title: The R-form of DNA does exist.
abstract: Oligonucleotide 5'-d(CATGCTAACT)-L-d(AGTTAGCATG)-L-d(CATGCTAACT)-3' [L = pO(CH2CH2O)3p] is shown to fold back on itself twice forming at pH 7 a sufficiently stable triplex (Tm is about 30 degrees C) with parallel-orientated identical strands (the recombinant or R-form of DNA). Experimental evidence was obtained by studying thermal denaturation, chemical modification and binding of fluorescent probes. The stability of the R-triplex increases in the presence of divalent ions or spermidine. Its structure is characterized by a certain heterogeneity that causes the cooperativity of a triplex-to-duplex transition to decrease. On the basis of conformational modeling, the possible types of base tripling in all four triplets are proposed. The experimental data as well as the molecular mechanic calculations indicate that the stabilities of triplets in the R-triplex decrease in the order: G:C-G = A:T-A >> T:A-T > C:G-C.
authors.affiliation: V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow.
authors.forename: A K
authors.initials: AK
authors.lastname: Shchyolkina
authors.forename: E N
authors.initials: EN
authors.lastname: Timofeev
authors.forename: O F
authors.initials: OF
authors.lastname: Borisova
authors.forename: I A
authors.initials: IA
authors.lastname: Il'icheva
authors.forename: E E
authors.initials: EE
authors.lastname: Minyat
authors.forename: E B
authors.initials: EB
authors.lastname: Khomyakova
authors.forename: V L
authors.initials: VL
authors.lastname: Florentiev
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D005454:Fluorescence Polarization; D006358:Hot Temperature; D006860:Hydrogen Bonding; D008274:Magnesium / Q000494:pharmacology; D008345:Manganese / Q000494:pharmacology; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D008345:Manganese; D004247:DNA; D008274:Magnesium