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Sequence specific fluorescence detection of double strand DNA

Rucker, Victor C. and Foister, Shane and Melander, Christian and Dervan, Peter B. (2003) Sequence specific fluorescence detection of double strand DNA. Journal of the American Chemical Society, 125 (5). pp. 1195-1202. ISSN 0002-7863. doi:10.1021/ja021011q.

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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.

Item Type:Article
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URLURL TypeDescription Information
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2003 American Chemical Society. Received July 23, 2002; Publication Date (Web): January 8, 2003. We are grateful to the National Institutes of Health for grant support (GM 27681), training grant support for V.C.R. (GM19789-02) and a postdoctoral fellowship to C.M., and to the National Science Foundation for a graduate research fellowship to S.F. We thank G.M. Hathaway for MALDI-TOF mass spectrometry.
Funding AgencyGrant Number
NIH Predoctoral FellowshipGM-19789-02
NSF Graduate Research FellowshipUNSPECIFIED
Issue or Number:5
Record Number:CaltechAUTHORS:20160510-081400599
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Official Citation:Sequence Specific Fluorescence Detection of Double Strand DNA Victor C. Rucker, Shane Foister, Christian Melander, and Peter B. Dervan Journal of the American Chemical Society 2003 125 (5), 1195-1202 DOI: 10.1021/ja021011q
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66810
Deposited By: Victoria Brennan
Deposited On:18 May 2016 16:32
Last Modified:11 Nov 2021 00:03

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