PT  - JOURNAL ARTICLE
AU  - Burcu Özay
AU  - Cara M Robertus
AU  - Jackson L Negri
AU  - Stephanie E McCalla
TI  - Biphasic, Switch-Like Isothermal DNA Amplification
AID  - 10.1101/169805
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 169805
4099  - http://biorxiv.org/content/early/2017/07/28/169805.short
4100  - http://biorxiv.org/content/early/2017/07/28/169805.full
AB  - Switches are common in biological systems due to their ability to give a definitive response to a specific target molecule in the presence of high concentration background. Synthetic systems aim to reproduce this effect for applications from DNA computing to molecular diagnostics. Exciting new systems can produce switch-like behavior, but typically respond to nanomolar input of target molecule. We report a novel DNA amplification chemistry that has two switch-like characteristics. First, the chemistry is biphasic, with a low-gain first phase and plateau followed by a high gain burst of signal. Second, the reaction kinetics can be tuned to give a large ultrasensitive jump in signal during the second phase. Reaction output at each stage can be rationally tuned based on DNA association thermodynamics. The chemistry is one-step, isothermal, and can be adapted to respond to a broad range of input target molecules. This biphasic DNA amplification reaction could potentially impact diagnostics, DNA circuits, or other sensor systems that require definitive digital outputs.Significance Statement Switch-like reactions are common in the natural world; they are vital to basic cellular operations such as signaling and genetic regulation. These responses are difficult to reproduce in synthetic biological systems, particularly for low concentrations of input molecules such as those seen in vivo. We have developed the first reported biphasic DNA amplification reaction, with the second amplification phase giving up to two orders of magnitude greater output than a standard oligonucleotide amplification reaction. Both reaction phases feature tunable kinetics based on DNA association thermodynamics, and the second phase can be tuned to produce ultrasensitive, switch-like signal output. This one-step isothermal reaction can potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.