A semi-empirical SCF-MO study on the base-pairing properties of 8-oxopurines: significance for mutagenicity

Venkateswarlu, Divi; Duncan, Richard H.; Bansal, Manju

doi:10.1039/a603927h

Cited by 13 publications

(4 citation statements)

References 37 publications

(40 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ROS or RNOS preferentially attack guanine in DNA probably as its ionization potential is least among those of all the bases. , Among the various ROS, the OH • radical is most reactive. , It is produced by a large number of enzymatic and nonenzymatic reactions , and can react with almost all biomolecules leading to DNA strand break, ,, DNA-protein cross-link, base pair mutation, , base oxidation, , and lipid peroxidation, etc. The OH • radical is involved in addition, hydrogen abstraction, and electron-transfer reactions. , Thus it can produce a wide variety of chemicals and can create genome instability and cellular damage. , The OH • radical is shown to attack the C4, C5, and C8 positions of guanine, the C8 position being most favored for the reaction. − When an OH • radical attacks 2‘-deoxyguanosine, hydrogen abstraction from the C4‘ position of deoxyribose or formation of the C4‘-OH • adduct takes place beside the formation of the C8-OH • adduct…”

Section: Introductionmentioning

confidence: 99%

“…Reactions of the OH • radical with organic molecules have been extensively studied. − Theoretical investigations of relative stabilities of the different tautomers of 8OG have been carried out by Venkateswarlu and Leszczynski, Venkateswarlu et al, and Cysewski. − It is found that stabilities of the 6,8-diketo and 6-enol, 8-keto forms of 8OG are comparable, the former being more stable in the gas phase than the latter while the reverse is true in aqueous media . The mechanism of OH • radical addition to imidazole and subsequent water elimination has been studied by Liano and Eriksson using density functional and ab initio methods .…”

Section: Introductionmentioning

confidence: 99%

“…13,28 The OH • radical is shown to attack the C4, C5, and C8 positions of guanine, the C8 position being most favored for the reaction. [29][30][31] When an OH • radical attacks 2′-deoxyguanosine, hydrogen abstraction from the C4′ position of deoxyribose or formation of the C4′-OH • adduct takes place beside the formation of the C8-OH • adduct. 32 Bruskov et al 33 have suggested that 8OG can be formed due to heat-mediated generation of ROS and their reactions with DNA.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH^• Radicals and the H₂O₂ Molecule with Guanine: A Quantum Computational Study

Jena

Mishra

2005

J. Phys. Chem. B

View full text Add to dashboard Cite

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH^• Radicals and the H₂O₂ Molecule with Guanine: A Quantum Computational Study

Jena

Mishra

2005

J. Phys. Chem. B

View full text Add to dashboard Cite

show abstract

“…However, the general approaches and methodologies used are relevant. Some of this work includes the study of stacking interactions,6 highly accurate pairing energies,7 cation binding to base pairs,8 radical ion forms of DNA base pairs,9–11 and modified DNA mispairs as a source of mutations 12, 13…”

Section: Introductionmentioning

confidence: 99%

Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search

Neihsial

Lyngdoh

2008

J Comput Chem

View full text Add to dashboard Cite

Density functional theory at the B3LYP/6-31G* level with counterpoise correction has been employed to study six sets of nitrogenous bases for the capacity of each to form H-bonded dimers restricted to a chosen pairing configuration. These results are augmented by MP2/6-311++G(d,p) single point calculations on the B3LYP/6-31G* optimized geometries. Each set has two bases, including substituted azoles, imidazoles, pyrimidines, and fused ring systems. This study aims to determine the suitability of each set to furnish H-bonded base pairs which may serve as repeat units for self-associative H-bonded macromolecular duplexes with the capacity to store and replicate information at the molecular level. Out of the various possibilities tested here, a set of two substituted pyrimidines best satisfies the prescribed criteria and may be put forward as a good candidate to yield isomorphic repeat units for designing such synthetic information-bearing macromolecular duplexes. The optimized configurations of these chosen base pairs as calculated at the B3LYP/6-31G* level compare well with those calculated at the B3LYP/6-31++G(d,p) and MP2/6-31G(d,p) levels, and indicate that isomorphism of the two base pairs is independent of method used. Assuming a one-to-one correspondence for encoding information in the macromolecule, such a set of two bases can allow the macromolecule to encode up to 8 types of encrypted species.

show abstract

Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

Das

Lyngdoh

2012

J Mol Model

View full text Add to dashboard Cite

Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.

show abstract

A semi-empirical SCF-MO study on the base-pairing properties of 8-oxopurines: significance for mutagenicity

Cited by 13 publications

References 37 publications

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH^• Radicals and the H₂O₂ Molecule with Guanine: A Quantum Computational Study

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH^• Radicals and the H₂O₂ Molecule with Guanine: A Quantum Computational Study

Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search

Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

Contact Info

Product

Resources

About

A semi-empirical SCF-MO study on the base-pairing properties of 8-oxopurines: significance for mutagenicity

Cited by 13 publications

References 37 publications

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH• Radicals and the H2O2 Molecule with Guanine: A Quantum Computational Study

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH• Radicals and the H2O2 Molecule with Guanine: A Quantum Computational Study

Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search

Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

Contact Info

Product

Resources

About

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH^• Radicals and the H₂O₂ Molecule with Guanine: A Quantum Computational Study

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH^• Radicals and the H₂O₂ Molecule with Guanine: A Quantum Computational Study