Quantum mechanical study of bases interactions in various associates in atomic dipole approximation

Kudritskaya, Z. G.; Danilov, V.I.

doi:10.1016/0022-5193(76)90172-7

Cited by 64 publications

(27 citation statements)

References 34 publications

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“…The mean data for forward and reverse promoter sequences (number of forward sequences equals 28 and number of reverse ones equals 34) are presented in Fig.2. The mean energy of nucleotide pair is −29.33 kJ/mol for AT-pair and −70.35 kJ/mol for GC-pair (Kudritskaya and Danilov, 1976). As Fig.2 data show that the distribution of pair free energy of interaction in promoter sequences have three minimums.…”

Section: Resultsmentioning

confidence: 78%

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence

Berezhnoy

Shckorbatov²

2005

J Zheijang Univ Sci B

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Abstract:The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at -35, -8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to -8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.

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Section: Resultsmentioning

confidence: 78%

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence

Berezhnoy

Shckorbatov²

2005

J Zheijang Univ Sci B

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“…We henceforth study a chain of N sites with periodic boundary conditions described by the Lagrangian (5), a dynamical system depending on the single parameter 2 ϵ 4D a 2 / k (henceforth called the Morse parameter). Using the values in the literature [13][14][15], we estimate a realistic biological value for to be = 6.3, and the scaling factors for the units of time and energy to be 0.810 −12 s and 2.010 −3 eV, respectively. For small amplitudes, the normal mode frequency spectrum of Eq.…”

Section: ͑4͒mentioning

confidence: 99%

“…The masses of the bases have a common value m, the constant k is the longitudinal elastic constant, and the parameters D and a define the Morse potential describing the transverse H bonds linking the two chains. The experimental values for these parameters have been discussed in the literature [3,[13][14][15]: the mass of the base pairs is about 300 a.m.u. = 5.010 −25 kg and the linear spring constant is 0.04 eV/ Å 2 .…”

Section: Introductionmentioning

confidence: 99%

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Energy localization in the Peyrard-Bishop DNA model

et al. 2004

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We study energy localization on the oscillator chain proposed by Peyrard and Bishop to model DNA. We search numerically for conditions with initial energy in a small subgroup of consecutive oscillators of a finite chain and such that the oscillation amplitude is small outside this subgroup on a long time scale. We use a localization criterion based on the information entropy and verify numerically that such localized excitations exist when the nonlinear dynamics of the subgroup oscillates with a frequency inside the reactive band of the linear chain. We predict a mimium value for the Morse parameter ͑ Ͼ 2.25͒ (the only parameter of our normalized model), in agreement with the numerical calculations (an estimate for the biological value is = 6.3). For supercritical masses, we use canonical perturbation theory to expand the frequencies of the subgroup and we calculate an energy threshold in agreement with the numerical calculations.

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“…Base-pair binding energies are presented by -ǫ AT and -ǫ GC for A-T and G-C, respectively, with ǫ AT , ǫ GC > 0, and stacking binding energies by −ǫ ν , ν = 1, ..., 16. Their values have been calculated using quantum chemistry methods [44,45]. In our computational study we used ǫ AT = 7 kcal/mol, ǫ GC = 16.79 kcal/mol, and the values given in Table I for the stacking energies.…”

Section: Denaturation Of Diblock Dnamentioning

confidence: 99%

Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies

Singh

Granek

2016

The Journal of Chemical Physics

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We study DNA denaturation by integrating elasticity — as described by the Gaussian network model — with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed “bubbles” (“loops”) is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.

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Quantum mechanical study of bases interactions in various associates in atomic dipole approximation

Cited by 64 publications

References 34 publications

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence

Energy localization in the Peyrard-Bishop DNA model

Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies

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