title: Distinguishing "looped-out" and "stacked-in" DNA bulge conformation using fluorescent 2-aminopurine replacing a purine base.
abstract: The conformation of a bulged DNA base, whether looped-out of the DNA helix or stacked-in between the flanking bases, can be distinguished using fluorescence spectroscopy of an inserted fluorescent base. If 2-aminopurine, a structural analog of adenine and guanine, is placed in duplex DNA as the bulged base replacing an adenine or guanine, it loops out of the DNA helix into solution. This is determined by the decrease or increase of 2-aminopurine fluorescence during DNA thermomelting: if the 2-aminopurine base stacks into the helix, its fluorescence increases or remains about the same during DNA duplex melting, but if the 2-aminopurine base loops out of the helix, its fluorescence decreases upon melting of the DNA duplex.
authors.affiliation: Department of Chemistry, Jackson State University, Jackson, MS 39217, USA.
authors.forename: Yugao
authors.initials: Y
authors.lastname: Jiao
authors.forename: Sandra
authors.initials: S
authors.lastname: Stringfellow
authors.forename: Hongtao
authors.initials: H
authors.lastname: Yu
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011193:Potassium Iodide / Q000737:chemistry; D011687:Purines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence / Q000379:methods; D013696:Temperature
chemical_list: D005456:Fluorescent Dyes; D011687:Purines; D011193:Potassium Iodide; D015075:2-Aminopurine; D004247:DNA