title: Oligodeoxynucleotides having a loop consisting of 3'-deoxy-4'-C-(2-hydroxyethyl)thymidines form stable hairpins.
abstract: Components that form stable hairpin loops are highly useful for the development of functional DNA and RNA molecules. We have designed and synthesized a sugar-modified thymidine analogue, 3'-deoxy-4'-C-(2-hydroxyethyl)thymidine (X), as a nucleosidic loop component stabilizing the hairpin structure. The ODNs I-1-4, 5'-d[CGAACG-X(n)-CGTTCG]-3' (I-1, n = 1; I-2, n = 2; I-3, n = 3; I-4, n = 4), forming the hairpin loop structures, of which the loop moiety consisted of the analogue X, and also the corresponding unmodified ODNs II-1-4, 5'-d[CGAACG-T(n)-CGTTCG]-3' (II-1, n = 1; II-2, n = 2;II-3, n = 3; II-4, n = 4), having a thymidine loop, were synthesized by the phosphoramidite method. The melting temperatures (T(m)) of the ODNs I-1-4 containing X in the loop moiety at 5 microM were 67.1, 68.1, 73.0, and 69.3 degrees C, respectively, and those of the control natural ODNs II-1-4 were 65.3, 67.0, 69.2, and 68.8 degrees C, respectively. Thus, the ODNs I-1-4 formed a more thermally stable hairpin than the corresponding unmodified ODNs II-1-4 having an equal number of loop residues. The hairpin structures of the modified ODNs I-1-4 and the unmodified ODNs II-1-4 were investigated by CD spectroscopy and molecular mechanics calculations. These results showed that the 4'-branched nucleoside X can stabilize hairpin structures when it is present in the loop moiety, probably due to the flexibility of the one-carbon-elongated 4'-branched structure.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Yamamoto
authors.forename: Satoshi
authors.initials: S
authors.lastname: Shuto
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Tamura
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Kodama
authors.forename: Shuichi
authors.initials: S
authors.lastname: Hoshika
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ichikawa
authors.forename: Yoshihito
authors.initials: Y
authors.lastname: Ueno
authors.forename: Eiko
authors.initials: E
authors.lastname: Ohtsuka
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Komatsu
authors.forename: Akira
authors.initials: A
authors.lastname: Matsuda
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D002241:Carbohydrates / Q000737:chemistry; D002942:Circular Dichroism; D006358:Hot Temperature; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009943:Organophosphorus Compounds / Q000138:chemical synthesis / Q000737:chemistry; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism; D013936:Thymidine / Q000031:analogs & derivatives* / Q000737:chemistry*
chemical_list: D002241:Carbohydrates; D009838:Oligodeoxyribonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D015719:Single-Strand Specific DNA and RNA Endonucleases; D013936:Thymidine