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The influence of exocyclic substituents of purine bases on DNA curvature.

Complementary oligonucleotides with 5' overhanging deoxyguanosine or deoxycytidine stretches, respectively, of the general form 5'-d(GGGCAARAAC).5'-d(CCCGTTYTTG), where R represents the bases adenine (A), hypoxanthine (base of inosine nucleoside, I), purine (R), 2-aminopurine (n2R), or 2,6-diaminopurine (n2,6(2)R) and where Y represents the pyrimidine bases thymine (T) or cytosine (C), have been chemically synthesized. After hybridization of complementary fragments, they were ligated to form multimers and analyzed by polyacrylamide gel electrophoresis. Anomalous gel migration was observed for the sequences 5'-d(AARAA) when the R.Y base pair was dA.dT, dI.dC, or dR.dT. All of these base pairs lack at least the amino group at position 2 of the purine base. The degree of anomalous gel migration was also related to the substituent at position 6 of the purine base. An amino group at position 6 was more effective than a carbonyl or a hydrogen in inducing anomalous gel migration. Additionally, the fragments 5'-d(GGGCAIAIAC).5'-d(CCCGTCTCTG), 5'-d(GGGCAIIIAC).5'-d(CCCGTCCCTG), and 5'-d(GGGCIIAIIC).5'-d(CCCGCCTCCG) were prepared in which increasing numbers of dA.dT base pairs are replaced by dI.dC base pairs. The degree of gel-migration anomaly of these sequences correlates with the number of dA.dT base pairs left in the five-base purine block. The data support the hypothesis that within the deoxyadenosine tracts, the base pairs fold into the minor groove at position 2 of the base to balance for the NH2 groups at position 6. This hypothesis explains the formation of a B'-form DNA structure for the deoxyadenosine tracts as well as DNA curvature.