New NTP analogs:: the synthesis of 4′-thioUTP and 4′-thioCTP and their utility for SELEX

The synthesis of the triphosphates of 4'-thiouridine and 4'-thiocytidine, 4'-thioUTP ( 7; thioUTP) and 4'-thioCTP ( 8; thioCTP), and their utility for SELEX ( systematic evolution of ligands by exponential enrichment) is described. The new nucleoside triphosphate ( NTP) analogs 7 and 8 were prepared from appropriately protected 4'-thiouridine and - cytidine derivatives using the one-pot method reported by J. Ludwig and F. Eckstein [( 1989) J. Org. Chem., 54, 631 - 635]. Because SELEX requires both in vitro transcription and reverse transcription, we examined the ability of 7 and 8 for SELEX by focusing on the two steps. Incorporation of 7 and 8 by T7 RNA polymerase to give 4'-thioRNA ( thioRNA) proceeded well and was superior to those of the two sets of frequently used modified NTP analogs for SELEX (2'- NH(2)dUTP and 2'-NH(2)dCTP; 2'-FdUTP and 20-FdCTP), when an adequate leader sequence of DNA template was selected. We revealed that a leader sequence of about +15 of DNA template is important for the effective incorporation of modified NTP analogs by T7 RNA polymerase. In addition, reverse transcription of the resulting thioRNA into the complementary DNA in the presence of 2'-deoxynucleoside triphosphates (dNTPs) also proceeded smoothly and precisely. The stability of the thioRNA toward RNase A was 50 times greater than that of the corresponding natural RNA. With these successful results in hand, we attempted the selection of thioRNA aptamers to human alpha-thrombin using thioUTP and thioCTP, and found a thioRNA aptamer with high binding affinity (K-d = 4.7 nM).