The use of 2-hydroperoxytetrahydrofuran as a reagent to sequence cytosine and to probe non-Watson-Crick DNA structures.
2-Hydroperoxytetrahydrofuran (THF-OOH) can be employed to sequence cytosine (C) and to probe for non-canonical DNA structures involving C. Using 32P-labeled oligomers and a DNA restriction fragment, it is demonstrated that THF-OOH has a strong preference for Cs in single-stranded (s-s) DNA regions, and in bulges, loops and mismatches. The reactivity of C is diminished below pH 6.0, but is not affected by substitution of 5-methylcytosine. To demonstrate the utility of the reagent, it is directly compared to methoxylamine and chloroacetaldehyde, two other reagents commonly used to chemically probe C residues in non-Watson-Crick DNA structures.
Liang
G
G
Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha 68198-6805.
Gannett
P
P
Gold
B
B
D044503:5-Methylcytosine; D000079:Acetaldehyde / Q000031:analogs & derivatives; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D005663:Furans; D006358:Hot Temperature; D006863:Hydrogen-Ion Concentration; D006898:Hydroxylamines; D007202:Indicators and Reagents; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D017422:Sequence Analysis, DNA
D004277:DNA, Single-Stranded; D005663:Furans; D006898:Hydroxylamines; D007202:Indicators and Reagents; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; C005214:methoxyamine; C004656:chloroacetaldehyde; D000079:Acetaldehyde; C092664:2-hydroperoxytetrahydrofuran