title: Thermodynamic, structural and fluorescent characteristics of DNA hairpins containing functionalized pyrrolo-2'-deoxycytidines.
abstract: Herein, we present comprehensive physicochemical and structural analysis of various DNA hairpins modified with pyrrolo-2'-deoxycytidine (Py-dC) derivatives. The introduction of modified Py-dC in most cases causes minor decrease of hairpin thermodynamic stability. The energetically unfavorable effect is more pronounced when modified residue is present within hairpin loop. Our studies indicate that thermodynamic effects induced by all Py-dC derivatives are net results of increased stacking interactions caused by larger surface of pyrrolo-2'-deoxycytidine aromatic ring and unfavorable effect implied by the presence of additional side chains. The CD spectra of all modified hairpins are similar to unmodified hairpin indicating that the presence of Py-dC derivatives does not disrupt the secondary structure of DNA. Interestingly, the presence of various side chains can increase fluorescent discrimination of paired and unpaired regions of DNA. The fluorescence observed for hairpins modified within loop is significantly quenched when Py-dC derivative is present in the stem region.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
authors.forename: Zofia
authors.initials: Z
authors.lastname: Jahnz-Wechmann
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
authors.forename: Jolanta
authors.initials: J
authors.lastname: Lisowiec-Wachnicka
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Framski
authors.affiliation: Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89 b, 61-614 Poznań, Poland.
authors.forename: Joanna
authors.initials: J
authors.lastname: Kosman
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
authors.forename: Jerzy
authors.initials: J
authors.lastname: Boryski
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland. Electronic address: apa@ibch.poznan.pl.
authors.forename: Anna
authors.initials: A
authors.lastname: Pasternak
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D005453:Fluorescence; D009690:Nucleic Acid Conformation; D011758:Pyrroles / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D011758:Pyrroles; C540526:pyrrolo-deoxycytidine; D003841:Deoxycytidine; D004247:DNA
keywords: Circular dichroism; DNA; Fluorescence; Hairpin; Nucleosides; Thermodynamics