Digital biology and chemistry

Abstract

This account examines developments in "digital" biology and chemistry within the context of microfluidics, from a personal perspective. Using microfluidics as a frame of reference, we identify two areas of research within digital biology and chemistry that are of special interest: (i) the study of systems that switch between discrete states in response to changes in chemical concentration of signals, and (ii) the study of single biological entities such as molecules or cells. In particular, microfluidics accelerates analysis of switching systems (i.e., those that exhibit a sharp change in output over a narrow range of input) by enabling monitoring of multiple reactions in parallel over a range of concentrations of signals. Conversely, such switching systems can be used to create new kinds of microfluidic detection systems that provide "analog-to-digital" signal conversion and logic. Microfluidic compartmentalization technologies for studying and isolating single entities can be used to reconstruct and understand cellular processes, study interactions between single biological entities, and examine the intrinsic heterogeneity of populations of molecules, cells, or organisms. Furthermore, compartmentalization of single cells or molecules in "digital" microfluidic experiments can induce switching in a range of reaction systems to enable sensitive detection of cells or biomolecules, such as with digital ELISA or digital PCR. This "digitizing" offers advantages in terms of robustness, assay design, and simplicity because quantitative information can be obtained with qualitative measurements. While digital formats have been shown to improve the robustness of existing chemistries, we anticipate that in the future they will enable new chemistries to be used for quantitative measurements, and that digital biology and chemistry will continue to provide further opportunities for measuring biomolecules, understanding natural systems more deeply, and advancing molecular and cellular analysis. Microfluidics will impact digital biology and chemistry and will also benefit from them if it becomes massively distributed.

Digital quantification of miRNA directly in plasma using integrated comprehensive droplet digital detection

“…Our hypothesis is that that the confinement of samples containing low-abundance miRNAs in picoliter droplets can significantly increase the effective miRNA concentration, provide a means for digital quantification (i.e., each droplet has 0 or 1 target miRNA) and minimizes the number of background molecules (interference) from plasma. 25 Indeed, we demonstrated that the IC 3D can robustly quantify target miRNA directly from unprocessed plasma as validated by RT-qPCR for the same samples (Figure 3f). RNase-treated plasma was also included as a negative control to confirm that the fluorescent droplets are due to the target Let-7a (Figure s5).…”

Building bio-assays with magnetic particles on a digital microfluidic platform

“…Optical single-molecule detection methods, also known as digital assays [68], have become valuable analytical techniques for a broad variety of bio-assays, enabling sensitive detection of relevant biomolecules down to the attomolar range. This ultrasensitive detection is possible by the isolation of individual target biomolecules into small reaction chambers where the signal is generated and detected.…”

The pumping lid: investigating multi-material 3D printing for equipment-free, programmable generation of positive and negative pressures for microfluidic applications

“…We found that pumping proceeded to completion despite the variation of pressure applied to the pumping lid by the volunteer. 30, 31 We expect the simplicity of the pumping lid to be valuable in both LRS and laboratory settings, e.g. for digital single-molecule measurements.…”