title: Self-Assembled Pico-Liter Droplet Microarray for Ultrasensitive Nucleic Acid Quantification.
abstract: Nucleic acid detection and quantification technologies have made remarkable progress in recent years. Among existing platforms, hybridization-based assays have the advantages of being amplification free, low instrument cost, and high throughput, but are generally less sensitive compared to sequencing and PCR assays. To bridge this performance gap, we developed a quantitative physical model for the hybridization-based assay to guide the experimental design, which leads to a pico-liter droplet environment with drastically enhanced performance and detection limit several order above any current microarray platform. The pico-liter droplet hybridization platform is further coupled with the on-chip enrichment technique to yield ultrahigh sensitivity both in terms of target concentration and copy number. Our physical model, taking into account of molecular transport, electrostatic intermolecular interactions, reaction kinetics, suggests that reducing liquid height and optimizing target concentration will maximize the hybridization efficiency, and both conditions can be satisfied in a highly parallel, self-assembled pico-liter droplet microarray that produces a detection limit as low as 570 copies and 50 aM. The pico-liter droplet array device is realized with a micropatterned superhydrophobic black silicon surface that allows enrichment of nucleic acid samples by position-defined evaporation. With on-chip enrichment and oil encapsulated pico-liter droplet arrays, we have demonstrated a record high sensitivity, wide dynamic range (6 orders of magnitude), and marked reduction of hybridization time from >10 h to <5 min in a highly repeatable fashion, benefiting from the physics-driven design and nanofeatures of the device. The design principle and technology can contribute to biomedical sensing and point-of-care clinical applications such as pathogen detection and cancer diagnosis and prognosis.
authors.affiliation: Department of Bioengineering, University of California San Diego , La Jolla, California 92093-0412, United States.
authors.forename: Tony M
authors.initials: TM
authors.lastname: Yen
authors.affiliation: Materials Science and Engineering Program, University of California San Diego , La Jolla, California 92093-0418, United States.
authors.forename: Tiantian
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Chemical Engineering Program, University of California San Diego , La Jolla, California 92093-0448, United States.
authors.forename: Ping-Wei
authors.initials: PW
authors.lastname: Chen
authors.affiliation: Department of Electrical and Computer Engineering, University of California San Diego , La Jolla, California 92093-0407, United States.
authors.forename: Ti-Hsuan
authors.initials: TH
authors.lastname: Ku
authors.affiliation: Materials Science and Engineering Program, University of California San Diego , La Jolla, California 92093-0418, United States.
authors.forename: Yu-Jui
authors.initials: YJ
authors.lastname: Chiu
authors.affiliation: Department of Biology, Lamar University , Beaumont, Texas 77710, United States.
authors.forename: Ian
authors.initials: I
authors.lastname: Lian
authors.affiliation: Department of Electrical and Computer Engineering, University of California San Diego , La Jolla, California 92093-0407, United States.
authors.forename: Yu-Hwa
authors.initials: YH
authors.lastname: Lo
mesh_terms: D004247:DNA / Q000032:analysis; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000032:analysis*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013997:Time Factors
chemical_list: D009696:Nucleic Acids; D004247:DNA
keywords: amplification-free; biophysics; hybridization efficiency; microarray; nucleic acid sensing; pico-liter; self-assembly