Synthesis and modelling of DNA junction and minor groove zipper motifs incorporating the double-headed nucleoside 5'(S)-C-(thymine-1-ylmethyl)thymidine.
A nucleoside with two nucleobases, a so-called double-headed nucleoside, 5'(S)-C-(thymine-1-ylmethyl)thymidine 3, is synthesised and incorporated into oligonucleotides. The additional nucleobase is hereby positioned in the minor groove of the duplexes, which are formed with complementary DNA and RNA-sequences. Slight thermal destabilisation of these duplexes as compared to unmodified duplexes is observed. With other target sequences forming bulged duplexes or three-way junctions, no additional influence of the additional base on the thermal stability is observed. On the other hand, a base-base stacking interaction and subsequent stabilisation is observed when two double-headed nucleotide moieties are positioned in two complementary DNA-sequences forming a DNA-zipper motif.
Christensen
Mikkel S
MS
Nucleic Acid Center, Department of Chemistry and Physics, University of Southern Denmark, 5230, Odense M, Denmark.
Madsen
Charlotte M
CM
Nielsen
Poul
P
D002626:Chemistry, Pharmaceutical / Q000379:methods; D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009705:Nucleosides / Q000737:chemistry*; D009711:Nucleotides; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics; D013936:Thymidine / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000494:pharmacology; D013941:Thymine / Q000737:chemistry*
C521750:5'(S)-C-(thymine-1-ylmethyl)thymidine; D009705:Nucleosides; D009711:Nucleotides; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D004247:DNA; D013941:Thymine; D013936:Thymidine