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American Journal of Biochemistry and Molecular Biology

Year: 2013 | Volume: 3 | Issue: 1 | Page No.: 175-181
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Authors

Md. Gias Uddin

A.T.M. Zafrul Azam

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Research Article

A Novel Oligo-DNA Probe Carrying Non-nucleosidic Silylated Pyrene Derivatives: Synthesis and Excimer Forming Ability

Md. Gias Uddin and A.T.M. Zafrul Azam
Sequence-selective DNA detection is an important tool for monitoring many biological processes and for other biotechnological applications. In this way, molecular beacons (MBs) are highly selective in detecting oligonucleotides that have got widespread applications in nucleic acids chemistry. Excimer formation is a fundamental property of pyrene that can be used for designing unique class of DNA probe such as molecular beacons. To develop a new DNA detection probe that gives specific excimer fluorescent signal before hybridization to the target, a novel 29mer stem-loop structured (molecular beacon) DNA was synthesized. Then two non-nucleosidic silylated pyrene units have been incorporated into this novel oligo-DNA by standard phosphoramidite method using automated DNA synthesizer. Molecular beacon probe with silylated pyrene has already been reported by our group where pyrene was used as a part of nucleobase. In the present case, pyrenes are incorporated as non-nucleobase that have successfully displayed excimer fluorescence signal. Interestingly, the resulting modified DNA exhibited strong excimer fluorescent signal both before and after hybridization to the fully matched complementary target. Careful selection of the nucleobases in the stem segment could result in a more efficient sequence discriminating oligo-DNA probe.
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