Del Mar Photonics - DNA Imaging with AFM Heron - AFM Heron

DNA related presentations at SPIE Defense and Security Sensing

Gold nanoparticle assays: toward single molecule unamplified DNA detection
Paper 7312-22 of Conference 7312
Date: Tuesday, 14 April 2009

Author(s): Remco Verdoold, Dorothee Wasserberg, Felicia Ungureanu, Jan Halamek, Rob Kooyman, Univ. Twente (Netherlands)

Light scattering and absorption properties of gold nanoparticles (GNPs) can be utilised for the detection of DNA. Binding of molecules to the GNP influences the local refractive index which can be detected as a red-shift of the GNP’s extinction maximum. Therefore GNPs are suitable for use as nanoparticle chemical sensors. Utilizing this method it is possible to detect unamplified DNA from e.g. pathogens.
Randomly immobilised particles were visualised with a darkfield microscope. For the detection of single hybridisation events a sandwich assay was developed, utilizing a second DNA-functionalized GNP. Simultaneous observation of large numbers of GNPs provides a quantitative assay.

Conducting polymer-based DNA biosensor for the detection of Bacillus cereus group species
Paper 7315-3 of Conference 7315
Date: Tuesday, 14 April 2009

Author(s): Vijayalakshmi Velusamy, Khalil I. Arshak, Olga Korostynska, Kamila Oliwa, Catherine Adley, Univ. of Limerick (Ireland)

There is an increasing demand for food safety worldwide and real time detection of microbial pathogens in food is the solution to the prevention and recognition of problems related to health and safety. Handheld DNA biosensor is one of the proposed solutions for the sensitive (<100 CFU/g) and real time detection of foodborne pathogens and it is being developed for the in situ detection of Bacillus cereus group species. The electrically conducting polymer, polypyrrole is used a platform for immobilizing DNA on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers.

eSensor®: an electrochemical detection-based DNA microarray technology enabling sample-to-answer molecular diagnostics
Paper 7306A-23 of Conference 7306A
Date: Wednesday, 15 April 2009

Author(s): Robin H. Liu, Osmetech Molecular Diagnostics (United States)

DNA microarrays are becoming a widespread tool used in life science and drug screening due to its many benefits of miniaturization and integration. Microarrays permit a highly multiplexed DNA analysis. Recently, the development of new detection methods and simplified methodologies has rapidly expanded the use of microarray technologies from predominantly gene expression analysis into the arena of diagnostics. Osmetech’s eSensor® is an electrochemical detection platform based on a low-to- medium density DNA hybridization array on a cost-effective printed circuit board substrate. We currently have two FDA cleared platforms: 1) eSensor® 4800 system for cystic fibrosis carrier screening; 2) eSensor® XT-8 for Warfarin sensitivity test [1] (see Figure. 1). Other genetic-based diagnostic and infectious disease detection tests are under development. The eSensor® platform eliminates the need for an expensive laser-based optical system and fluorescent reagents. In addition, it allows one to perform hybridization and detection in a single and small instrument without any fluidic processing and handling. Furthermore, the eSensor® platform is readily adaptable to on-chip sample-to-answer genetic analyses using microfluidics technology (Figure 2). We demonstrated feasibility of integrated sample preparation, PCR, and microarray detection on a single device that consists of novel microfluidic valves, pumps, and mixers [2]. The devices are completely self-contained: no external pressure sources, fluid storage, mechanical pumps, or valves are necessary for fluid manipulation. The eSensor® platform provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus have a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

DNA enzyme-based detection of metals in water
Paper 7306A-51 of Conference 7306A
Date: Thursday, 16 April 2009

Author(s): David G. Kellner, Yi Lu, DzymeTech, Inc. (United States)

DzymeTech has developed a DNA enzyme based detection scheme for metals, and other toxic chemicals, in water. DNA is isolated that has a high binding affinity for a specific target. This DNA is then tagged with a flourescent dye. A complementary strand is tagged with a quencher. When lead, or another target is present, the lead binds the DNA, and cleaves the strand with the quencher, releasing it. The change in flourescense is then monitored determining the presence and concentration of the lead. This system is hand-held, portable, and can detect lead at below the EPA limits for drinking water.

Label-free DNA methylation analysis using the optofluidic ring resonator sensor
Paper 7322-7 of Conference 7322
Date: Thursday, 16 April 2009

Author(s): Jonathan D. Suter, Xudong Fan, Daniel J. Howard, Charles W. Caldwell, Huidong Shi, Univ. of Missouri, Columbia (United States)

Abnormal DNA methylation patterns are an important phenomenon underlying the development of many cancers. We propose a new label-free sensing platform for the study and quantitative detection of methylated DNA strands called the opto-fluidic ring resonator (OFRR). Leveraging the ability of the anti-5-methylcytosine antibody to discriminate methylated and non-methylated cytosine bases, this work demonstrates the characterization of the OFRR to different oligonucleotide strands based on concentration and variable methylation. It is observed that the sensor signal is highly dependent on the number of methylation sites per oligonucleotide, which supports the utility of the OFRR as a tool for methylation analysis.

