title: Nucleic acid structure and sequence probing using fluorescent base analogue tC(O).
abstract: The fluorescent cytosine analog tC(O) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(O), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tC(O) is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transitions of such systems, tC(O) represents a new method of characterization. Furthermore, we find that tC(O) may be used to detect bulges and loops in nucleic acids as well as to distinguish a matched base-pair from several of the mismatched.
authors.affiliation: Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
authors.forename: Karl
authors.initials: K
authors.lastname: Börjesson
authors.forename: Peter
authors.initials: P
authors.lastname: Sandin
authors.forename: L Marcus
authors.initials: LM
authors.lastname: Wilhelmsson
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D005615:Freezing; D055029:Inverted Repeat Sequences; D009690:Nucleic Acid Conformation; D013696:Temperature
chemical_list: D005456:Fluorescent Dyes; D003596:Cytosine; D004247:DNA