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Biomolecular computation with molecular beacons for quantitative analysis of target nucleic acids
Lim, H.W.,Lee, S.H.,Yang, K.A.,Yoo, S.I.,Park, T.H.,Zhang, B.T. North-Holland Pub. Co ; Elsevier Science Ltd ; Els 2013 Bio systems Vol.111 No.1
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.
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Non-linear molecular pattern classification using molecular beacons with multiple targets
Lee, I.H.,Lee, S.H.,Park, T.H.,Zhang, B.T. North-Holland Pub. Co ; Elsevier Science Ltd ; Els 2013 Bio systems Vol.114 No.3
In vitro pattern classification has been highlighted as an important future application of DNA computing. Previous work has demonstrated the feasibility of linear classifiers using DNA-based molecular computing. However, complex tasks require non-linear classification capability. Here we design a molecular beacon that can interact with multiple targets and experimentally shows that its fluorescent signals form a complex radial-basis function, enabling it to be used as a building block for non-linear molecular classification in vitro. The proposed method was successfully applied to solving artificial and real-world classification problems: XOR and microRNA expression patterns.
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