LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures.

Background: We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs.

Results: LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regions for LAMP signatures with loop primers, which can be used as LAMP signatures.

Development and initial results of a low cost, disposable, point-of-care testing device for pathogen detection.

Development of small footprint, disposable, fast, and inexpensive devices for pathogen detection in the field and clinic would benefit human and veterinary medicine by allowing evidence-based responses to future out breaks. We designed and tested an integrated nucleic acid extraction and amplification device employing a loop-mediated isothermal amplification (LAMP) or reverse transcriptase-LAMP assay. Our system provides a screening tool with polymerase-chain-reaction-level sensitivity and specificity for outbreak detection, response, and recovery.

Aptamer-based SERRS sensor for thrombin detection.

We describe an aptamer-based surface enhanced resonance Raman scattering (SERRS) sensor with high sensitivity, specificity, and stability for the detection of a coagulation protein, human alpha-thrombin. The sensor achieves high sensitivity and a limit of detection of 100 pM by monitoring the SERRS signal change upon the single-step of thrombin binding to immobilized thrombin binding aptamer. The selectivity of the sensor is demonstrated by the specific discrimination of thrombin from other protein analytes.

Diagnostic evaluation of multiplexed reverse transcription-PCR microsphere array assay for detection of foot-and-mouth and look-alike disease viruses.

A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and-mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV.

Single-step electronic detection of femtomolar DNA by target-induced strand displacement in an electrode-bound duplex.

We report a signal-on, electronic DNA (E-DNA) sensor that is label-free and achieves a subpicomolar detection limit. The sensor, which is based on a target-induced strand displacement mechanism, is composed of a "capture probe" attached by its 5' terminus to a gold electrode and a 5' methylene blue-modified "signaling probe" that is complementary at both its 3' and 5' termini to the capture probe. In the absence of target, hybridization between the capture and signaling probes minimizes contact between the methylene blue and electrode surface, limiting the observed redox current.

Sequence-specific, electronic detection of oligonucleotides in blood, soil, and foodstuffs with the reagentless, reusable E-DNA sensor.

The ability to detect specific oligonucleotides in complex, contaminant-ridden samples, without the use of exogenous reagents and using a reusable, fully electronic platform could revolutionize the detection of pathogens in the clinic and in the field. Here, we characterize a label-free, electronic sensor, termed E-DNA, for its ability to simultaneously meet these challenging demands. We find that because signal generation is coupled to a hybridization-linked conformational change, rather than to only adsorption to the sensor surface, E-DNA is selective enough to detect oligonucleotides in complex, multicomponent samples, such as blood serum and soil.

An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids.

Whereas spectroscopic and chromatographic techniques for the detection of small organic molecules have achieved impressive results, these methods are generally slow and cumbersome, and thus the development of a general means for the real-time, electronic detection of such targets remains a compelling goal. Here we demonstrate a potentially general, label-free electronic method for the detection of small-molecule targets by building a rapid, reagentless biosensor for the detection of cocaine. The sensor, based on the electrochemical interrogation of a structure-switching aptamer, specifically detects micromolar cocaine in seconds.

G-factor analysis of protein secondary structure in solutions and thin films.

The biological activity of proteins is structure dependent. In this discussion, we describe development of g-factor analysis for characterizing the secondary structure of proteins in solutions and films. In g-factor analysis, experimental circular dichroism (CD) and UV absorbance spectra are converted to dimensionless g-factor spectra by dividing the differential absorbance of circularly polarized light (AL - AR) by the UV absorbance (A) at each wavelength.