Synthesis and monitored selection of 5'-nucleobase-capped oligodeoxyribonucleotides

Oligodeoxynucleotides bearing 5′-appendages consisting of a nucleobase and an amide linkage were prepared from 5′-amino-5′-deoxyoligonucleotides, amino acid building blocks and thymine or uracil derivatives. Small chemical libraries of 5′-modified oligonucleotides bearing the nucleobase moieties via five, three or two atom linkages were subjected to spectrometrically monitored nuclease selections to identify members with high affinity for target strands. The smallest of the appendages tested, a uracil acetic acid substituent, was found to convey the greatest duplex stabilizing effect on the octamer 5′-T*GGTTGAC-3′, where T* denotes the 5′-amino-5′-deoxythymidine residue. Compared to 5′-TTGGTTGAC-3′, the modified sequence 5′-u-T*GGTTGAC-3′ gives a duplex with 5′-GTCAACCAA-3′ that melts 4°C higher. The duplex-stabilizing effect of this 5′-substituent does not require a specific residue at the 3′-terminus of the complement and the available data suggest that the uracil moiety is located in the major groove of the duplex.