Pretend I’m Not Here: Minimally-Interfering Fluorescent Dye-Quenchers for DNA Reaction Networks
Abstract
Many disease-related biomarkers have been detected in the blood stream. However, detection of such low-concentration molecules requires expensive and time-consuming analytical techniques. In the past decade, the programmability of Watson-Crick base-pairing has been used to develop DNA-based molecular circuits that can detect and amplify low-concentration, disease-related biomarkers. These DNA-based circuits consist of coupled reaction networks, and the interactions between network components can be difficult to predict. Operation of such networks is normally monitored by measuring the fluorescence of separate molecular probes. Such probes are used to minimized the interference of fluorescent dye-quencher pairs, which may bind strongly and impact network operation; however, the probe sequences may also interfere with network operation. To simplify amplification circuitry and improve network performance, we performed of a series of experiments to establish a fluorescent dye-quencher system that can be directly incorporated within a DNA-based amplifying circuit with minimal impact on circuit performance.
Pretend I’m Not Here: Minimally-Interfering Fluorescent Dye-Quenchers for DNA Reaction Networks
Many disease-related biomarkers have been detected in the blood stream. However, detection of such low-concentration molecules requires expensive and time-consuming analytical techniques. In the past decade, the programmability of Watson-Crick base-pairing has been used to develop DNA-based molecular circuits that can detect and amplify low-concentration, disease-related biomarkers. These DNA-based circuits consist of coupled reaction networks, and the interactions between network components can be difficult to predict. Operation of such networks is normally monitored by measuring the fluorescence of separate molecular probes. Such probes are used to minimized the interference of fluorescent dye-quencher pairs, which may bind strongly and impact network operation; however, the probe sequences may also interfere with network operation. To simplify amplification circuitry and improve network performance, we performed of a series of experiments to establish a fluorescent dye-quencher system that can be directly incorporated within a DNA-based amplifying circuit with minimal impact on circuit performance.