A fiber optic microarray for the detection of pathogenic microorganisms
Paper 7312-9 of Conference 7312
Date: Monday, 13 April 2009

Author(s): Jason R. E. Shepard, Univ. at Albany (United States)

The past decade has seen the initiation and development of DNA analysis for detection of pathogenic microrganisms. The genomic information in databases now allows analysis of DNA to proceed in a manageable fashion, and along with new technologies addresses key issues involved in DNA analysis of pathogenic microorganisms. We have employed a high density fiber optic microarray, housing DNA sequences for detection of such species as E. coli, C. botulinum, and B. anthracis. Each organism is analyzed with multiple sequences and is sub-typed against other closely related organisms. For public health labs, culture and growth are still considered the gold standard. High throughput technologies are better suited to capitalize on the limitless potential garnered from sequence information. Our array platform is reusable, allowing repetitive tests on a single array, providing an increase in throughput and decrease in cost, along with a certainty of detection down to the individual strain level.

SmartHEALTH: a microfluidic multisensor platform for POC cancer diagnostics
Paper 7313-10 of Conference 7313
Date: Thursday, 16 April 2009

Author(s): Cornelia Carstens, Holger Becker, Claudia Gärtner, Microfluidic ChipShop GmbH (Germany)

We present a microfluidics based POC multisensor platform for the detection of breast, cervical and colorectal cancer markers. It will perform multi-analyte sensing and interpretation for nucleic acids and proteins and will handle multiple biological sample types. This paper concentrates on the microfluidics technology which allows the development of a fully integrated disposable cartridge which contains functional design elements for the following functions:
• On-chip reagent storage
• Sample preparation, including steps of sample extraction, mixing, filtering and cell lysis
• DNA extraction and purification
• DNA amplification
• Separation
• Detection
• Waste storage

Photonic crystal slab and waveguide design for biological detection
Paper 7322-10 of Conference 7322
Date: Thursday, 16 April 2009

Author(s): Elizabeth A. Tanner, Juronica Arch, Anne-Marie Dorsett, Digital Fusion Inc. (United States); Derek Strembicke, Milan C. Buncick, AEgis Technologies Group, Inc. (United States); Jian Han, HudsonAlpha Institute for Biotechnology (United States); Scott T. Retterer, Darrell K. Thomas, Oak Ridge National Lab. (United States)

Digital Fusion has designed, fabricated, and tested a photonic crystal slab (PCS) with a line defect waveguide for measurement of DNA. PCS devices with a lattice defect close to a photonic band edge have demonstrated a measureable change in optical transmission as a result of small refractive index changes (~2x10-4), which makes them an ideal candidate for biosensing applications. In order to uniquely identify pathogens critical to medical and homeland defense applications, the PCS can be functionalized to capture DNA.

We will discuss design parameters and the tools used to optimize the PCS, and we will also report preliminary experimental results.

Electrochemical aptamer-based sensor optimization: from benchtop to bedside
Paper 7321-5 of Conference 7321
Date: Monday, 13 April 2009

Author(s): Ryan J. White, Kevin W. Plaxco, Univ. of California, Santa Barbara (United States)

Electrochemical aptamer-based (E-AB) sensors have emerged as a promising biosensing platform that could readily be adapted to a multitude of sensing applications such modern healthcare, defense, and environmental applications. E-AB sensors comprise of an electrode modified with surface immobilized, redox-tagged DNA aptamers, which have been selected in vitro to bind to a specific target. In order to further improve this technology to develop such sensors we have systematically studied optimization parameters that provide a general means for optimization of future E-AB sensors.

Time-resolved FRET for single-nucleotide polymorphism genotyping
Paper 7320-39 of Conference 7320
Date: Tuesday, 14 April 2009

Author(s): Alessandra Andreoni, Univ. degli Studi dell'Insubria (Italy); Maria Bondani, National Lab. for Ultrafast and Ultraintense Optical Science (ULTRAS) (Italy); Luca Nardo, Univ. degli Studi dell'Insubria (Italy)

By tens-of-picosecond resolved fluorescence detection (TCSPC, time-correlated single-photon counting) we study Förster resonance energy transfer between a donor and a black-hole-quencher acceptor bound at the 5’- and 3’-positions of a synthetic DNA oligonucleotide. This dual labelled oligonucleotide is annealed with either the complementary sequence or with sequences that mimic single-nucleotide polymorphic gene sequences: they differ in one nucleotide at positions near either the ends or the centre of the oligonucleotide. We find donor fluorescence decay times whose values are definitely distinct and discuss the feasibility of single nucleotide polymorphism genotyping by this method.

