Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Target-assembled Exciplex Detectors for Detecting DNA Sequences and Mismatches

Detection of specific target nucleic acid sequences through hybridization to a complementary probe oligonucleotide with a fluorescent label usually suffers from large background fluorescence. Decreased background is possible by using two short oligonucleotide probes, complementary to neighboring sites of the same DNA target, which form a pyrene excimer on suitable juxtaposition of the partners (A = B = pyrene in Figure 1A). Excitation of one of the pyrene partners forms an excimer that emits at long wavelength. Thus, the target sequence itself assembles its own detector from components that are non-fluorescent at the detection wavelength, giving massive improvement in terms of the decreased background. For excimer-DNA systems, A and B must be identical. More variability in properties and potential applications would be possible if A and B were different from each other and could be varied (i.e., exciplexes). However, organic exciplexes do not usually emit with reasonable strength in solvents more polar than acetontrile. We will describe the experimental conditions required for the first exciplex-based split-probe systems for detection of nucleic acids (ExciProbes), and how such exciplexes can register the presence of mismatches as required in SNP analysis.

Figure 1: Split-probe oligonucleotides self-assembled by their DNA target. A and B represent exci-partners capable of forming an excimer (A=B) or exciplex (AB).

References and Footnotes
  1. Ebata, K., Masuko, M., Ohtani, H., & Jibu, M. Nucl. Acids Symp. Ser. 34, 187-188 (1995).
  2. Paris, P. L., Langenhan, J. M., & Kool, E. T. Nucleic Acids Research 26, 3789-3793 (1998).
  3. K. T. Douglas, E. V. Bichenkova, H. Savage, A. Sardarian, 2004-GB1803[2004097043], 105-20041111, WO23-4-2004.

E. V. Bichenkova
H. E. Savage
A. R. Sardarian
C. Rogert
A. Gbaj
L. Walsh
K. T. Douglas*

Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics
School of Pharmacy and Pharmaceutical Sciences
University of Manchester
Manchester, M13 9PL, U.K

*Corresponding author
Fax: +44 (0) 161 275 2481
Email: Ken.Douglas@.man.ac.uk