DNA receptor recognition

Abstract differences between the high intensity fields contoured at — 2570 kJ mol-1 for the different ordering of C and G. The general distribution close to the phosphates is similar, with the bulk of the high potential lying in the wide groove. However, the details differ slightly in that the area contoured by each section plane is dependent on the proximity of a base carbonyl group. Thus, the field strength in the phosphate region is modified to some extent by the arrangement of bases. The spiral nature of the fields in the grooves is not so clearly defined as that of those in the homopolymer. This is evident in the central region of the helix, where the narrow groove — 2570 kJ contour is absent at the right-hand side of the middle base pairs of figure 3 a. A possible explanation for this finding may be produced by examining the positions of the carbonyl groups in the two grooves. For G-C sequences the carbonyl groups of adjacent base pairs are situated further apart in the narrow than in the wide groove; consequently, the local field suffers a directional distortion introduced by the alternating sequence in the narrow groove. The — 2508 kJ mol-1 contour of figure 3b has a 3-D shape very similar to that in the homopolymer. Large volumes of potential are found in the wide groove with coupling of the phosphate and carbonyl generated fields. Figure 4a, b shows the fields in the narrow groove at the front of the box for the homopolymer and the alternating sequence respectively. With poly(dG) • poly(dC) the — 2570 k J mol-1 contours in the narrow groove are found only on one edge and lie close to the oxygen atoms of cytosine and the furanose oxygen of the sugar ring. For the alternating polymer a band of high potential bridges the groove from the oxygen atoms of the sugar ring and a neighbouring cytosine on one side to analogous atoms associated with the next base pair. This base sequence corresponds to the complementary guanine oxygen atoms being stacked in the wide groove. A similar pattern of electrostatic potential distribution can just be discerned when this sequence is next encountered.