Phosphoramidate linkage stability

BNA (also known as LNA) has been used in TFOs in a pyrimidine motif at neutral pH. The binding constant of the BNA TFO was about 20 times larger than that of DNA as a result of a large decrease in the dissociation rate constant. A 3 -amino-2, 4 -BNA nucleotide has been prepared to introduce N3 -P5 phosphoramidate linkages. It is introduced as a dinucleotide unit (61), and in thermal stability studies was shown to exhibit superior duplex and triplex stability compared to either BNA or DNA, and shows enhanced resistance to digestion by SVPDE. These properties have previously been observed for N3 -P5 phosphoramidate linkages in DNA. ... 

The conformationally-locked 3 -amino thymidine derivative (47) was prepared and incorporated into DNA as a dimer unit, attaching the amino group via a carbamate or phosphoramidate linkage.Both modifications were found to be destabilising towards both RNA and DNA targets. The hybridisation properties of an amino-modified bicyclic thymine nucleotide (48) have been exam-ined. Using alternate T and (48) residues there is an increase in duplex stability with d(A)io, with no pH dependence. When the amino group is acetylated, the duplex stability is decreased. The locked C-nucleoside oxazole derivative (49) has been incorporated into TFOs where it was found to selectively enhance the stability with a C.G base pair. ... 

Amino-LNA has been incorporated into oligonucleotides with a N3 - P5 phosphoramidate linkage. " The presence of the phosphor-amidate linkage gave quite signiflcant increases in thermal stabilities... 

Phosphorothioate-modified DNA aptamers have been selected for binding to NF-kB, ° and phosphoramidate ODNs for binding to TAR to inhibit Tat-mediated transcription. Deoxyribozymes that cleave RNA have been modified with 3 -3 inverted linkages, phosphorothioate linkages, 2 0-methyl sugars and LNA in an attempt to enhance stability and cleavage activity. " ... 

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