scholarly journals The Watson-Crick rare tautomer hypothesis of mutations and reality

Background: In their Nature's seminal work (Nature. 1953;171:737), J.D. Watson and F.H.C. Crick noted that the structure of DNA admits a so-called tautomeric model of spontaneous point mutations. This work reported at the conference "Nanobiophysics-2019" (Kiev) as a plenary report, is actually an attempt to answer the following questions: (i) "Yes, the tautomerism of the bases is a very attractive model, but how important is it in mutagenesis?" by Morgan (Morgan AR. Trends Biochem. Sci. 1993;18:160–163); (ii) What reality does the rare tautomeric mutation model describe? The structure [А×Т]WC was selected in the work. Developing the previously proposed mutation model×of the Watson-Crick pair [А×Т]WC due to the shift of the bases in the pair relative to each other and the interconnection hydrogen bonds (Kryachko ES, Sabin JR. Int. J. Quantum Chem. 2003;91:695–710), it is shown that some resultant structures possess the electron affinity that is 1.7 times higher compared to the canonical pair, which is definitely of interest in the view of the numerous phenomena associated with a charge transfer in and attachment of an electron to DNA. Objectives: Answer the questions raised in the Background, and show the realism of the tautomeric [А×Т]WC-mutation model modified in the present work on the example of the Watson-Crick pair [А×Т]WC that is dubbed as a pair-tautomerism model. Materials and Methods: The key method is a computer simulation based on the density functional method. All calculations performed in the present work use the package of programs GAUSSIAN with the density functional method invoking the Becke-Lee-Yang-Parr density functional, B3LYP. Results: The paper shows the existence and stability of paired tautomeric mutations in a pair of adenine-thymine and investigates to what wobble pairs it can lead. It is also shown that, due to the specific structure of the paired tautomeric mutation of the adenine-thymine pair, the mutation possesses a larger electronic affinity in comparison with the pair that it generates, and thus can be observed in reality and through it one can explain a number of phenomena of charge transfer in DNA, which, again, emphasizes its reality. Conclusions: On the one hand, a generalization of the Watson-Crick tautomeric hypothesis, proposed in this work, specifically for the adenine-thymine pair, the name of the paired tautomeric mutation. This mutation refers to dipole-binding-electron systems, which implies their high adiabatic electron affinity. The latter, on the other hand, emphasizes the realism of the proposed mutational model and its possible application to the explanation of the phenomena of charge transfer in DNA and the processes of attachment electron to DNA.

2003 ◽  
Vol 17 (18n20) ◽  
pp. 3329-3338 ◽  
Author(s):  
E. P. Stoll ◽  
P. F. Meier ◽  
T. A. Claxton

The electronic structure of La 2 CuO 4 has been studied by first-principles cluster calculations before and after doping. Clusters containing up to five planar copper atoms were investigated using the density functional method. At variance with band-structure calculations, we have been able to determine the charge and spin distributions from molecular orbitals expressed as linear combinations of atomic orbitals localised at the nuclear sites. Doping is achieved by subtracting an electron from the cluster which, although there is a change of spin state, produces a charge distribution which is remarkably similar to the charge distribution of the peripheral charge method which does not involve changes in spin state. The peripheral charge method is designed to simulate doping by placing a carefully chosen set of point charges beyond the periphery of the cluster and relies on the supposition that the hole distribution is closely related to the charge distribution. More importantly the peripheral charge method enables charge distribution changes to be obtained for fractional changes in doping. The results show that with fixed nuclear positions, doping not only depopulates the 2pσ orbitals but also affects other orbitals. This redistribution of charges influences the electric field gradients and hyperfine coupling parameters. The theoretical values for the field gradients are compared to values derived from experiments.


2019 ◽  
Vol 26 (09) ◽  
pp. 1950064
Author(s):  
PEIYING HUO ◽  
XIURONG ZHANG ◽  
ZHICHENG YU ◽  
KUN GAO

A theoretical study was carried out of CumCon-O2-H2O ([Formula: see text]) clusters using density functional method. The results indicate that O2 and H2O molecules are adsorbed at top sites. The presence of H2O promotes more charge transfer to anti-bonding orbitals of O2 molecules which can lead to the elongation of O–O bond. And the effect of charge transfer suggests the occurrence of chemisorption. Comparison between CumCon-O2 and CumCon-O2-H2O, PDOS are also discussed.


Background: As Yu.P. Blagoi, the memory of who is dedicated to this work, once said: "The molecular structure of DNA — the famous double helix — is stabilized by water molecules and metal ions". The central, key interaction that determines both the double-helix structure of DNA and its functioning (the genetic code, replication, mutagenesis) is hydrogen-bonded interaction. Objectives: Demonstration of the diverse manifestations of the hydrogen bond in the structure and functioning of DNA. Materials and Methods: A computer simulation based on the density functional method was used. Results: This paper identifies a wide range of hydrogen-bonded interactions that determine key aspects of both DNA structures and functional features related to heredity (replication, mutagenesis). Conclusions: The preopeness of DNA base pairs with an embedded water molecule on the exterior hydrogen bond create more favorable conditions for proton transitions between bases along the central hydrogen bond. In this case, the hydrogen bonds of the bases to a lesser extent hinder the transition of the proton due to the smaller electrostatic repulsion (due to a larger distance) between them. Therefore, the preopened pairs are likely to form tautomeric forms of nucleic acid bases and to originate a probable mechanism for the formation of point mutations in DNA. At the same time, the central hydrogen bonds with the imino groups of bases in pairs remain intact.


2006 ◽  
Vol 139 (5) ◽  
pp. 847-855 ◽  
Author(s):  
Takeyuki Tanaka ◽  
Haruhiko Tamaoki ◽  
Yasuzo Nishina ◽  
Kiyoshi Shiga ◽  
Takashi Ohno ◽  
...  

2018 ◽  
Vol 25 (07) ◽  
pp. 1950008 ◽  
Author(s):  
PEI-YING HUO ◽  
XIU-RONG ZHANG ◽  
ZHI-CHENG YU ◽  
KUN GAO ◽  
JUN ZHU

A theoretical study was carried out of CO2 adsorption on CumCon(2[Formula: see text]7) clusters using density functional method. Generally CO2 are located at top or bridge sites, while CO2 of Cu2Co4CO2, Co6CO2 and Cu2Co5CO2 clusters are absorbed at hollow sites. Co3CO2 and CuCo2CO2 clusters are more stable than their neighbors, while Cu2CO2 and Cu6CO2 clusters display stronger chemical stability. After adsorption, CO2 is activated with the elongation of the C–O bond owing to electrons transfer from Cu–Co clusters to 2[Formula: see text] anti-bonding orbit of CO2. More charge transfer often corresponds to longer C–O bond and larger adsorption energy, and the chemical activity is stronger correspondingly. Magnetic and electronic properties are also discussed.


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