Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs

Komarov, V. M.; Polozov, R. V.; Konoplev, G. G.

doi:10.1016/s0022-5193(05)80600-9

Cited by 15 publications

(10 citation statements)

References 23 publications

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“…Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. The DNA bases were believed to be planar for many years, until the nonplanarity of their amino groups has been predicted in the 1990s (Aamouche et al, 1997;Hobza & Šponer, 1999;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Komarov & Polozov, 1990;Komarov et al, 1992;Šponer & Hobza, 1994;Šponer et al, 2001). Direct experimental results for the nucleic acid bases amino moieties are not available, but indirect experimental evidence does exist.…”

Section: Dna Bases With Amino Group: Planar or Nonplanar?mentioning

confidence: 99%

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

Brovarets’¹,

Kolomiets²,

Hovorun³

2012

Quantum Chemistry - Molecules for Innovations

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Section: Dna Bases With Amino Group: Planar or Nonplanar?mentioning

confidence: 99%

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

Brovarets’¹,

Kolomiets²,

Hovorun³

2012

Quantum Chemistry - Molecules for Innovations

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“…C Watson-Crick base pair could be intrinsically slightly nonplanar, as was recently obtained at the ab initio SCF/MINI-~ level [ 121. Semiempirical calculations can also yield nonplanar base pairs [66,67]. Because the reliability of these methods is questionable, the respective results should be used with care.…”

Section: Nonplanar Amino Groups and The Base-base Interactionsmentioning

confidence: 99%

DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations

Šponer

Hobza

1996

Int. J. Quantum Chem.

212

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Interactions of DNA bases frequently involve the DNA base amino groups. In contrast to the empirical force fields, the ab initio calculations predict nonplanar DNA base amino groups. The same conclusion also follows from the density functional theory (DFT) calculations. Both local and nonlocal density approximations were used. Optimized geometries of two other molecules with nonplanar amino groups (aniline, formamidine) are presented for comparison. The influence of nonplanar DNA base amino groups on the conformational variability of DNA is discussed. 6 3 1996 John Wiley & Sons, Inc. small systems. The use of the ab initio method in studies of biopolymers is not straightforward [l]. The important advantage of ab initio calculations ydrogen-bonding and stacking interactions is the fact that they can reveal which energy H of DNA bases represent an important source contributions are properly, improperly, or not at all of conformational variability and flexibility of covered by the empirical potentials. Further, they DNA. These interactions were studied mostly are useful in (re)parametrization of the classical using empirical potential calculations, because force fields [2-41. Last, but not least, ab initio sophisticated ab initio calculations are limited to calculations on small model systems can be

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“…The refore the nonplanarity of isolated DNA rare base pairs as well as that of the isolated Watson-Crick ones (see [7]) is their intrinsic property. The propeller base twisting and buckling in isolated rare base pairs has been obtained without any attraction of the stacking perturbation hypothesis that was marked earlier [7,17].…”

Section: Table 3 the Geometrical And Energetical (Kcallmol) Charactermentioning

confidence: 94%

“…According to the geometric selection mechanism of bases as a principal determinant of DNA rep lication fidelity [17][18][19][20] the geometrical and electro static properties of the polymerase active site are likely to have a profound influence on nucleotideinsertion specificities. This influence would strongly favor the insertion of bases having an optimal geo metry, such that the C1'(N9)-C1'(N1) distances and bond angles most closely approximate those of the Watson-Crick base pairs.…”

Section: Structures Of the Rare Base Pairs Determined By Mp2mentioning

confidence: 99%

The molecular mechanism of the spontaneous substitution mutations caused by tautomerism of bases: Post Hartree-Fock study of the DNA rare base pairs

2005

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Gas-phase gradient optimization of the DNA rare base pairs containing lactam-lactim and amino-imino tautomers was carried oat using the Hartree-Fock (HF), Density Functional Theory (DFT) and the second-order Moller-Plesset perturbation (MP2) methods at the 6-31G(d, p) basis set. It is shown that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G*-T and G-T* base pairs. The nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The comparison of the formation energies for the rare base pairs shows the energetical preference of the G*-T and A-C* base pairs as compared with the G-T* and A*-C ones, respectively. It is detected that the stabilization energies of the G-T* and A*-C base pairs describing the interaction between monomers are essentially larger than those of the G*-T and A-C* base pairs, respectively. An analysis of the decomposition members for molecular HF interaction energies by Morokuma-Kitaura (MK) and the Reduced Variational Space (RVS) methods showed that the nature of a larger stability of the G-T* and A*-C base pairs as compared to the G*-T and A-C* ones is due to the electrostatic interactions by 60-65 % and the polarization and charge transfer interactions by 35-40 %.

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Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs

Cited by 15 publications

References 23 publications

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations

The molecular mechanism of the spontaneous substitution mutations caused by tautomerism of bases: Post Hartree-Fock study of the DNA rare base pairs

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