Xylo-Configured oligonucleotides (XNA, xylo nucleic acid): synthesis of conformationally restricted derivatives and hybridization towards DNA and RNA complements.
Xylo-Configured oligonucleotides (XNA) containing a novel conformationally restricted 2'-deoxy-2'-fluoro-beta-D-xylofuranosyl nucleotide monomer, a novel conformationally locked 2'-amino-2'-deoxy-2'-N,4'-C-methylene-beta-D-xylofuranosyl nucleotide monomer, and a known 2'-deoxy-beta-D-xylofuranosyl nucleotide monomer (XNA monomers) have been synthesized and their hybridization towards DNA and RNA complements studied. Thermal denaturation studies of nine-mer mixed-base sequences composed of a mixture of XNA monomers and DNA monomers revealed preferential hybridization towards RNA complements relative to DNA complements. For 14-mer homo-thymine XNAs containing thirteen XNA monomers, stable complexes towards single-stranded DNA and RNA were formed at pH 7. Gel-shift experiments revealed these complexes to involve at least two XNA strands per DNA or RNA target strand.
Poopeiko
Nicolai E
NE
Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
Juhl
Martin
M
Vester
Birte
B
Sørensen
Mads D
MD
Wengel
Jesper
J
D004247:DNA / Q000187:drug effects*; D016521:Electrophoresis, Gel, Pulsed-Field; D024202:Electrophoretic Mobility Shift Assay; D005461:Fluorine; D007202:Indicators and Reagents; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry*; D012313:RNA / Q000187:drug effects*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D007202:Indicators and Reagents; D009841:Oligonucleotides; D005461:Fluorine; D012313:RNA; D004247:DNA