title: Synthesis of oligodeoxynucleotides with 5'-caps binding RNA targets.
abstract: Protocols for the synthesis of oligodeoxynucleotides with a short peptidyl substituent linked to the 5'-O-terminus through a phosphodiester bond are presented. The example given is a peptidyl cap consisting of the residues of L-prolinol, glycine, and the acyl residue of oxolinic acid. DNA probes with this cap, also known as ogOA cap, give melting point increases for duplexes with RNA targets and improve mismatch discrimination at the terminus. The cap is either introduced in one step, using a newly developed phosphoramidite reagent, or assembled on the DNA chain. The step-wise assembly of the peptidyl chain is advantageous for combinatorial studies aimed at the optimization of a cap structure. The block coupling method, introducing the preassembled cap in one step, is attractive for routine use of a cap already optimized for a given application. Cap-bearing probes can increase fidelity of hybridization in a genomic context. They can be synthesized by automated DNA synthesis.
authors.affiliation: Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany.
authors.forename: Simone
authors.initials: S
authors.lastname: Egetenmeyer
authors.forename: Clemens
authors.initials: C
authors.lastname: Richert
mesh_terms: D020137:Base Pair Mismatch; D020029:Base Pairing; D001483:Base Sequence; D020650:Combinatorial Chemistry Techniques / Q000379:methods*; D015342:DNA Probes / Q000138:chemical synthesis* / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D015345:Oligonucleotide Probes; D009943:Organophosphorus Compounds / Q000138:chemical synthesis / Q000737:chemistry; D010093:Oxolinic Acid / Q000737:chemistry; D011759:Pyrrolidines / Q000737:chemistry; D012313:RNA / Q000737:chemistry*
chemical_list: D015342:DNA Probes; D009838:Oligodeoxyribonucleotides; D015345:Oligonucleotide Probes; D009943:Organophosphorus Compounds; D011759:Pyrrolidines; C434331:phosphoramidite; C010509:prolinol; D012313:RNA; D010093:Oxolinic Acid; D005998:Glycine