Solvation effect on the vertical ionization energy of adenine‐thymine base pair: From microhydration to bulk

2019 ◽  
Vol 120 (6) ◽  
Author(s):  
Madhubani Mukherjee ◽  
Soumi Haldar ◽  
Achintya K. Dutta
Keyword(s):  
Base Pair ◽  
Ionization Energy ◽  
Solvation Effect ◽  
Vertical Ionization Energy ◽  
Adenine Thymine

scholarly journals Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences

2010 ◽  
Vol 133 (6) ◽  
pp. 064302 ◽  
Author(s):  
Yue-Jie Ai ◽  
Feng Zhang ◽  
Gang-Long Cui ◽  
Yi Luo ◽  
Wei-Hai Fang
Keyword(s):  
Base Pair ◽  
Similarities And Differences ◽  
Adenine Thymine

scholarly journals The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase

2004 ◽  
Vol 381 (3) ◽  
pp. 709-717 ◽  
Author(s):  
Harry P. RAPPAPORT
Keyword(s):  
Dna Polymerase ◽  
Rate Constant ◽  
Base Pair ◽  
Apparent Rate Constant ◽  
Polymerase Activity ◽  
Exonuclease Activity ◽  
Base Pairs ◽  
Error Frequency ◽  
Steady State Kinetics ◽  
Adenine Thymine

With the goal of constructing a genetic alphabet consisting of a set of three base pairs, the fidelity of replication of the three base pairs TH (5-methyl-2-pyrimidinone)/HS (6-thiopurine; thiohypoxanthine), C/H (hypoxanthine) and T/A was evaluated using T7 DNA polymerase, a polymerase with a strong 3′→5′ exonuclease activity. An evaluation of the suitability of a new base pair for replication should include both the contribution of the fidelity of a polymerase activity and the contribution of proofreading by a 3′→5′ exonuclease activity. Using a steady-state kinetics method that included the contribution of the 3′→5′ exonuclease activity, the fidelity of replication was determined. The method determined the ratio of the apparent rate constant for the addition of a deoxynucleotide to the primer across from a template base by the polymerase activity and the rate constant for removal of the added deoxynucleotide from the primer by the 3′→5′ exonuclease activity. This ratio was designated the eni (efficiency of net incorporation). The eni of the base pair C/H was equal to or greater than the eni of T/A. The eni of the base pair TH/HS was 0.1 times that of A/T for TH in the template and 0.01 times that of A/T for HS in the template. The ratio of the eni of a mismatched deoxynucleotide to the eni of a matched deoxynucleotide was a measure of the error frequency. The error frequencies were as follows: thymine or TH opposite a template hypoxanthine, 2×10−6; HS opposite a template cytosine, <3×10−4. The remaining 24 mismatched combinations of bases gave no detectable net incorporation. Two mismatches, hypoxanthine opposite a template thymine or a template TH, showed trace incorporation in the presence of a standard dNTP complementary to the next template base. T7 DNA polymerase extended the primer beyond each of the matched base pairs of the set. The level of fidelity of replication of the three base pairs with T7 DNA polymerase suggests that they are adequate for a three-base-pair alphabet for DNA replication.

Effects of monohydration on an adenine–thymine base pair

2015 ◽  
pp. 205-216
Author(s):  
Sara Watanabe ◽  
Yudai Ogata ◽  
Tsutomu Kawatsu ◽  
Yukio Kawashima ◽  
Masanori Tachikawa
Keyword(s):  
Base Pair ◽  
Adenine Thymine

The Readout of Base-Pair Information in Adenine-Thymine α-D-Arabinonucleosides

2014 ◽  
Vol 20 (47) ◽  
pp. 15473-15481 ◽  
Author(s):  
Shiliang He ◽  
Hang Zhao ◽  
Xiurong Guo ◽  
Xiaoping Xu ◽  
Xinglong Zhou ◽  
...  
Keyword(s):  
Base Pair ◽  
Adenine Thymine
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