Synthesis of Oligodeoxynucleotides Containing 5-(β-D-Glucopyranosyloxymethyl)-2′-deoxyuridine, a Modified Nucleoside in the DNA ofTrypanosoma Brucei

Abstract

The synthesis of the recently discovered modified DNA base 5‐(β‐D‐glucopyranosyloxymethyl)‐2′‐deoxyuridine (β‐dJ, 1) is described. TMSOTf mediated β‐glucosylation of 5‐hydroxymethyl‐2′‐deoxyuridine (5‐HMdU) derivative 10 (obtained in 20% from 2′‐deoxyuridine) with trichloroacetimidate 12 gave dimer 13 in 47% yield. On the other hand, condensation of 12with N3‐POM‐protected derivative 20, readily available from thymidine in 48%, afforded the fully protected nucleoside 22 in 96% yield. The latter compound was converted into phosphoramidite 3 which was applied in the automated solid phase synthesis of several biological interesting β‐dJ containing DNA fragments.

Chemical and Enzymatic Synthesis of DNA Fragments Containing 5-(β-D-Glucopyranosyloxymethyl)-2′-deoxycytidine − a Modified Nucleoside in T4 Phage DNA

“…NH 4 OH, 60 °C, 60 h) required for complete removal of the cyanoethyl group was an incentive for replacing the cyanoethyl group with an acetyl moiety and for using thymidine as the starting material. The synthesis of target compound 4 is presented in Scheme and commences with radical bromination15 of the known13a bis‐silylated thymidine derivative 6 . Substitution of the resulting crude allylic bromide with cesium acetate in DMF afforded 5‐HMdU derivative 7 , which was transformed into 5‐HMdC 8 by the following three‐step sequence.…”

“…An alternative route to the 5‐GlcMdC derivative 5 would entail transformation of the known13a glucosylated 5‐HMdU building block 15 (Scheme ). Surprisingly, subjection of the benzoylated gluconucleoside 15 to the same conditions as used for the synthesis of 8 did not produce the expected intermediate triazolide 16 .…”

“…It did, however, prove possible to obtain 16 , in a poor yield (29%), by prolonged treatment of 15 with excess POCl 3 and 1,2,4‐triazole at elevated temperature. Alternatively, treatment of the tetra‐ O ‐acetyl derivative 18 , easily accessible by conversion of N 3 ‐pivaloyloxymethyl (POM)‐protected 17 ,13a could readily be converted under the originally applied mild conditions (cf. 7 → 9 ) into the requisite triazolide 19 , in 86% yield.…”

“…Firstly, attention was focused on the synthesis of the DNA 20‐mer 5′‐GTT TAC TTC X TC GGT TAG TG‐3′ ( 23 , X= 5‐HMdC), the length and sequence of which was based on a molecular modeling study using the X‐ray structure of T4 BGT4,5,20 to select suitable candidates for co‐crystallization experiments. The appropriate deoxynucleoside, immobilized by means of a 3′‐ O ‐succinyl bond to controlled pore glass (CPG), was elongated according to previously reported13a methodology for the solid‐phase synthesis of oligodeoxynucleotides containing dJ ( 3 ). After completion of the elongation cycles, the immobilized DNA fragment was deprotected and simultaneously cleaved from the resin by ammonolysis (50 °C, 16 h).…”

O‐Glycoside Orientation Is an Essential Aspect of Base J Recognition by the Kinetoplastid DNA‐Binding Protein JBP1

“…The N 3 ‐unprotected phosphoramidite analogues 2 b – h (Figure 1) were prepared based upon an original method for the N 3 ‐unprotected phosphoramidite 2 a , developed by van Boom and co‐workers (Scheme ) 14–16. Thus, bis‐silylation of dT ( 1 i ), followed by radical allylic bromination gave allylic bromide 3 in good yield (67 % over two steps).…”