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DNA duplexes containing an ethyl interstrand crosslink that bridges the N3 atoms of thymidines on the opposite strands have been synthesized using an approach that combines conventional solid phase oligonucleotide synthesis and the selective removal of protecting groups of a crosslinked thymidine dimer. This approach allows for the assembly of a crosslinked duplex directly on the solid support. Duplexes that contain a N3T-ethyl-N3T interstrand crosslink in a staggered orientation at either a -TA- or -AT-step in a duplex have been prepared. When placed in an -AT- step of a duplex the effect was stabilizing relative to the non-crosslinked control duplex (deltaTm= +24 degrees C) and this crosslinked duplex was found to efficiently form multimers in the presence of T4 ligase. In the case of the -TA- crosslinked duplex the stabilizing effect was less pronounced (deltaT.= +6 degrees C) and likewise did not undergo self ligation under identical conditions. Molecular modeling studies suggested that the -AT- containing lesion had little deviation in structure relative to the non-crosslinked duplex DNA control, whereas the -TA- crosslinked duplex exhibited significant buckling of the base pairs flanking the lesion.

Chimeric oligodeoxyribonucleotides where the phosphodiester linkage -C3'-O-PO2--O-CH2-C4'- of DNA is substituted by the amide linkage -C3'-CH2-CH*(CH3)-CO-NH-CH2-C4' (*either R or S stereochemistry) have been prepared and their binding to RNA targets have been investigated. Incorporation of a single amide unit increases the Tm by approximately 1.4-1.9 degrees C. Circular dichroic spectra of these modified duplexes are similar to the wildtype DNA/RNA.

Inversion of configuration of the C2' position of RNA leads to a very unique nucleic acid structure: arabinonucleic acid (ANA). ANA, and its 2'-fluoro derivative (2'F-ANA) from hybrids with RNA that are capable of activating RNase H, resulting in cleavage of the RNA strand. In this paper, we review the properties of duplexes formed between ANA (or 2'F-ANA) and its RNA complement. These studies support the notion that RNase H is sensitive to the minor groove dimensions of the hybrid substrate.