The calculations of interaction energy between complementary base pairs of nucleic acids in the function of 5 variables determining parameters of double helix (Arnott's parameters) have been carried out by the method of atom-atom potential functions. Four of these parameters are essential in the case of mutual positions of bases corresponding to conformational A-family, and only two parameters (the distance between pairs along helical axis and the angle of rotation around this axis)--in the case of B-family. Positions of the interaction energy minima over each of the essential variables are close to experimentally determined parameters. The interaction energy minima are more pronounced for A-family conformations. The positions of minima in this case are determined by dispersion and short range repulsion energy.

Adenine↗

PubMedDate not supplied

[The influence of complementary base pair interactions on secondary structure formation and conformational transitions in polynucleotides].

The calculations have been carried out of interaction energy between complementary base pairs of nucleic acids in the function of conformational parametres of double helix (Arnott's parameters) by the method of atom-atom potential functions. Interaction energy as a function of conformational parametres is valley-like and varies little along the bottom of the valley. The regions of interaction energy minima are compared with experimentally determined conformational parametres of nucleic acid double helices. On the basis of calculation results the pathways of conformational transitions between different forms of double-helical polynucleotides are discussed.

Binding Sites↗

PubMedDate not supplied

[Interactions between nucleic acid bases. New parameters of potential functions and energy minima].

The parameters of atom-atom potential functions suggested by one of the authors in 1979-1986 were slightly changed. The changes were performed to achieve a better agreement with experimental data of interaction energy values in global minima and hydrogen bond lengths. These changes resulted in better accord with experimental values of distances between the layers in DNA monomer crystals and between the base pairs in oligonucleotide duplexes. The refined potential functions were used to calculate the energy of interactions between nucleic acid bases in various mutual positions. The calculations revealed a few types of mutual base arrangements in minima of interaction energy for each pairwise base combination. A new type of minima was found, which correspond to a nearly perpendicular arrangement of base rings and the formation of the intermolecular hydrogen bond.

Algorithms↗

PubMedDate not supplied

[Theoretical conformational analysis of doulble-stranded polynucleotides].

Calculations of intramolecular interaction energy of two-stranded helical homopolynucleotide in the function of nine conformational variables have been carried out by the method of atom-atom potential functions. Four of these variables determine mutual position of base pairs, other four--deoxiribose ring conformation and other one--orientation of this ring with respect to the base. For this purpose an algorythm connecting dependent variables with independent ones has been developed. The investigation of energy function has shown that in the space of conformational parameters there are two valleys, which correspond to A-and B-families of conformations. Experimentaly determined conformations of two-stranded helical polynucleotides are located along the bottoms of these valleys. Along the bottom of each valley the intramolecular interaction energy changes rather little when conformational parameters change within a wide range. The valleys are separated by an energetical barrier.

Models, Chemical↗

PubMedDate not supplied

[Interaction of caffeine with basic nucleic acids my a molecular mechanic method].

To understand some aspects of the biological action of caffeine (CAF), the interaction energies for various mutual positions of CAF and DNA bases or basepairs were calculated. Three types of mutual CAF-base (CAF-basepair) arrangements corresponding to the minima of interaction energy were revealed. One type of minima correspond to the stacking arrangement of molecules. This type is important for interactions of CAF with DNA monomers and single-stranded fragments. The other two types of minima correspond to the formation of intermolecular hydrogen bonds. Some of these minima may occur during the interaction of CAF with the double helix. One of these types corresponds to the nearly in-plane position of molecules. The other type of minima correspond to the nearly perpendicular arrangement of molecule planes. The minima of the last type are supposed to be the most important for the interaction of CAF with the DNA duplex, and interaction energies for this type of minima have the most negative values.

Caffeine↗

PubMedDate not supplied

[Possible configuration of dimers of Gua-Cyt bases. Computation by molecular mechanic models and density functional theory].

The energies of interactions between guanine and cytosine in various mutual positions were calculated by the methods of molecular mechanics with refined atom-atom potential functions and the quantum mechanics theory of density functional. Both methods indicate three types of mutual positions of bases in local energy minima. These types correspond to (1) nearly coplanar base positions with intermolecular hydrogen bond formation (base pairing); (2) arrangements of two bases in nearly parallel planes one above another (base stacking); and (3) nearly perpendicular positions of base planes. According to the calculations, the global energy minimum corresponds to the Watson-Crick base pair with three hydrogen bonds. A specific feature of the pair is a transition from many positions of type (2) to positions of type (1) without any energy barrier. This feature is revealed by both methods. Another special feature of this pair is a deviation, for most of mutual base positions, of the amine group atoms from the ring plane, the deviation being more pronounced for Gua. These features are important for understanding the conformational behavior of DNA fragments and the RNA structure.

Cytosine↗

PubMedDate not supplied

[Modeling of hydration of incorrect nucleic acid base pairs by the Monte Carlo method].

The hydration of water bridged base pairs of nucleic acids have been simulated via the Monte Carlo method. The simulation have shown that water molecules forming H-bonds with both bases preserve this H-bonding with large probability in the water surrounding. This fact supports the supposition about the important role of water molecules in wrong base pair formation and about the role of these base pairs in the structure and functioning of nucleic acids.

Base Composition↗

PubMedDate not supplied

[Monte-Carlo simulation of hydration of nucleic acid fragments].

