Biomolecular computation with molecular beacons for quantitative analysis of target nucleic acids

• Published in: BioSystems 2013-01, Vol.111 (1), p.11-17
• Main Authors: Lim, Hee-Woong, Lee, Seung Hwan, Yang, Kyung-Ae, Yoo, Suk-In, Park, Tai Hyun, Zhang, Byoung-Tak
• Format: Article
• Language: English
• Subjects: Base Sequence; Biomolecular computation; Computational Biology - methods; DNA Probes - genetics; DNA Probes - metabolism; Fluorescence; Molecular beacon; Molecular Sequence Data; Nucleic Acids - analysis; Oligonucleotides - genetics; Quantitative analysis; Weighted-sum
• ISSN: 0303-2647; 1872-8324
• DOI: 10.1016/j.biosystems.2012.09.004

Molecular beacons are efficient and useful tools for quantitative detection of specific target nucleic acids. Thanks to their simple protocol, molecular beacons have great potential as substrates for biomolecular computing. Here we present a molecular beacon-based biomolecular computing method for quantitative detection and analysis of target nucleic acids. Whereas the conventional quantitative assays using fluorescent dyes have been designed for single target detection or multiplexed detection, the proposed method enables us not only to detect multiple targets but also to compute their quantitative information by weighted-sum of the targets. The detection and computation are performed on a molecular level simultaneously, and the outputs are detected as fluorescence signals. Experimental results show the feasibility and effectiveness of our weighted detection and linear combination method using molecular beacons. Our method can serve as a primitive operation of molecular pattern analysis, and we demonstrate successful binary classifications of molecular patterns made of synthetic oligonucleotide DNA molecules.