Base Pair Combinations Research Articles

Selection of DNA binding sites by regulatory proteins: II. The binding specificity of cyclic AMP receptor protein to recognition sites

The statistics of base-pair usage within known recognition sites for a particular DNA-binding protein can be used to estimate the relative protein binding affinities to these sites, as well as to sites containing any other combinations of base-pairs. As has been described elsewhere, the connection between base-pair statistics and binding free energy is made by an equal probability selection assumption; i.e. that all base-pair sequences that provide appropriate binding strength are equally likely to have been chosen as recognition sites in the course of evolution. This is analogous to a statistical-mechanical system where all configurations with the same energy are equally likely to occur. In this communication, we apply the statistical-mechanical selection theory to analyze the base-pair statistics of the known recognition sequences for the cyclic AMP receptor protein (CRP). The theoretical predictions are found to be in reasonable agreement with binding data for those sequences for which experimental binding information is available, thus lending support to the basic assumptions of the selection theory. On the basis of this agreement, we can predict the affinity for CRP binding to any base-pair sequence, albeit with a large statistical uncertainty. When the known recognition sites for CRP are ranked according to predicted binding affinities, we find that the ranking is consistent with the hypothesis that the level of function of these sites parallels their fractional saturation with CRP-cAMP under in-vivo conditions. When applied to the entire genome, the theory predicts the existence of a large number of randomly occurring “pseudosites” with strong binding affinity for CRP. It appears that most CRP molecules are engaged in non-productive binding at non-specific or pseudospecific sites under in-vivo conditions. In this sense, the specificity of the CRP binding site is very low. Relative specificity requirements for polymerases, repressors and activators are compared in light of the results of this and the first paper in this series.

Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology.

A series of potential energy calculations have been carried out to estimate base sequence dependent structural differences in B-DNA. Attention has been focused on the simplest dimeric fragments that can be used to build long chains, computing the energy as a function of the orientation and displacement of the 16 possible base pair combinations within the double helix. Calculations have been performed, for simplicity, on free base pairs rather than complete nucleotide units. Conformational preferences and relative flexibilities are reported for various combinations of the roll, tilt, twist, lateral displacement, and propeller twist of individual residues. The predictions are compared with relevant experimental measures of conformation and flexibility, where available. The energy surfaces are found to fit into two distinct categories, some dimer duplexes preferring to bend in a symmetric fashion and others in a skewed manner. The effects of common chemical substitutions (uracil for thymine, 5-methyl cytosine for cytosine, and hypoxanthine for guanine) on the preferred arrangements of neighboring residues are also examined, and the interactions of the sugar-phosphate backbone are included in selected cases. As a first approximation, long range interactions between more distant neighbors, which may affect the local chain configuration, are ignored. A rotational isomeric state scheme is developed to describe the average configurations of individual dimers and is used to develop a static picture of overall double helical structure. The ability of the energetic scheme to account for documented examples of intrinsic B-DNA curvature is presented, and some new predictions of sequence directed chain bending are offered.

Theoretical studies of the structure and energies of base-paired nucleotides and the dissociation kinetics of a proflavine-dinucleotide complex.

We presented calculations of base-paired dinucleoside phosphates and hexanucleoside pentaphosphates of varying compositions. Complete energy minimizations were performed for (a) the ten base-pair combinations of dinucleoside phosphates, starting from a B-DNA conformation, (b) six hexanucleoside pentaphosphates--base-paired CGCGCG, GCGCGC, G6-C6, TATATA, ATATAT, and A6-T6--starting with a B-DNA geometry, and (c) the four hexanucleoside pentaphosphates that have alternating pyrimidine-purine sequences, starting with a Z-DNA geometry. In addition, we studied the proflavine-base-paired CpG complex, using both complete energy minimization and energetic constraints to force the drug to dissociate from the dinucleoside phosphate. In many of these calculations, we examined the dependence of the calculated energies and structures on the potential function, focusing mainly on the effect of nonbonded potentials, the effective dielectric constant, and the role of counterions. These calculations allow us to explain why pur-(3',5')-pyr sequence isomers are more stable than pyr-(3'-5')-pur isomers. Both base-base and base-backbone energies are important in this differentiation, with the former being mainly van der Waals attraction and the latter mainly electrostatic energies. The calculations also allow us to understand the differences in double helical stabilities found by Wells et al. These differences, caused by electrostatic interactions between those bases not Watson-Crick hydrogen bonded, allow us to explain the following experimental data: poly(dG-dC) melts 12 degrees C higher than poly dG-poly dC, poly(dA-dT) melts 6 degrees C lower than poly dA-poly dT, and poly(dA-dG)-poly(dC-dT) melts 6 degrees C lower than poly(dA-dC)-poly(dT-dG). These results have interesting implications for drug binding: they imply that simple intercalators, such as ethidium, will exhibit a greater affinity for hetero- than for homopolymers and that this preference will be greater in the AT polymers than it is in the GC polymers. Our calculations allow us to explain the fact that Z-DNA is more stable than B-DNA under high salt conditions and to suggest some sequence dependence for the Z to B transition. We found that the activation energy for proflavine dissociating from dCpG is almost equal to the dissociation energy.

ChemInform Abstract: ELECTROSTATIC POTENTIALS OF DEOXYDINUCLEOSIDE MONOPHOSPHATES. 1. DEOXYDINUCLEOSIDE MONOPHOSPHATES AND ACTINOMYCIN CHROMOPHORE INTERACTIONS

We present electrostatic potential maps for the ten Watson-Crick base-pair combinations of dinucleoside monophosphates in a conformation appropriate for intercalation of drugs to occur. These maps reveal interesting differences among the base-pair combinations and suggest reasons for the base-pair specificities often observed upon intercalation. Simple electrostatic calculations on the intercalation energy of substituted actinomycin chromophores correlate qualitatively with the relative biological activity of these compounds, although the correlation with binding affinity is not as satisfactory.

Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions.

We present electrostatic potential maps for the ten Watson-Crick base-pair combinations of dinucleoside monophosphates in a conformation appropriate for intercalation of drugs to occur. These maps reveal interesting differences among the base-pair combinations and suggest reasons for the base-pair specificities often observed upon intercalation. Simple electrostatic calculations on the intercalation energy of substituted actinomycin chromophores correlate qualitatively with the relative biological activity of these compounds, although the correlation with binding affinity is not as satisfactory.