Monte-Carlo simulation of the systems containing a stack of 6 complementary base pairs and 180 water molecules has been performed. Characteristic of the hydration shell structure in major and minor grooves has been found for the stacks of repeating A : U and G : C base pairs as well as alternating (A : U, U : A) and (G : C, C : G) ones. Probabilities of the formation of bridges, formed by 1, 2 and 3 water molecules, between hydrophilic centres of the bases have been estimated. One water molecule forms an H-bonded bridge between two adjacent hydrophilic centres with high probability if N...N, N...O or O...O distance between these centres is close to 4.3 A. Hydration shell structure was found to depend significantly on the stack sequence and configuration, while global hydration characteristics (average energy, the number of water-water and water-base H-bonds) are only slightly dependent on the stack sequence and configuration. For the stacks in A conformation the number of water molecules forming more than one H-bonds with the bases is greater in comparison with the stacks in B-like conformation. This result is discussed in connection with the concept of hydration economy during B to A transition.

Base Composition↗

PubMedDate not supplied

[Additional possibilities of the formation of incorrect nucleotide pairs].

Calculations of intermolecular interaction energies for the systems consisting of two nitrogen bases and one or two molecules of water have been performed by the atom--atom potential function method. In some energy minima corresponding to the arrangement of the bases with one of the bases being in the syn-orientation with respect to the sugar two bases are linked through one H-bond and one or two water bridges. Such pairs provide an additional possible pathway for the appearance of errors during template biosynthesis.

Base Composition↗

PubMedDate not supplied

[Study of the hydration characteristics of nucleic acid bases and their complementary pairs using the Monte-Carlo method].

To elucidate the role of certain atomic groups in the formation of the nucleic acid hydrate shell, we simulated the systems involving a base or a complementary pair (the base molecules are methylated in N9 of purines and in N1 of pyrimidines) and 25 water molecules using the Monte-Carlo method. All hydrophilic centers, except for N1 purines and N3 pyrimidines in complementary pairs, form hydrogen bonds (H-bonds) with water molecules. The mean numbers of H-bonds formed by different centers, and distributions of the geometric characteristics of these bonds, which appeared similar to those in crystals, have been calculated. The formation of bridges of one, two of three water molecules between hydrophilic centers was shown. The probabilities of formation of these bridges have been calculated.

DNA↗

PubMedDate not supplied

[Structure of poly(dA).poly(dT) from data of x-ray diffraction, energy calculations and nuclear magnetic resonance].

The results of X-ray diffraction studies of poly(dA).poly(dT) have been compared with the results of energy optimization and with the NMR data in solution. Slight refinement of the X-ray and energetically optimal models leads to a very good quantitative agreement with the NMR data, that suggests similarity of the poly(dA).poly(dT) structure in a condensed state and in solution. One of the features distinguishing these models from the classic B form is a narrowed minor groove of the double helix. The anomalous properties of DNA with this sequence can be related specific organization of the water molecules near the polynucleotide.

Magnetic Resonance Spectroscopy↗

PubMedDate not supplied

[Base interaction and conformation manifestations of repetitive nucleotide sequences].

To understand why different nucleotide sequences prefer different double helical conformations and to predict conformational behaviour of definite sequences the base-base interaction energy in regular helices consisting of A:U, A:T, G:C and I:C (hypoxanthine-cytosine) base pairs was calculated. Interaction energy was assumed to be a function of eight conformational parameters: H, the distance between adjacent pairs along helix axes; tau, turn angle of one pair relative to the neighbouring one; angles between base planes in a pair (TW, propeller twist and BL, buckle) and position of pairs with respect to helix axes (D and SL, displacements in the plane normal to helix axes, and TL and RL, inclinations to this plane, tilt and roll, respectively). For H and tau characteristic of A- and B-families of nucleic acid conformations (2.5 A less than H less than or equal to 3.5 A, 30 degrees less than or equal to tau less than or equal to 45 degrees) the ranges of conformational parameters corresponding to energy values close to minimal ones (valleys) and correlations between conformational parameters were revealed. Valleys for different sequences largely coincide but have distinctive characteristics for each sequence. Reasons for base pair planarity distortion in double-stranded helices were considered. The calculations permit to account for A-phility of G:C sequences and B-phility for A:T sequences. The valley for I:C sequence branches. This corresponds to A:T-like behaviour in some cases and G:C-like in the others.

DNA↗

PubMedDate not supplied

[Interaction of nucleic acid bases with water molecules and formation of mismatched nucleotide pairs].

The possibility of the inclusion of water molecules in the formation of mismatched nucleotide pairs was considered in relation to the mechanisms of point errors in template directed biosynthesis. Calculations of the intermolecular interaction energy for systems containing two bases and one water molecule were carried out by the method of atom-atom potential functions. There exist energy minima for each base pair, corresponding to a single N--H...O or N--H...N H-bond between the bases and H-bonding of the water molecule with both bases. The relative positions of glycosyl bonds in some of these minima are closer to those for Watson--Crick pairs, than the positions of minima for these pairs without water. For other minima, the H-bond formation between the water molecule and the two bases additionally stabilizes the relative base position in wobble-pairs with two H-bonds between the bases. The base and water positions in energy minima are compared with the positions in some pairs proposed on the basis of NMR and X-ray data for double helical oligonucleotides.

Base Composition↗

PubMedDate not supplied

[Semiempirical calculation of the energy of interaction between nitrogenous bases].

Explore the source record for details and available documents.

Adenine↗