Why Carba-LNA-Modified Oligonucleotides Show Considerably Improved 3 '-Exonuclease Stability Compared to That of the LNA Modified or the Native Counterparts: A Michaelis-Menten Kinetic Analysis
2010 (English)In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 75, no 7, 2341-2349 p.Article in journal (Refereed) Published
In this study, 12 different native or LNA, carba-LNA-modified dinucleoside phosphates were designed as simple chemical models to study how carba-LNA modifications improve the 3'-exonuclease (SVPDE in this study) resistance Of internucleotidic phosphate compared to those exhibited by LNA-modified and the native counterparts. Michaelis-Menten kinetic studies for dimers 3 - 7, in which the LNA or carba-LNA modifications are located at the 5'-end, showed that (i) increased 3'-exonuclease resistance of (5')[LNA-T](p)T (3) compared to the native (TpT)-T-5' (1) was mainly attributed to steric hindrance imposed by the LNA modification that retards the nuclease binding (K-M) and (ii) digestion of (5')[carba-LNA-dT](p)T (4) and (5')[LNA-T](p)T (3), however, exhibit similar K(M)s, whereas the former shows a 100x decrease in K-cat and is hence more stable than latter. By studying the correlation between log k(cat) and pK(a) of the departing 3'(or 6')-OHs for 3-7, we found the pK(a) of 3'-OH of carba-LNA-T was 1.4 pK(a) units higher than that of LNA-T, and this relatively less acidic character of the 3'-OH in the former leads to the 100x decrease in the catalytic efficiency for the digestion Of (5')[Carba-LNA-T](p)T (4). In contrast, Michaelis-Menten kinetic studies for dimers 9-12, with the LNA or carba-LNA modifications at the 3'-end, showed that the digestion of T-5'(p)[LNA-T] (9) exhibited similar K-M but k(cat) decreased around 40 times compared to that of the native (TpT)-T-5' (1). Similar k(cat) values have been observed for digestion of T-5'(p)[carba-LNA-T] (10) and T-5'(p)[LNA-T] (9). The higher stability of carba-LNA modified dimer 10 compared with LNA modified dimer 9 comes solely from the increased K-M.
Place, publisher, year, edition, pages
2010. Vol. 75, no 7, 2341-2349 p.
IdentifiersURN: urn:nbn:se:uu:diva-136649DOI: 10.1021/jo100170gISI: 000275884400023PubMedID: 20225808OAI: oai:DiVA.org:uu-136649DiVA: diva2:377329