title: Sequence specific fluorescence detection of double strand DNA.
abstract: Methods for the fluorescent detection of specific sequences of double strand DNA in homogeneous solution may be useful in the field of human genetics. A series of hairpin polyamides with tetramethyl rhodamine (TMR) attached to an internal pyrrole ring were synthesized, and the fluorescence properties of the polyamide-fluorophore conjugates in the presence and absence of duplex DNA were examined. We observe weak TMR fluorescence in the absence of DNA. Addition of >/=1:1 match DNA affords a significant fluorescence increase over equimolar mismatch DNA for each polyamide-TMR conjugate. Polyamide-fluorophore conjugates offer a new class of sensors for the detection of specific DNA sequences without the need for denaturation. The polyamide-dye fluorescence-based method can be used to screen in parallel the interactions between aromatic ring pairs and the minor groove of DNA even when the binding site contains a non-Watson-Crick DNA base pair. A ranking of the specificity of three polyamide ring pairs-Py/Py, Im/Py, and Im/Im-was established for all 16 possible base pairs of A, T, G, and C in the minor groove. We find that Im/Im is an energetically favorable ring pair for minor groove recognition of the T.G base pair.
authors.affiliation: The Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
authors.forename: Victor C
authors.initials: VC
authors.lastname: Rucker
authors.forename: Shane
authors.initials: S
authors.lastname: Foister
authors.forename: Christian
authors.initials: C
authors.lastname: Melander
authors.forename: Peter B
authors.initials: PB
authors.lastname: Dervan
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D004247:DNA / Q000032:analysis* / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009757:Nylons / Q000737:chemistry*; D012235:Rhodamines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013379:Substrate Specificity
chemical_list: D005456:Fluorescent Dyes; D009757:Nylons; D012235:Rhodamines; D004247:DNA