Niridazole: Evidence for promutagenic events involving guanine-cytosine and adenine-thymine base pairs

1985 ◽  
Vol 7 (4) ◽  
pp. 429-437 ◽  
Author(s):  
William T. Speck ◽  
Howard S. Carr ◽  
Herbert S. Rosenkranz
Keyword(s):  
Base Pairs ◽  
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.

scholarly journals Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid

1968 ◽  
Vol 109 (4) ◽  
pp. 543-557 ◽  
Author(s):  
K. J. Thrower ◽  
A. R. Peacocke
Keyword(s):  
Ionic Strength ◽  
Rate Constant ◽  
Base Pairs ◽  
Phage Dna ◽  
Dna Strands ◽  
Entropy Of Activation ◽  
T7 Phage ◽  
Kinetics Of ◽  
Rate Controlling Step ◽  
Adenine Thymine

The kinetics of the renaturation of Escherichia coli DNA in 0·4–1·0m-sodium chloride at temperatures from 60° to 90° have been studied. The extent of renaturation was a maximum at 65° to 75° and increased with ionic strength, and the rate constant increased with both ionic strength and temperature. The energy and entropy of activation of renaturation were calculated to be 6–7kcal.mole−1 and −40cal.deg.−1mole−1 respectively. It has been shown that renaturation is a second-order process for 5hr. under most conditions. The results are consistent with a reaction in which the rate-controlling step is the diffusion together of two separated complementary DNA strands and the formation of a nucleus of base pairs between them. The kinetics of the renaturation of T7-phage DNA and Bordetella pertussis DNA have also been studied, and their rates of renaturation related quantitatively to the relative heterogeneity of the DNA samples. By analysis of the spectra of DNA at different stages during renaturation it was shown that initially the renatured DNA was rich in guanine–cytosine base pairs and non-random in base sequence, but that, as equilibrium was approached, the renatured DNA gradually resembled native DNA more closely. The rate constant for the renaturation of guanine–cytosine base pairs was slightly higher than for adenine–thymine base pairs.

Intriguing radical–radical interactions among double-electron oxidized adenine–thymine base pairs

2015 ◽  
Vol 619 ◽  
pp. 223-229 ◽  
Author(s):  
Mei Wang ◽  
Jing Zhao ◽  
Laibin Zhang ◽  
Xiyu Su ◽  
Hanlei Su ◽  
...  
Keyword(s):  
Base Pairs ◽  
Double Electron ◽  
Adenine Thymine

A STOCHASTIC MECHANISM FOR DNA MELTING

2013 ◽  
Vol 24 (11) ◽  
pp. 1350077
Author(s):  
SENCER TANERI
Keyword(s):  
Hydrogen Bond ◽  
Potential Energy ◽  
Quantum Fluctuation ◽  
Base Pairs ◽  
Hydrogen Bond Interaction ◽  
Total Potential ◽  
Bond Interaction ◽  
Bose Einstein ◽  
Stochastic Mechanism ◽  
Adenine Thymine

Deoxyribonucleic acid (DNA) is a kind of nucleic acid consisting of two strands which are made up of two Watson–Crick base pairs: adenine–thymine (AT) and guanine–cytosine (GC). There are three components of the total energy. These are the inharmonic stacking interaction, hydrogen bond interaction and the kinetic energy. Morse potential is used to mimic the hydrogen bond interaction between bases on the opposite strands for the overlapping π electrons, when two neighboring bases move out of the stack. The AT pair has 2 hydrogen bonds and the GC pair has 3 of them. The π electrons obey Bose–Einstein (BE) statistics, and the overlapping of them results in quantum fluctuation. It will be shown that this can be simplified into 〈Δy(t)Δy(t)〉 = 2DqΔt type fluctuation between the base pairs. Thus, a metropolis algorithm can be developed for the total potential energy by superposing two potential energy terms as well as including the quantum fluctuation in terms of random displacement of the π electrons. So, one can calculate the melting temperature of base pairs.

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