title: Quencher-free multiplexed monitoring of DNA reaction circuits.
abstract: We present a simple yet efficient technique to monitor the dynamics of DNA-based reaction circuits. This technique relies on the labeling of DNA oligonucleotides with a single fluorescent modification. In this quencher-free setup, the signal is modulated by the interaction of the 3'-terminus fluorophore with the nucleobases themselves. Depending on the nature of the fluorophore's nearest base pair, fluorescence intensity is decreased or increased upon hybridization. By tuning the 3'-terminal nucleotides, it is possible to obtain opposite changes in fluorescence intensity for oligonucleotides whose hybridization site is shifted by a single base. Quenching by nucleobases provides a highly sequence-specific monitoring technique, which presents a high sensitivity even for small oligonucleotides. Compared with other sequence-specific detection methods, it is relatively non-invasive and compatible with the complex dynamics of DNA reaction circuits. As an application, we show the implementation of nucleobase quenching to monitor a DNA-based chemical oscillator, allowing us to follow in real time and quantitatively the dephased oscillations of the components of the network. This cost-effective monitoring technique should be widely implementable to other DNA-based reaction systems.
authors: LIMMS/CNRS-IIS, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
authors: Adrien
authors: A
authors: Padirac
authors: Teruo
authors: T
authors: Fujii
authors: Yannick
authors: Y
authors: Rondelez
mesh_terms: D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides; D004247:DNA