External electric field promotes proton transfer in the radical cation of adenine–thymine

2016 ◽  
Vol 30 (21) ◽  
pp. 1650276 ◽  
Author(s):  
Guiqing Zhang ◽  
Shijie Xie
Keyword(s):  
Electric Field ◽  
Proton Transfer ◽  
External Electric Field ◽  
Radical Cation ◽  
Base Pair ◽  
Low Temperatures ◽  
Room Temperature ◽  
Theoretical Calculations ◽  
Base Pairs ◽  
Adenine Thymine

According to [Formula: see text] measurements, it has been predicted that proton transfer would not occur in the radical cation of adenine–thymine (A:T). However, recent theoretical calculations indicate that proton transfer takes place in the base pair in water below the room temperature. We have performed simulations of proton transfer in the cation of B-DNA stack composed of 10 A:T base pairs in water from 20 K to 300 K. Proton transfer occurs below the room temperature, meanwhile it could also be observed at the room temperature under the external electric field. Another case that interests us is that proton transfer bounces back after [Formula: see text][Formula: see text]300 fs from the appearance of proton transfer at low temperatures.

scholarly journals Electric Field Dependence of the Fluorescence Intensity of Solute Molecules and Fourth Order Effects

1985 ◽  
Vol 40 (9) ◽  
pp. 874-876
Author(s):  
Hilmar Bischof ◽  
Wolfram Baumann
Keyword(s):  
Electric Field ◽  
External Electric Field ◽  
Field Dependence ◽  
Fourth Order ◽  
Fluorescence Intensity ◽  
Room Temperature ◽  
Order Effects ◽  
Electric Field Dependence ◽  
Total Fluorescence

Abstract The effect of an external electric field on the total fluorescence of solute molecules is studied up to fourth order theoretically, and is checked experimentally with 4´-N,N-dimethylamino- 4-nitrostilbene in dioxane at room temperature.

Proton Transfer in Adenine−Thymine Radical Cation Embedded in B-Form DNA

2010 ◽  
Vol 1 (9) ◽  
pp. 1403-1407 ◽  
Author(s):  
Colin Kinz-Thompson ◽  
Esther Conwell
Keyword(s):  
Proton Transfer ◽  
Radical Cation ◽  
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.

Proton Transfer in the Adenine-Thymine Base Pair

1994 ◽  
Vol 116 (4) ◽  
pp. 1457-1460 ◽  
Author(s):  
Jan Florian ◽  
Vojtech Hrouda ◽  
Pavel Hobza
Keyword(s):  
Proton Transfer ◽  
Base Pair ◽  
Adenine Thymine

Elektrochemische Synthesen, XIV [1] Radikalkation-Salze des Naphthalins / Electrochemical Syntheses, XIV [1]. Radical Cation Salts of Naphthalene

1978 ◽  
Vol 33 (5) ◽  
pp. 498-506 ◽  
Author(s):  
Heinz P. Fritz ◽  
Helmut Gebauer ◽  
Peter Friedrich ◽  
Peter Ecker ◽  
Reinhold Artes ◽  
...  
Keyword(s):  
Radical Cation ◽  
Low Temperatures ◽  
Room Temperature ◽  
Specific Conductivity ◽  
Columnar Structure ◽  
Screw Axis ◽  
Radical Cation Salts ◽  
Difference Fourier ◽  
Pure Hydrocarbon

Abstract By anodic oxidation of naphthalene in H2CCl2/O.O2m Bu4NPF6 at -45 °C dark red-violet crystals of (C10H8)2PF6 can be obtained by electrocrystallisation. They are stable at low temperatures, however, decompose on warming. In solution and in the polycrystalline state these radical cation salts show only narrow e.p.r. signals without h.f.s. The specific conductivity of a polycrystalline pellet at room temperature was determined to be 0.12 ±0.046 Ohm-1 cm-1 . The structure determination of (C10H8)2PF6 yielded the tetragonal space group P42/n, Z = 2, a = b = 1156(2), c = 640(1) pm. Patterson synthesis and difference Fourier analyses showed the compound to have a columnar stacking of C10H8 units the long molecular axes of which are twisted alternately by 90° around a screw axis in c-direction, and the molecular planes of which are 320 pm apart. The PF6-ions have four nearest C10H8 neighbours lying in pairs in parallel planes 63 pm above and below that plane of PF6- perpendicular to the c-axis and containing a PF4 group. This is the first established case for a columnar structure of a pure hydrocarbon radical cation. (C10H8)2AsF6 is isomorphous.

