Base Pair Complexes Research Articles

Configurational specificity of stacking interactions in DNA base pairs: A computational analysis

AbstractA theoretical study of stacking patterns of various hydrogen‐bonded base pair complexes has been undertaken. Modified Rayleigh‐Schrodinger perturbation theory for intermediate range interactions, has been employed to evaluate the stacking interactions using multicentered‐multipole expansion method. Net atomic charge and corresponding dipole components located at each of the atomic centers have been computed by CNDO/2 method. An analysis of the intermolecular forces involved in the stable formation of the various base pair complexes, has been presented and the results have been discussed in the light of experimental as well as other theoretical observations. The possibility of relative preference of the left‐handed configuration for alternating sequences has been quantitatively explored.

Base-pairing properties of O-methylated bases of nucleic acids. Energetic and steric considerations.

Base-pairing properties of O-methylated nucleic-acid bases have been systematically investigated using both semi-empirical quantum-mechanical methods and a second-order perturbation formalism. The energetic, steric and electronic properties of (a) the individual methylated bases, (b) possible base-pairs formed between O-methylated and normal bases, and (c) mini-helices incorporating O-methylated bases were calculated. Two types of base-paired complexes were obtained: Those involving classical linear hydrogen bonds, and those involving bifurcated hydrogen-donor-hydrogen-acceptor interactions. In most complexes the presence of mispairs in the helical structure of nucleic acids is expected to create a local perturbation in the structure of the helix. Even though the most stable planar configurations of the mispairs may deviate markedly from those in the regular double helix, the induced deformations in the structure of the backbone are relatively small. Internal energies and geometries of mispairs are strongly affected by the conformation of the exocyclic group of the methylated bases. Another important contribution to the stability of various base-pairing schemes comes from stacking interactions.

High sensitivity of amide V bands in uracil and its derivatives to the strengths of hydrogen bonding

Bands due to CO, CH and NH out-of-plane bending modes have been identified and studied as a function of temperature in the cis-amide uracil and its derivatives. Only the bands due to NH out-of-plane bending modes, the so-called amide V bands, are found to be sensitive to the strengths of hydrogen bonds. This sensitivity is found to be as great as that of NH stretching bands. It is shown that the amide V bands could be used, among other things, to detect the possibility and/or extent of hydrogen bonding in Hoogsteen-type base-pairs. This provides a very simple way to detect the presence of undesirable uncomplexed bases in the study of base-paired complexes. These results point to the need to understand better the origin of amide V bands.

Left handed double helices: effect of sequence on the spatial configuration of high anti nucleic acids.

The conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates in which the glycosidic torsion is fixed to congruent to 120 degree by the formation of a covalent link between the base and the sugar ring are explored by 1H NMR spectroscopy in order to obtain information about the spatial configuration of high anti nucleic acids. The intramolecular stack of the high anti dimers were found to be left handed, in contrast to that (right handed) for natural oligomers, which are low anti. Even though both the high anti pyrimidine-purine and purine-pyrimidine dimers have similar backbone torsion angles, they display widely different relative geometry between the bases; thus in the former there is extensive base-base overlap in the stack, and in the latter there is negligible intramolecular base-base overlap. In addition it was found that purine-pyrimidine systems form miniature double helices in which there is substantial interstrand purine-purine interaction; on the other hand the pyridine-purine high anti dinucleosides have no proclivity to form such base-paired complexes in solution. Mathematical polymerization of the conformation of the high anti purine-pyrimidine dinucleoside monophosphates generates a left handed helix for high anti polynucleotides. This also means that the double helix for high anti-nucleic acids containing purine-pyrimidine repeated units may also be left handed, as had been suggested [Sundaralingam, M., & Yathindra, N. (1977) Int. J. Quantum Chem., Quantum Biol. Symp. 4, 285]. It is suggested that the plasticity in the structure of genomic DNA is such that, if under certain conditions of interactions the sugar-base torsion of certain domains assume high anti values, that domain will become left handed, and this in turn can be a mechanism for the control of expression by genomic DNA.

Radicals in irradiated monocrystals of the base-pair complex 9-ethyl adenine: 1-methyl uracil.

SummaryRadical formation in monocrystals of equimolar complexes of 9-ethyl adenine: 1-methyl uracil by irradiation with X-rays was investigated at 77 K and 300 K using e.s.r.-spectroscopy at 9·5 GHz and 35 GHz. Five different types of spectrum were identified, which corresponded to spectra of the irradiated components. A hydrogen abstraction radical (I and III) and a hydrogen addition radical (II and IV) were assigned to each of the two constituents. The fifth species, with an unidentified singlet after irradiation at 77 K, has also been found in irradiated single crystals of 9-ethyl adenine. By bleaching with U.V.-light or heating to about 150 K, it is decomposed irreversibly. After a crystal irradiated at 77 K is warmed to room temperature only pyrimidine radicals I and II are left. At 77 K the two types of radical (I and II) in 1-methyl uracil are present in addition to the singlet line; at 300 K the addition radicals (II and IV) predominate in comparable proportions, but the abstraction radicals (I an...

Binding of complementary pentanucleotides to the anticodon loop of transfer RNA

The conformation of the anticodon loop of tRNA (yeast) was studied by detecting the most strongly binding pentanucleotide among the pentamers obtained by digestion of ribosomal RNA with T 1 RNase. This pentamer was identified as UUCAG which is complementary to the anticodon and the two pyrimidines on the 5′ side of the anticodon loop. Gel electrophoresis was used to detect binding. Control experiments employing other tRNA's showed that UUCAG formed a five base-pair complex with the tRNA. This indicates that the pentamer binds to the anticodon and the two pyrimidines to the 5′ side of it and lends support to a model for the tRNA loop which was recently proposed by Woese (1970).

Two- and three-stranded complexes containing homopolymers polyriboadenylic acid and polyribobromouridylic acid

The formation, dissociation and interconversion of two- and three-stranded complexes composed of the homopolymers rA † † Abbreviations used: A, T, U, BU, C, BC, G, I: adenine, thymine, uracil, bromouracil, cytosine, bromocytosine, guanine, hypoxanthine (the ribonucleotide of which is inosine), respectively. Ribonucleoside diphosphates are denoted as XDP. The conventions for designating synthetic polynucleotides and polynucleotide complexes proposed by Inman & Baldwin (1962) are followed: rA, the homopolymer polyriboadenylate; rBU, polyribobromouridylate, rABU, the alternating copolymer of riboadenylic acid and ribobromouridylic acid. Base paired complexes are designated with a colon as in rA:rBU, the homopolymer pair, or rAU: rAU, the base paired alternating copolymer. and rBU have been studied. The effects of temperature and pH at 0.1 m-sodium ion concentration on the equilibria between the homopolymers and the two possible complexes have been investigated, and areas of stability of the different forms have been delineated. The effect of relative amounts of the two polymers on the nature of the complex formed has been studied. The results have been discussed in relation to those obtained in the rA-rU system. The three-stranded complex, rA:rBU 2, is more stable relative to the two-stranded complex, rA:rBU, than is the case for the analogous rA-rU homopolymer complexes. The effect of bromine in stabilizing ribopolynucleotide complexes containing BU is not dependent on base sequence when the helix-coil transition occurs at alkaline pH. However, at neutral pH the homopolymer complex rA:rBU 2 is found to be significantly more stable than the copolymer complex rABU:rABU, suggesting that a base sequence effect on the stabilization conferred by bromine may exist at neutral pH.