Synthesis and biophysical properties of oligodeoxynucleotides containing 2'-deoxy-5-(4-nitro-1H-imidazol-1-yl)-beta-D-uridine and 2'-deoxy-5-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)-beta-D-uridine monomers.
Detection of single-nucleotide polymorphisms (SNPs) of biologically relevant DNA and RNA samples remain a scientific and practical challenge. We have synthesized phosphoramidite building blocks and oligodeoxynucleotide probes containing novel 2'-deoxyuridine monomers modified by 5-(4-nitro-1H-imidazol-1-yl; (monomer X) or 2'-deoxy-5-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl; monomer Y) substituents. The effects of monomers X and Y on duplex thermal stability, and their capability towards discrimination of single-base mismatches were furthermore studied. Encouraging results were obtained with respect to thermal mismatch discrimination using oligodeoxynucleotides containing monomer X and fluorescence-based discrimination using oligodeoxynucleotides containing monomer Y.
Gondela
Andrzej
A
Department of Organic Chemistry, Biochemistry and Biotechnology, Selisian University of Technology, Krzywoustego 4, PL-44-100 Gliwice.
Kumar
Thatikonda Santhosh
TS
Walczak
Krzysztof
K
Wengel
Jesper
J
D020137:Base Pair Mismatch; D015342:DNA Probes / Q000138:chemical synthesis* / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D020641:Polymorphism, Single Nucleotide; D013696:Temperature; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry
C549410:2'-deoxy-5-(1,3-dioxo-1H-benzo(de)isoquinolin-2(3H)-yl)uridine; C549409:2'-deoxy-5-(4-nitro-1H-imidazo-1-yl)uridine; D015342:DNA Probes; D009838:Oligodeoxyribonucleotides; D014529:Uridine