title: Hairpin formation of d(CGCG-TA-CGCG), d(CGCG-TG-CGCG) and their cytosine methylated analogs.
abstract: Hairpin formations of decamers d(CGCG-TA-CGCG), d(CGCG-TG-CGCG), and their m5dC analogs are evidenced by the existence of biphasic absorbance melting profiles in which the lower transition temperature increases with increasing oligomer concentration, whereas the higher melting temperature is concentration independent. The corresponding temperature dependent CD intensity at 285 nm exhibits a maximum around 55 degrees C. These observations are consistent with the interpretation that the lower temperature transition corresponds to the duplex to hairpin transformation while the melting of hairpins into single strands constitutes the higher temperature transition. The CD spectrum of the hairpin conformation appears to be characterized by a couplet with nearly equal positive and negative intensities at 285 and 255 nm, respectively, while a significantly smaller intensity at 285 nm is apparent for the duplex form. The hairpin conformation is suspected to contain a two-nucleotide loop. Titrations with NaCl further suggest that, in contrast to the TA sequence, the TG sequence with wobble base pairing favors Z formation under high salt conditions.
authors.affiliation: Department of Chemistry, Tennessee State University, Nashville 37209-1561.
authors.forename: F M
authors.initials: FM
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D055598:Chemical Phenomena; D002621:Chemistry; D003596:Cytosine; D004247:DNA; D008745:Methylation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides; D013696:Temperature; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D003596:Cytosine; D004247:DNA