Development of novel C-nucleoside analogues for the formation of antiparallel-type triplex DNA with duplex DNA that includes TA and dUA base pairs

2020 ◽  
Vol 18 (15) ◽  
pp. 2845-2851 ◽  
Author(s):  
Yosuke Taniguchi ◽  
Yuya Magata ◽  
Takayuki Osuki ◽  
Ryotaro Notomi ◽  
Lei Wang ◽  
...  
Keyword(s):  
Nucleoside Analogues ◽  
Triplex Dna ◽  
Duplex Dna ◽  
Base Pairs

We report the formation of stable triplex DNA for TA duplex sites by using triplex-forming oligonucleotides (TFOs) with novel C-nucleoside analogues.

scholarly journals Design and synthesis of purine nucleoside analogues for the formation of stable anti-parallel-type triplex DNA with duplex DNA bearing the 5mCG base pair

RSC Advances ◽  
2021 ◽  
Vol 11 (35) ◽  
pp. 21390-21396
Author(s):  
Ryotaro Notomi ◽  
Lei Wang ◽  
Shigeki Sasaki ◽  
Yosuke Taniguchi
Keyword(s):  
Base Pair ◽  
Purine Nucleoside ◽  
Nucleoside Analogues ◽  
Triplex Dna ◽  
Duplex Dna ◽  
Design And Synthesis ◽  
Direct Recognition ◽  
First Time ◽  
Parallel Type

We herein demonstrated for the first time the direct recognition of duplex DNA bearing the 5-methyl-2′-deoxycytosine and 2′-deoxyguanosine base pair by triplex DNA formation.

scholarly journals Transient Hoogsteen base pairs in canonical duplex DNA

Nature ◽  
2011 ◽  
Vol 470 (7335) ◽  
pp. 498-502 ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Eunae Kim ◽  
Abigail A. Wise ◽  
Patrick J. O’Brien ◽  
Ioan Andricioaei ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Base Pairs

scholarly journals A historical account of hoogsteen base-pairs in duplex DNA

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Huiqing Zhou ◽  
Federico L. Gottardo ◽  
Heidi S. Alvey ◽  
Isaac J. Kimsey ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Historical Account ◽  
Base Pairs

scholarly journals 2-Chloro-2′-deoxyadenosine monophosphate residues in DNA enhance susceptibility to 3′ → 5′ exonucleases

1994 ◽  
Vol 302 (2) ◽  
pp. 567-571 ◽  
Author(s):  
P Hentosh ◽  
P Grippo
Keyword(s):  
Dna Polymerase ◽  
Nucleoside Analogues ◽  
Duplex Dna ◽  
Exonuclease Activity ◽  
Klenow Fragment ◽  
Purine Nucleotide ◽  
Nucleotide Analogue ◽  
Pyrimidine Dimers ◽  
Deoxyadenosine Triphosphate ◽  
Dna Polymerase Ii

2-Chloro-2′-deoxyadenosine triphosphate, a purine nucleotide analogue and potent antileukaemic agent, was incorporated into double-stranded 36-mers in place of dATP to investigate the effects of 2-chloroadenine (ClAde) on DNA polymerase-associated 3′-->5′ exonuclease activity. ClAde residues within one strand of duplex DNA did not inhibit exonuclease activity; on the contrary, ClAde-containing minus strands were digested to a greater extent than was control DNA in the absence of deoxyribonucleoside triphosphates by Escherichia coli Klenow fragment, yeast DNA polymerase II and T4 DNA polymerase. After a 30 min incubation with 5 units of Klenow fragment, approximately 65% of control DNA remained in DNA fragments of 26 bases or larger compared with only approximately 25% of ClAde-substituted substrates. Unsubstituted plus strands opposite a ClAde-containing strand were likewise digested more quickly by 3′-->5′ exonuclease, but only in the vicinity of the ClAde sites. Approx. 63% of the plus strands from ClAde-containing oligomers were less than 24 bases in length after a 25 min digestion period with Klenow fragment compared with only approximately 32% of control DNA. Such results indicate that, unlike other base modifications such as pyrimidine dimers, methoxy psoralen adducts and certain nucleoside analogues, all of which inhibit or decrease the rate of strand degradation by 3′-->5′ exonucleases, incorporated ClAde enhances strand degradation of duplex DNA.

Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

2012 ◽  
Vol 532 ◽  
pp. 28-35 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Yukako Miyakawa ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Specific Binding ◽  
Duplex Dna ◽  
Base Pairs ◽  
Positive Cooperativity

scholarly journals DNA polymerase β: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes1

1998 ◽  
Vol 331 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Jinwoo AHN ◽  
Vadim S. KRAYNOV ◽  
Xuejun ZHONG ◽  
Brian G. WERNEBURG ◽  
Ming-Daw TSAI
Keyword(s):  
Conformational Change ◽  
Dna Polymerase ◽  
Catalytic Efficiency ◽  
Duplex Dna ◽  
Gap Filling ◽  
Dna Polymerase Β ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Dna Substrates ◽  
Gapped Dna

Pre-steady-state kinetic analysis was used to compare the catalytic properties of DNA polymerase β (Pol β) for single-base gap-filling and regular duplex DNA synthesis. The rate of polymerization (kpol) and the apparent equilibrium dissociation constant of dNTP (Kd) were determined with single-nucleotide gapped DNA substrates for all four possible correct base pairs and twelve possible incorrect base pairs, and the results were compared with those obtained previously with non-gapped primer/template duplex DNA substrates. For correct dNTP incorporation, the use of single-nucleotide gapped DNA led to significant decreases in the Kd of dNTP. Although kpol was little affected, the catalytic efficiency kpol/Kd increased significantly owing to the decreases in Kd. In contrast, for incorrect dNTP incorporation, the use of single-nucleotide gapped DNA substrates did not affect the Kd of dNTP appreciably but caused the kpol (and thus kpol/Kd) for incorrect dNTP incorporation to increase. As a consequence the fidelity of Pol β was not significantly affected by the use of single-nucleotide gapped DNA substrates. In addition we show that under processive polymerization conditions the processivity of Pol β increases in the gap-filling synthesis owing to a decreased rate of DNA dissociation. Finally, with a single-nucleotide gapped DNA substrate the rate-limiting conformational change step before chemistry was also observed. However, the preceding fast conformational change observed with duplex DNA substrates was not clearly detected. A possible cause is that in the complex with the gapped DNA, the 8 kDa N-terminal domain of Pol β already exists in a closed conformation. This interpretation was supported by tryptic digestion experiments.

Preferential binding of anticancer drugs to triplex DNA compared to duplex DNA: a spectroscopic and calorimetric study

RSC Advances ◽  
2016 ◽  
Vol 6 (46) ◽  
pp. 39903-39917 ◽  
Author(s):  
Neelam Lohani ◽  
Moganty R. Rajeswari
Keyword(s):  
Anticancer Drugs ◽  
Promoter Region ◽  
Binding Study ◽  
Triplex Dna ◽  
Calorimetric Study ◽  
Duplex Dna ◽  
Calorimetric Technique ◽  
Preferential Binding

Binding study of adriamycin and actinomycin to triplex DNA formed on the promoter region of hmgb1 gene using spectroscopic and calorimetric technique.

scholarly journals Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Heidi S. Alvey ◽  
Federico L. Gottardo ◽  
Evgenia N. Nikolova ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Duplex Dna ◽  
Base Pairs
Sign in / Sign up

Export Citation Format

Share Document