Theoretical Investigation of the Hydrogen Bond Strengths in Guanine-Cytosine and Adenine-Thymine Base Pairs

1994 ◽  
Vol 116 (6) ◽  
pp. 2493-2499 ◽  
Author(s):  
Ian R. Gould ◽  
Peter A. Kollman
Keyword(s):  
Hydrogen Bond ◽  
Theoretical Investigation ◽  
Base Pairs ◽  
Bond Strengths ◽  
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.

scholarly journals DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA

2020 ◽  
Author(s):  
Maria Izabel Muniz ◽  
Hershel Lackey ◽  
Jennifer Heemstra ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Thermodynamic Properties ◽  
Stacking Interactions ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Mesoscopic Modeling ◽  
Bond Strengths ◽  
Purine Pyrimidine

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.

Hydrogen Bond Mediated Association of Dinucleotide Analogs

2003 ◽  
Vol 217 (12) ◽  
pp. 1463-1472 ◽  
Author(s):  
Eline M. Basílio Janke ◽  
Klaus Weisz
Keyword(s):  
Hydrogen Bond ◽  
Acetic Acid ◽  
Chloroform Solution ◽  
Pair Formation ◽  
Spectroscopic Techniques ◽  
Base Pairs ◽  
Base Interaction ◽  
Ambient Temperatures ◽  
H Nmr ◽  
Adenine Thymine

AbstractSeveral dinucleotide analogs, in which two of the nucleobases adenine, thymine and uracil are connected by a hexadecamethylene linker have been synthesized and studied for their base-base interaction in a chloroform solution. Using 1H NMR spectroscopic techniques intramolecular base pair formation through hydrogen bonding is observed at ambient temperatures but found to strongly depend on the identity of paired bases. Thus, whereas cyclization through intramolecular base-base interactions predominate for adenine–(CH2)16–thymine and adenine–(CH2)16–uracil, no intramolecular adenine-adenine pairing was observed. Upon addition of acetic acid to adenine–(CH2)16–thymine, strong adenine-acetic acid interactions result in the disruption of preformed intramolecular adenine-thymine base pairs.

Theoretical investigation of the proton transfer mechanism in guanine-cytosine and adenine-thymine base pairs

2012 ◽  
Vol 137 (19) ◽  
pp. 195101 ◽  
Author(s):  
Shiyan Xiao ◽  
Lei Wang ◽  
Yuan Liu ◽  
Xiangsong Lin ◽  
Haojun Liang
Keyword(s):  
Proton Transfer ◽  
Theoretical Investigation ◽  
Transfer Mechanism ◽  
Base Pairs ◽  
Adenine Thymine

scholarly journals DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA

2020 ◽  
Author(s):  
Maria Izabel Muniz ◽  
Hershel Lackey ◽  
Jennifer Heemstra ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Thermodynamic Properties ◽  
Stacking Interactions ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Mesoscopic Modeling ◽  
Bond Strengths ◽  
Purine Pyrimidine

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.

Study of the hydrogen bond in different orientations of adenine-thymine base pairs: An ab initio study

2005 ◽  
Vol 70 (3) ◽  
pp. 366-376 ◽  
Author(s):  
M. Monajjemi ◽  
B. Chahkandi ◽  
K. Zare ◽  
A. Amiri
Keyword(s):  
Hydrogen Bond ◽  
Ab Initio ◽  
Ab Initio Study ◽  
Base Pairs ◽  
Adenine Thymine
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