Analysis of sequences of twist angles in DNA double helix

The study of stacking energy for natural DNA sequences

The stacking energies between bases of DNA for both A and B conformation have been calculated by Aida & Nagata (1986, Int. J. Quantum Chem. 29, 1253-1261). For naturally occurring DNA sequences, by assuming that the average stacking energy of A conformation is completely identical with that of B, the lowest average stacking energy for double strand DNA has been calculated and found to be equal to -7.38 kcal M-1. This conclusion has been confirmed by the data of stacking energy of 112 promoter sequences of Escherichia coli and some other natural DNA sequences. Our result shows that the natural DNA sequences are bi-stable. One stable-state is the A conformation, the other is B. It is shown that the result is only applicable to the transcription processes that regulate the gene expression. Through the interaction with RNA polymerase in the processes of transcription, the conformation of DNA might undergo a transition of B----A----B.

Environment-induced changes in DNA conformation as probed by ethidium bromide fluorescence

The interaction of the ethidium cation with calf thymus DNA is investigated in solutions of different ionic strength and temperature by observation of the enhancement of fluorescence of ethidium upon intercalation in the duplex structure. The quantum yield of the fluorescence of the intercalated dye is found to increase either upon lowering the Na+ concentration or upon increasing the temperature. The existence of a correlation between the geometry of the intercalation complex and the features of the secondary structure of DNA is suggested. Binding isotherms under corresponding environmental conditions are also quantitated by fluorescence enhancement and interpreted in terms of the neighbor exclusion model. Large contributions from change in hydration to the thermodynamics of binding are demonstrated by the temperature dependences of the equilibrium constants. The neighbor exclusion range is found to be practically independent of the salt concentration but its value increases from an average of 2.4 around room temperature to 4-5 at 80 degrees C, as inferred from the binding curves in 0.15 and 0.5 M [Na+] or from the DNA hypochromism vs temperature profiles of complexes at 10(-3) M [Na+]. All the data point to a possible sequence-conformation specificity in the intercalation of ethidium which in heterogeneous DNA is mediated by environmental changes.

Analysis of patterns of twist angles in DNA double helix

We have analysed theoretically the patterns of twist angles of B-DNA by the Tung-Harvey model mainly. It is shown that for a sequence of twist angles a smaller twist angle tends to follow a larger one and vice versa. Therefore the sequence of twist angles always takes a gentle zig-zag form. For simplicity we convert the sequence of twist angles to a symbolic sequence consisting of L and S, where L or S represents a large or a small angle, respectively. The -10 and -35 regions of 112 well-defined promoters for E. coli RNA polymerase, which were compiled by Hawley and McClure, have been analysed in terms of LS sequences in detail. The results shows that the number of LS sequences for promoters is considerably limited and the promoter mutations do not change the patterns of LS sequences in most cases. Several new ideas, which are believed to be useful in the further study, have been presented.