Specific solvation effects on the structures and properties of Watson–Crick and reverse Watson–Crick isocytosine–cytosine and guanine–cytosine base pairs: a theoretical ab initio study

Zhanpeisov, Nurbosyn U.; Leszczyński, Jerzy

doi:10.1016/s0166-1280(99)00144-x

Cited by 30 publications

(29 citation statements)

References 17 publications

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“…7). These sites are coplanar to the base planes, in agreement with ab initio geometry optimizations performed by Moroni et al [51] using the SCF-MI formalism and, independently, by Leszczinski and colleagues [51,53] using the DFT approach. Thus, it is possible to build "hydrated" VB/HF fragments [X-mH 2 O] n , including m extra water molecules to the usual VB/HF X fragment.…”

Section: Beyond the Rigid Gas-phase Supramoleculesupporting

confidence: 81%

From organic superconductors to DNA: Fragment orbital‐based model

Castet

Ducasse

Fritsch

2005

Int J of Quantum Chemistry

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ABSTRACT:A semi-empirical valence bond/Hartree-Fock (VB/HF) method is developed to calculate one-and two-electron interactions between molecular fragments in conducting supramolecular stacks. This fragment orbital-based formalism allows for consistent extraction of an effective Hamiltonian defined as a "frontier orbital" model. This Hamiltonian quantitatively describes transfer and electrostatic interactions between conducting electrons, while reducing the active space so dramatically that the electronic eigenstates of very large systems may be investigated. The capabilities of the VB/HF method are illustrated on two different supramolecular stacks involving ainteracting fragment. In the first part of this study, the framework of the VB/HF method is used to evaluate the relative magnitude of the electronic interactions between conduction electrons in organic conductors and superconductors derived from Bechgaard salts. In the second part of this study, the VB/HF formalism is extended to derive an effective model for conduction holes along doped DNA double strands. Transferable intra-and intersite parameters were first evaluated from VB/HF calculations carried out on nucleoside pairs. From this interaction databank, the effective Hamiltonian of any type of nucleoside sequence can be defined. The thermalized charge distribution for a single hole delocalized along a DNA sequence containing 240 Watson-Crick pairs is then calculated and compared with the experimental yields of damage revealed by photocleavage experiments.

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Section: Beyond the Rigid Gas-phase Supramoleculesupporting

confidence: 81%

From organic superconductors to DNA: Fragment orbital‐based model

Castet

Ducasse

Fritsch

2005

Int J of Quantum Chemistry

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“…This indicates very clearly that one single configuration cannot represent the structure of the hydrogen bond hydration shell in the liquid. The recent interest in the influence of this hydration shell led to studies of geometryoptimized complexes of GC (and similar systems) and a few water molecules [11,31,32]. These studies required eight water molecules in a complex-optimized structure to obtain a sizable decrease in the interaction energy and increase in the interplanar angle [31].…”

Section: Theoretical Methodologymentioning

confidence: 99%

Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair

2004

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We present a computer simulation study of the hydration of the guanine-cytosine (GC) hydrogen-bonded complex. Using first principles density-functional theory, with gradient-corrected exchange-correlation and Monte Carlo simulation, we include thermal contribution, structural effects, solvent polarization, and the water-water and water-GC hydrogen bond interaction to show that the GC interaction in an aqueous environment is weakened to about 70% of the value obtained for an isolated complex. We also analyze in detail the preferred hydration sites of the GC pair and show that on the average it makes around five hydrogen bonds with water.

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“…Adenine and uracil are nucleic acid bases, while isocytosine is a structural isomer of cytosine that is able to recognize cytosine through a Watson-Crick hydrogen bonding pattern similar to that of the natural guanine/cytosine pair, thus possibly mimicking guanine in an alternative primordial genetic alphabet (Zhanpeisov and Leszczynski 1999). Moreover, compound 5 also recognizes guanine by a reversed Watson-Crick interaction, further enlarging the possibility of hydrogen bond interactions in alternative pre-RNA molecules (Gupta et al 2004).…”

Section: Prebiological Significance Of Formamide Productsmentioning

confidence: 99%

Catalytic effects of Murchison Material: Prebiotic Synthesis and Degradation of RNA Precursors

Saladino

Crestini

Cossetti

et al. 2011

Orig Life Evol Biosph

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Mineral components of the Murchison meteorite were investigated in terms of potential catalytic effects on synthetic and hydrolytic reactions related to ribonucleic acid. We found that the mineral surfaces catalyzed condensation reactions of formamide to form carboxylic acids, amino acids, nucleobases and sugar precursors. These results suggest that formamide condensation reactions in the parent bodies of carbonaceous meteorites could give rise to multiple organic compounds thought to be required for the emergence of life. Previous studies have demonstrated similar catalytic effects for mineral assemblies likely to have been present in the early Earth environment. The minerals had little or no effect in promoting hydrolysis of RNA (24mer of polyadenylic acid) at 80°C over a pH range from 4.2 to 9.3. RNA was most stable in the neutral pH range, with a half-life ~5 h, but at higher and lower pH ranges the half-life decreased to ~1 h. These results suggest that if RNA was somehow incorporated into a primitive form of RNA-based thermophilic life, either it must be protected from random hydrolytic events, or the rate of synthesis must exceed the rate of hydrolysis.

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Specific solvation effects on the structures and properties of Watson–Crick and reverse Watson–Crick isocytosine–cytosine and guanine–cytosine base pairs: a theoretical ab initio study

Cited by 30 publications

References 17 publications

From organic superconductors to DNA: Fragment orbital‐based model

From organic superconductors to DNA: Fragment orbital‐based model

Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair

Catalytic effects of Murchison Material: Prebiotic Synthesis and Degradation of RNA Precursors

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