Base Pair Opening Probability Research Articles

Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA

Local opening of the DNA double helix is required in many fundamental biological processes and is, in part, controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed a program that predicts the locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties with other available datasets. Source codes freely available for download at http://www.cbp.ens-lyon.fr/doku.php?id=developpement:productions:logiciels:twistdna, implemented in Fortran90 and supported on any Unix-based operating system (Linux, Mac OS X).

Sequence-Dependent Basepair Opening in DNA Double Helix

Preservation of genetic information in DNA relies on shielding the nucleobases from damage within the double helix. Thermal fluctuations lead to infrequent events of the Watson-Crick basepair opening, or DNA “breathing”, thus making normally buried groups available for modification and interaction with proteins. Fluctuational basepair opening implies the disruption of hydrogen bonds between the complementary bases and flipping of the base out of the helical stack. Prediction of sequence-dependent basepair opening probabilities in DNA is based on separation of the two major contributions to the stability of the double helix: lateral pairing between the complementary bases and stacking of the pairs along the helical axis. The partition function calculates the basepair opening probability at every position based on the loss of two stacking interactions and one basepairing. Our model also includes a term accounting for the unfavorable positioning of the exposed base, which proceeds through a formation of a highly constrained small loop, or a ring. Quantitatively, the ring factor is found as an adjustable parameter from the comparison of the theoretical basepair opening probabilities and the experimental data on short DNA duplexes measured by NMR spectroscopy. We find that these thermodynamic parameters suggest nonobvious sequence dependent basepair opening probabilities.

Melting profile and temperature dependent binding constant of an anticancer drug daunomycin-DNA complex.

We calculate thermal fluctuational base pair opening probability and the drug binding constant of a daunomycin-bound Poly d(CGTA).Poly d(TACG) at temperatures from room temperature to its melting temperature. For comparison we also carry out a calculation on a drug-free DNA with the same sequence. Our calculations are carried out by means of a statistical approach using microscopic structures and established force fields and with cooperative effects incorporated into the algorithm. Both hydrogen bond disruption probabilities and drug unstacking probability are determined self-consistently. These probabilities are then used to determine temperature dependent base pair opening probabilities and the drug binding constant. The calculated base pair opening probabilities and drug binding constant are found to be in fair agreement with experiments carried out at room temperature. Our calculation shows cooperative base pair disruption and drug dissociation at certain critical temperatures close to the observed melting temperatures for similar helices. We find that the temperature dependence of the drug binding constant fits well to the van't Hoff relation, in agreement with observations. Our calculation indicates the occurrence of a premelting transition in the drug-bound DNA helix. Some comments are made about this premelting transition.

Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT).poly d(ATGC) complex

We calculate room temperature thermal fluctuational base pair opening probability of a daunomycin-poly d(GCAT).poly d(ATGC) complex. This system is constructed at an atomic level of detail based on x-ray analysis of a crystal structure. The base pair opening probabilities are calculated from a modified self-consistent phonon approach of anharmonic lattice dynamics theory. We find that daunomycin binding substantially enhances the thermal stability of one of the base pairs adjacent the drug because of strong hydrogen bonding between the drug and the base. The possible effect of this enhanced stability on the drug inhibition of DNA transcription and replication is discussed. We also calculate the probability of drug dissociation from the helix based on the selfconsistent calculation of the probability of the disruption of drug-base H-bonds and the unstacking probability of the drug. The calculations can be used to determine the equilibrium drug binding constant which is found to be in good agreement with observations on similar daunomycin-DNA systems.

Salt dependent premelting base pair opening probabilities of B and Z DNA Poly [d(G-C)] and significance for the B-Z transition

We calculate room temperature thermal fluctuational base pair opening probabilities of B and Z DNA Poly[d(G-C)] at various salt concentrations and discuss the significance of thermal fluctuation in facilitating base pair disruption during B to Z transition. Our calculated base pair opening probability of the B DNA at lower salt concentrations and the probability of the Z DNA at high salt concentrations are in agreement with observations. The salt dependence of the probabilities indicates a B to Z transition at a salt concentration close to the observed concentration.

Theory of pressure-dependent melting of the DNA double helix: Role of strained hydrogen bonds.

