title: Synthesis and hybridization studies of alpha-configured arabino nucleic acids.
abstract: Synthesis of alpha-L-arabino- and alpha-D-arabino-configured pentofuranosyl nucleosides of four of the natural bases [thymine (ara-T), adenine (ara-A), cytosine (ara-C) and guanine (ara-G)] is reported together with hybridization properties of oligonucleotides containing alpha-L-ara-T and -A, alpha-D-ara-T and -A, and 2'-amino-alpha-L-ara-T monomers. 2'-O-Acetylated alpha-L-ara-T, -A, -C and -G, alpha-D-ara-T, -A, -C and -G, and N2'-acylated-alpha-L-ara-T phosphoramidite building blocks were synthesized and used together with standard DNA phosphoramidites for solid-phase synthesis of 18-mer oligonucleotides. Thermal denaturation experiments showed that incorporation of three or six of the arabino-configured monomers into DNA-oligonucleotides reduced the binding affinity towards antiparallel DNA/RNA complements. Fully modified alpha-L-ara-oligonucleotides did not hybridize with DNA/RNA complements, whereas hybridization of fully modified alpha-D-ara-oligonucleotides with complementary DNA/RNA in parallel strand orientation was confirmed.
authors.affiliation: Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Gupta
authors.forename: Jyotirmoy
authors.initials: J
authors.lastname: Maity
authors.forename: Gaurav
authors.initials: G
authors.lastname: Shakya
authors.forename: Ashok K
authors.initials: AK
authors.lastname: Prasad
authors.forename: Virinder S
authors.initials: VS
authors.lastname: Parmar
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
mesh_terms: D001087:Arabinonucleosides / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000378:metabolism; D013237:Stereoisomerism
chemical_list: D001087:Arabinonucleosides; D009696:Nucleic Acids; D012313:RNA; D004247:DNA