Synthesis of 5‐(β‐D‐glucopyranosyloxymethyl)‐2′‐deoxyuridine and derivatives thereof. A modified d‐nucleoside from the DNA of Trypanosoma brucei

Abstract

Abstract. An appropriately protected 3'-phosphoramidite and 5'-phosphate derivative of the modified 2'-deoxyuridine were obtained by P-glycosylation of a properly protected 5-hydroxymethyl-2'-dcoxyuridine, and subsequent elaboration of the resulting intermediates using standard protocols dcvised in nucleic acids chemistry.

The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1

“…The geometry of that structure was idealized in REFMAC5 ( 37 ) using interval restraints ( 44 ) for describing the hydrogen bonds of the J-base to the N -1-phosphoryl oxygen and between all other Watson–Crick base pairs. The 7 nt bracketing the J-base in the J-containing strand ( 9–15 ) of this idealized 20-mer were then superposed to the DNA in the MogR complex, ‘sliding’ it in various positions to find a placement that would allow the J-base to be located close to Asp525 of the recognition helix; a unique suitable solution was found and was used to create the DB-JBP1:J-DNA complex. In that complex, both C4 and C6 hydroxyls were very close to Asp525, whereas Arg517, Lys522, Lys524 were all close to DNA and available for interactions.…”

“…Synthesis of the J nucleotide ( 11 ) and J-base containing (J-DNA) oligonucleotides by chemical methods ( 12 , 13 ), allowed the identification of a 93 kDa J-binding protein 1 (JBP1) in extracts of T. brucei , Leishmania species and Crithidia fasciculata ( 14 ). JBP1 binds specifically to base J in duplex DNA ( 15 ).…”

Preparation of 5‐Hydroxymethyl‐pyrimidine Based Nucleosides: A Reinvestigation

“…[22,23] Van Boom's group described the first synthesis of the suitably protected base J phosphoramidite building unit from the 5-O-acetyl derivative of 5hmdU as intermediate using the Sower's procedure (Figure 1A). [24] This method offers several advantages: it requires inexpensive reagents and starting material, and is simple to implement. However, using this pathway, the fully deprotected 5hmdU is obtained, which makes selective protection of the 5-hydroxyl group tricky.…”

Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2′-Amino-LNA Monomers

“…They can be installed terminally during ON synthesis either at the 5′-end via phosphoramidite chemistry, or used together with a solid support in the 3′-end as has been realized for the previous described triantennary carbohydrate linkers. The groups of Hrdlicka and Kobayashi have modified LNA-U and 2′-deoxyuridine, respectively, in the C5 position of the pyrimidine base with an acetylene linked monosaccharide under Sonogashira conditions. , As in base J, formation of a direct glycosidic bond between a carbohydrate and a hydroxyl modified base of the nucleoside is also possible. , The group of Lönnberg exchanged the whole nucleobase by a triantennary carbohydrate linker using oxime and azide–alkyne cycloaddition chemistry . Beigelman and co-workers introduced several galactosamines in the 2′-position of deoxyribose through an amide linker strategy .…”