scholarly journals Preparation of vertically aligned ZnO crystal rods in aqueous solution at external electric field

2014 ◽  
Vol 32 (2) ◽  
pp. 157-163 ◽  
Author(s):  
B. Prijamboedi ◽  
E. Maryanti ◽  
T. Haryati
Keyword(s):  
Aqueous Solution ◽  
Electric Field ◽  
External Electric Field ◽  
Indium Tin Oxide ◽  
Room Temperature ◽  
Negative Electrode ◽  
Glass Substrates ◽  
Ito Glass ◽  
Vertically Aligned ◽  
Zno Crystal

AbstractIn this study, an external electric field was used to facilitate the growth of vertically aligned ZnO crystal rods on the surface of indium tin oxide (ITO) glass substrates in an aqueous solution. We used Zn(NO3) and C6H12N4 as precursor and reagent. We found that the external electric field generated by DC potential of 5 kV between two electrodes that were placed outside the bottle could facilitate the growth of homogeneous, high density and vertically aligned ZnO crystal rods. Position of the substrate during the growth of crystal was found to be important to obtain well aligned crystal. The crystals that were grown near the negative electrode had the best properties. Photoluminescence measurement at room temperature revealed sharp peaks at around 360 and 380 nm and a broad peak around 420 nm that indicated good properties of ZnO crystals grown with external electric field.

scholarly journals Trapping and transport of charges in DNA by mobile discrete breathers

2018 ◽  
Vol 13 (1) ◽  
pp. 1-12 ◽  
Author(s):  
A.P. Chetverikov ◽  
K.S. Sergeev ◽  
V.D. Lakhno
Keyword(s):  
Numerical Simulation ◽  
Wave Function ◽  
Charged Particle ◽  
Electric Field ◽  
External Electric Field ◽  
Base Pair ◽  
Quasi Particle ◽  
Dna Molecule ◽  
Discrete Breathers

Numerical simulation of trapping and transport of a charged particle (electron or hole) by mobile discrete breathes (mobile DB, MDB) in DNA molecule has been provided. Mobile DBs have been excited by disturbance of displacements or velocities of adjacent nucleotide pairs dislocated near one of fixed ends of the molecule. It is shown that effective forming of a stable quasi-particle “MDB + electron” occurs when a few of nucleotide pairs at the end of DNA are excited. Breathes may be excited by disturbances of displacements and velocities directed both to axis and from axis of the molecule. A wave function of an electron must be located initially in a region of disturbance of the molecule. It has been found that a metastable quasi-particle may be transported at a distance up to 200 of a rise per base pair. The mechanism of transport of a charged particle presented is not in need of an external electric field and may be considered as an alternative one to the polaronic mechanism.

Transient proton transfer of base pair hydrogen bonds induced by intense terahertz radiation

2020 ◽  
Vol 22 (17) ◽  
pp. 9316-9321
Author(s):  
Kaicheng Wang ◽  
Lixia Yang ◽  
Shaomeng Wang ◽  
Lianghao Guo ◽  
Jialu Ma ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Terahertz Radiation ◽  
Base Pair ◽  
Quantum Simulation ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

Intense terahertz radiation was applied to trigger transient proton transfer in DNA base pairs through quantum simulation.

Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand

2020 ◽  
Vol 22 (26) ◽  
pp. 14875-14888 ◽  
Author(s):  
Yan Sun ◽  
May Myat Moe ◽  
Jianbo Liu
Keyword(s):  
Mass Spectrometry ◽  
Proton Transfer ◽  
Radical Cation ◽  
Base Pair ◽  
Hydrogen Transfer ◽  
Theoretical Study ◽  
Computational Study ◽  
Collision Induced Dissociation ◽  
Water Ligand

A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.

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