Synthesis and physical and physiological properties of 4'-thioRNA: application to post-modification of RNA aptamer toward NF-kappaB

We report herein full details of the preparation of 4′-thiouridine, -cytidine, -adenosine and -guanosine phosphoramidites based on our synthetic protocol via the Pummerer reaction. Fully modified 4′-thioRNAs containing four kinds of 4′-thioribonucleoside units were prepared according to the standard RNA synthesis. The T_m values and thermodynamic parameters of a series of duplexes were determined by UV melting and differential scanning calorimetry (DSC) measurements. The resulting overall order of thermal stabilities for the duplexes was 4′-thioRNA:4′-thioRNA >> 4′-thioRNA:RNA > RNA:RNA > RNA:DNA > 4′-thioRNA:DNA. In addition, it was shown that the dominant factor in the stability of the duplexes consisting of 4′-thioRNA was enthalpic in character. The CD spectra of not only 4′-thioRNA:RNA and 4′-thioRNA:4′-thioRNA but also 4′-thioRNA:DNA were all similar to those of duplexes in the A-conformation. The stability of 4′-thioRNA in human serum was 600 times greater than that of natural RNA. Neither the RNA:RNA nor the 4′-thioRNA:4′-thioRNA duplexes were digested under the same conditions. The first example of a post-modification of an RNA aptamer by 4′-thioribonucleoside units was demonstrated. Full modification of the aptamer thioRNA3 resulted in complete loss of binding activity. In contrast, modifications at positions other than the binding site were tolerated without loss of binding activity. The post-modified RNA aptamer thioRNA5 was thermally stabilized and resistant toward nuclease digestion. The results presented in this paper will, it is hoped, contribute to the development of 4′-thioRNA as a new generation of artificial RNA.