Self-quenching DNA probes based on aggregation of fluorescent dyes

Gabriela Schafer; Matthias Muller; Bernhard Hafner; Gregor Habl; Oliver Nolte; Nicole Marme; Jens-Peter Knemeyer

doi:10.1117/12.588257

4 April 2005 Self-quenching DNA probes based on aggregation of fluorescent dyes

Gabriela Schafer, Matthias Muller, Bernhard Hafner, Gregor Habl, Oliver Nolte, Nicole Marme, Jens-Peter Knemeyer

Proceedings Volume 5704, Genetically Engineered and Optical Probes for Biomedical Applications III; (2005) https://doi.org/10.1117/12.588257
Event: SPIE BiOS, 2005, San Jose, CA, United States

Abstract

Here we present a novel class of self-quenching, double-labeled DNA probes based on the formation of non fluorescent H-type dye dimers. We therefore investigated the aggregation behavior of the red-absorbing oxazine derivative MR121 and found a dimerization constant of about 3000 M-1. This dye was successfully used to develop hairpin-structured as well as linear self-quenching DNA probes that report the presence of the target DNA by an increase of the fluorescence intensity by a factor of 3 to 12. Generally fluorescence quenching of the hairpin-structure probes is more efficient compared to the linear probes, whereas the kinetic of the fluorescence increase is significantly slower. The new probes were used for the identification of different mycobacteria and their antibiotic resistant species. As a test system a probe for the identification of a DNA sequence specific for the Mycobacterium xenopi was synthesized differing from the sequence of the Mycobacterium fortuitum by 6 nucleotides. Furthermore we developed a method for the discrimination between the sequences of the wild type and an antibiotic resistant species of Mycobacterium tuberculosis. Both sequences differ by just 2 nucleotides and were detected specifically by the use of competing olignonucleotides.

Citation Download Citation

Gabriela Schafer, Matthias Muller, Bernhard Hafner, Gregor Habl, Oliver Nolte, Nicole Marme, and Jens-Peter Knemeyer "Self-quenching DNA probes based on aggregation of fluorescent dyes", Proc. SPIE 5704, Genetically Engineered and Optical Probes for Biomedical Applications III, (4 April 2005); https://doi.org/10.1117/12.588257

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available