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Proceedings Paper

Short non-coding RNAs as bacteria species identifiers detected by surface plasmon resonance enhanced common path interferometry
Author(s): Charles Greef; Viatcheslav Petropavlovskikh; Oyvind Nilsen; Boris Khattatov; Mikhail Plam; Patrick Gardner; John Hall
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Paper Abstract

Small non-coding RNA sequences have recently been discovered as unique identifiers of certain bacterial species, raising the possibility that they can be used as highly specific Biowarfare Agent detection markers in automated field deployable integrated detection systems. Because they are present in high abundance they could allow genomic based bacterial species identification without the need for pre-assay amplification. Further, a direct detection method would obviate the need for chemical labeling, enabling a rapid, efficient, high sensitivity mechanism for bacterial detection. Surface Plasmon Resonance enhanced Common Path Interferometry (SPR-CPI) is a potentially market disruptive, high sensitivity dual technology that allows real-time direct multiplex measurement of biomolecule interactions, including small molecules, nucleic acids, proteins, and microbes. SPR-CPI measures differences in phase shift of reflected S and P polarized light under Total Internal Reflection (TIR) conditions at a surface, caused by changes in refractive index induced by biomolecular interactions within the evanescent field at the TIR interface. The measurement is performed on a microarray of discrete 2-dimensional areas functionalized with biomolecule capture reagents, allowing simultaneous measurement of up to 100 separate analytes. The optical beam encompasses the entire microarray, allowing a solid state detector system with no scanning requirement. Output consists of simultaneous voltage measurements proportional to the phase differences resulting from the refractive index changes from each microarray feature, and is automatically processed and displayed graphically or delivered to a decision making algorithm, enabling a fully automatic detection system capable of rapid detection and quantification of small nucleic acids at extremely sensitive levels. Proof-of-concept experiments on model systems and cell culture samples have demonstrated utility of the system, and efforts are in progress for full development and deployment of the device. The technology has broad applicability as a universal detection platform for BWA detection, medical diagnostics, and drug discovery research, and represents a new class of instrumentation as a rapid, high sensitivity, label-free methodology.

Paper Details

Date Published: 17 April 2008
PDF: 7 pages
Proc. SPIE 6954, Chemical, Biological, Radiological, Nuclear, and Explosives (CBRNE) Sensing IX, 695410 (17 April 2008); doi: 10.1117/12.779459
Show Author Affiliations
Charles Greef, AlphaSniffer, LLC (United States)
Viatcheslav Petropavlovskikh, AlphaSniffer, LLC (United States)
Oyvind Nilsen, AlphaSniffer, LLC (United States)
Boris Khattatov, AlphaSniffer, LLC (United States)
Mikhail Plam, AlphaSniffer, LLC (United States)
Patrick Gardner, Western Carolina Univ. (United States)
John Hall, Hall Stable Lasers LLC (United States)


Published in SPIE Proceedings Vol. 6954:
Chemical, Biological, Radiological, Nuclear, and Explosives (CBRNE) Sensing IX
Augustus Way Fountain; Patrick J. Gardner, Editor(s)

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