Monitored Selection of DNA-Hybrids Forming Duplexes with Capped Terminal C:G Base Pairs

Abstract

Reported here are the results of a search for modified oligodeoxynucleotides with a 5‘-terminal cytidine residue whose affinity for target strands is enhanced by 5‘-acylamido groups. These acylamido groups were envisioned to act as molecular caps that bind to the exposed terminal base pair of the duplex with the target strand. A total of 52 capped oligonucleotides of the sequence R-C*GGTTGAC, where R denotes the 5‘-appendage and C* a 5‘-amino-2‘,5‘-dideoxycytidine residue, were tested. Among the building blocks employed to modify the 5‘-amino group of the DNA strand were carboxylic acid residues, either appended directly or via an amino acid residue, and aromatic aldehydes, coupled via reductive amination. The carboxylic acids employed ranged from Fmoc-glycine to (Fmoc)₂-vancomycin and included a number of aromatic acids and bile acids. Small libraries were subjected to MALDI-monitored nuclease selection experiments, and selected compounds were tested in UV-melting assays with target strands. Cholic acid appendages stabilized terminal C:G base pairs to the greatest extent, with melting point increases of up to 10 °C. Further, the cholic acid residue enhanced base pairing fidelity at the terminus, as determined in melting analyses with target strands containing a mismatched nucleobase at the 3‘-terminus.