478812-28-1Relevant articles and documents
Sequence specific fluorescence detection of double strand dna
Rucker, Victor C.,Foister, Shane,Melander, Christian,Dervan, Peter B.
, p. 1195 - 1202 (2003)
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. Polyamidefluorophore 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.