Structural effects of internucleotide linkage modification at mismatch site in DNA/RNA duplex: Raman study

Two types of DNA oligonucleotide modifications, namely lengthening of the internucleotide linkage by insertion of CH2 methylene group and substitution of deoxyribose by deoxyxylose, were studied with respect to their possible impact on the oligonucleotide binding specificity. Structural effects of the modifications at the mismatched site of DNA/RNA hybrid duplex were monitored via Raman spectroscopy by using a molecular model system consisting of a DNA nonamer (5′-GTG ATA TGC-3′) with the modification at the site of the central thymidine and of RNA counterparts with altered central nucleotide (5′-GCA UNU CAC-3′, N = A or U). A novel approach based on single and double difference Raman spectra allowed extraction and analysis of spectroscopic signatures introduced by chemical modification and mismatched basepairs in NA duplexes. The double difference spectra revealed that substitution of 2′-deoxy-d-deoxyribose by 2′-deoxy-d-deoxyxylose supports bending of the modified dA-dT-dA segment in the mismatched duplex, while lengthening of the internucleotide linkage by insertion of the CH2 methylene group induces irregular distortion of this track. The modifications do not induce a better stacking interaction of the mismatched uracil and thus do not increase the stability of the T·U mismatched duplexes.