
Naoko Kotera ◽  
Florent Poyer ◽  
Anton Granzhan ◽  
Marie-Paule Teulade-Fichou
Keyword(s):  
Macrocyclic Ligands ◽  
Abasic Site ◽  
Ap Endonuclease ◽  
Abasic Sites ◽  
Ap Endonuclease 1 ◽  
Site Binding

Bis-naphthalene macrocycles bind to abasic sites in DNA, leading to efficient inhibition of their cleavage by human AP endonuclease 1 (APE1).

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