Crystal Structures of Oligodeoxyribonucleotides Containing 6‘-α-Methyl and 6‘-α-Hydroxy Carbocyclic Thymidines

Abstract

The X-ray crystal structures of two self-complementary DNA duplexes with the sequence d(CGCGAAtMe/OHtMe/OHCGCG) containing four 6‘-α-methyl (tMe) or four 6‘-α-hydroxy carbocyclic thymidines (tOH), respectively, have been determined. Both structures are isomorphous to the native Dickerson−Drew dodecamer duplex [d(CGCGAATTCGCG)]2. The cyclopentane moieties of the modified carbocyclic thymidine residues lacking the deoxyribose 4‘-oxygen adopt either C2‘-endo or C1‘-exo B-DNA type puckers. The dodecamer duplex incorporating 6‘-α-methyl carbocyclic thymidines shows an enlarged minor groove relative to both the unmodified duplex and the one with incorporated 6‘-α-hydroxy carbocyclic thymidines. The pairing of oligonucleotides containing single or multiple 6‘-α-substituted carbocyclic thymidines with complementary DNA is discussed on the basis of the structural data.