In this paper we study the effect of hydrostatic pressure on the thermal stability of DNA base pairs. The thermal stability of a base pair is predominantly determined by the fluctuational motion of the interbase hydrogen bonds in the base pair. We postulate that the pressure exerted on the surface of DNA creates a compressive stress in the interbase hydrogen bonds. This stress in turn induces a strain in these hydrogen bonds. The effect of this compressive stress on the thermal fluctuational motion of the strained interbase hydrogen bonds in DNA can be analyzed by the modified self-consistent phonon approximation theory. We calculate individual hydrogen bond disruption probabilities and base pair opening probabilities of two B-conformation DNA polymers, an adenine-thymine copolymer and a guanine-cytosine homopolymer, at various pressures and at temperatures both in the premelting region and in the helix-coil transition region. Our calculated pressure dependence of the melting temperature for both polymers is in fair agreement with experimental observations. Our values for the melting temperatures are also in agreement with observation and our theory is successful as a theory of cooperative melting.

Calculated enhancement of open base pair probability downstream of a (TATA)2 box

The modified self-consistent phonon approximation is generalized to calculate the open base pair probability of a (TATA)2 insert between two semi-infinite poly(dA-dC) . poly(dG-dT) helices. An iterative method based entirely on the Green's function method is developed to compute the open interbase hydrogen bond probability of the insert and near bases versus temperature. The open interbase hydrogen bond probability is calculated for two temperatures and compared with perfect homopolymer open base pair probabilities at room temperature. The probability of opening is enhanced by a factor of two for the major groove bond of the AT pair at the transcriptional downstream end of the (TATA)2 insert. The total base pair opening probability of that pair is enhanced by 54%. The probability of the next inline GC base pair to be open is increased by a factor of ten.

The role of a minor groove spine of hydration in stabilizing poly(dA). poly(dT) against fuctuational interbase H-bond disruption in the premelting temperature regime

Experimental estimates of the premelting Adenine-Thymine base pair opening probability for some B-DNA sequences are two orders of magnitude smaller than those of other B-DNA sequences. The AT pairs in the sequence with smaller open probability seem to be those that have a well defined spine of hydration in the minor groove. We show that this spine of hydration can significantly enhance the thermal stability of the base pairs to which they are attached. The effect of this spine of hydration coupled with the possible stabilization effect contributed from neighboring GC pairs can explain the differences in the observed AT pair opening probability for different AT containing B-DNA sequences.

Premelting thermal fluctuational base pair opening probability of poly(dA).poly(dT) as predicted by the modified self-consistent phonon theory.

We employ a mean field, modified, self-consistent phonon theory to evaluate the single base-pair opening rate and the probability of a base pair in the amino proton exchangeable state for the homopolymer poly(dA).poly(dT) at temperatures below the helix-coil transition region. Our calculated premelting single base-pair opening probabilities are in general agreement with several available experimental estimates from imino proton exchange and formaldehyde-induced DNA melting measurements. These calculated opening probabilities, however, are in disagreement with the prediction of the helix-coil transition theory. Possible reasons for the differences are discussed, especially the possible different definition of a meaningful open state in the premelting region. The premelting open state of the modified self-consistent phonon approximation theory seems to be appropriate to describe a solvent-accessible open configuration that is sufficient to facilitate important chemical reactions such as imino proton exchange and formaldehyde reaction with the bases. This can be compared with the completely unstacked open state of the helix-coil transition theory originally defined in the helix-coil transition region. We propose that the amino proton exchangeable state is different from the open state associated with melting and only involves the breaking of the amino interbase H bond. The agreement between the calculated and experimentally estimated probability of a base pair in the amino proton exchangeable state seems to support this hypothesis.

Fluctuations in superhelical DNA

The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations. In the range of physiological superhelix densities sigma (-sigma=0.05-0.09) the base-pair opening probability markedly increases. However, within this range of sigma the base-pairs are opened only transiently and permanently open regions are not formed. Permanently opened regions appear at higher negative superhelix densities (-sigma greater than 0.10). At the values of -sigma higher than 0.06 a cruciform structure in the palindromic region centred in position 3965 proves to be the most probable fluctuational disturbance in the 0x174 duplex DNA. Different experimental approaches used for probing the fluctuations in superhelical DNA have been analysed. The results suggest that most direct quantitative information can be derived from data on the nicking of closed DNA by single strand-specific endonucleases. Such data (Wang, 1974) accord with the results of theoretical calculations. Calculations show that, due to base-pair opening, the total free energy of superhelical DNA should depend parabolically on sigma only up to some critical value of sigma=sigmac. If negative superhelicity exceeds this critical value, which under physiological conditions proves to be -sigma=0.085, the free energy should increase linearly with -sigma. The biological role of supercoiling is discussed in the light of obtained results.