Properties of 5- and/or 2-modified 2'-O-cyanoethyl uridine residue: 2'-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component.

We systematically synthesized eight types of 5- and/or 2-modified uridine derivatives and evaluated their effect on duplex stability. The incorporation of 2'-O-cyanoethyl-2-thio-5-propynyluridine (p(5)s(2)UOCE) into RNA was significantly effective for stabilization of RNA/RNA (+8.5 °C) and DNA/RNA (+10.

Prediction of the stability of modified RNA duplexes based on deformability analysis: oligoribonucleotide derivatives modified with 2'-O-cyanoethyl-5-propynyl-2-thiouridine as a promising component.

We describe a method to predict the stability of a modified RNA duplex. Ten unique modified RNA duplexes showed a linear relationship between the calculated and experimentally determined duplex stabilities.

Linear relationship between deformability and thermal stability of 2'-O-modified RNA hetero duplexes.

We describe the relationship between the experimentally determined melting temperatures of 2'-O-modified-RNA/RNA duplexes and their deformability estimated from molecular dynamics simulations. To clarify this relationship, we synthesized several fully modified oligoribonucleotides such as 2'-O-cyanoethyl RNAs and 2'-O-methoxyethyl RNAs and compared the actual melting temperatures of the duplexes with their calculated deformabilities. An increase of the melting temperatures by 2'-O-modifications was found to correlate strongly with an increase of the helical elastic constants in U(14)/A(14), (CU)(7)/(AG)(7), and (GACU)(3)/(AGUC)(3) sequences.