TIRF-EC technology for rapid and accurate diagnostics and discovery of synthetic receptors
Paper 7306A-22 of Conference 7306A
Date: Wednesday, 15 April 2009

Author(s): Alexander N. Asanov, Tirf Technologies Inc. (United States)

Total Internal Reflection Fluorescence (TIRF) combined with ElectroChemistry and Electric field Control (TIRF-EC) is novel platform technology, which is capable of detecting hundreds of DNA/RNA and protein markers in a matter of several seconds and with limit of detection at the level of single molecules. Due to unique combination of advantages, TIRF-EC has the potential to become an indispensable tool for rapid and accurate molecular diagnostics. In this presentation we describe benchtop, portable and handheld TIRF-EC devices and present novel application of TIRF-EC for rapid discovery of synthetic receptors from combinatorial libraries of peptoids and nucleic acid oligomers.

Using of SAMs technology for label-free detection of pathogenic micro-organisms
Paper 7318-15 of Conference 7318
Date: Wednesday, 15 April 2009

Author(s): Erhan Piskin, Hacettepe Üniv. (Turkey)

Bioanalytical systems based on optical detection of biosensing elements could find wide applications in DNA analysis, drug discovery, medical diagnostics, environmental monitoring as well as in protection against bioterrorism. Here, we will demonstrate that our experience related to preparation of SAMs having various ending groups (i.e., amino, thiol, methyl, hydroxyl) on the different solid substrates and also different lithography techniques based on photolithography and template synthesis method using nano-structured anodic alumina films for the patterning of surfaces to detect microorganisms (i.e., Mycobacterium tuberculosis and Avian influenza) were investigated by surface Plasmon Resonance (SPR) and Ellipsometric biosensors.

Approaches to detection of airborne biological agents
Paper 7321-6 of Conference 7321
Date: Monday, 13 April 2009

Author(s): An-Cheng Chang, Mary Beth Tabacco, Smiths Detection (United States)

Three approaches to detection of biological agents based on biological processes will be presented. The first example is based on the use of dendrimers to deliver a membrane-impermeable fluorescent dye into live bacteria, similar to viral infection and delivery of viral DNA/RNA into a bacterial cell. The second example mimics collection and capture of airborne biological particles by the respiratory mucosa through the use of a hygroscopic sensing membrane. The third example is based on the use of multiple fluorescent probes with diverse functionalities to detect airborne biological agents in a manner similar to the olfactory receptors in the nasal tract.

Direct detection of biomarkers, nanoparticles, bacteria, and virus in blood and other biological samples
Paper 7312-5 of Conference 7312
Date: Monday, 13 April 2009

Author(s): Michael J. Heller, Univ. of California, San Diego (United States)

In many research and diagnostic applications it is a significant challenge to directly isolate and identify rare cells, bacteria, virus, nanoparticles and other important biomarkers directly in blood and plasma. Dielectrophoresis (DEP) offers a particularly attractive mechanism for high resolution separation of cells and nanoparticles. Unfortunately, DEP requires considerable dilution of the sample making it impractical for diagnostic applications. We have now clearly demonstrated the DEP separation and detection of nanoparticles and DNA directly in un-diluted whole blood. This DEP detection technology is now being used for the direct detection of bacteria and virus in blood.

Handheld and portable test systems for immunodiagnostics and nucleic acid detection
Paper 7306A-18 of Conference 7306A
Date: Wednesday, 15 April 2009

Author(s): Konrad Faulstich, Klaus Haberstroh, Roman Gruler, Michael Eberhard, Thomas Wiest, Dirk Lentzsch, ESE GmbH (Germany)

Emergency Diagnostics, Homeland Security, Epidemiological Preparedness and the high cost of the Health Care Systems have increased demand for affordable and mobile point of care (POC) devices with highest sensitivity, specificity and rapid time to result. We have developed pocket sized systems for point of care and field based tests based on fluorescence read-out. The core consists of battery operated, 90 gram electro-optical units with optional wireless data transfer, which have been optimized to achieve highest accuracy and sensitivity paired with simplicity of use. The robust systems have been applied to molecular diagnostics such as DNA based testing, immunodiagnostics as well as environmental monitoring and agricultural testing.

Isothermal nucleic acid diagnostics for the rapid detection of biological agents
Paper 7306A-25 of Conference 7306A
Date: Wednesday, 15 April 2009

Author(s): Andrew Miller, Ionian Technologies Inc. (United States)

Ionian’s technology provides for rapid detection of bacterial or viral genomes. Both DNA and RNA sequences can be detected, with the sensitivity and specificity of the amplification reactions providing improved performance relative to immunoassays. Sample prep requirements are minimal, reducing the time and expense of a complex sample purification. Results can be read-out with a variety of methods. Our detection technology is combined with a simple heating and fluorescent detection unit, providing nucleic acid testing in a field-use format, without requiring laboratory-trained personnel. Ionian is leveraging this technology in a variety of applications, including biodefense, healthcare, agriculture, and food safety.

Novel nanorod array substrates for high-sensitivity biomolecular sensing
Paper 7321-3 of Conference 7321
Date: Monday, 13 April 2009

Author(s): Richard A. Dluhy, Jeremy Driskell, Yiping Zhao, Ralph A. Tripp, The Univ. of Georgia (United States)

Development of diagnostic methods for rapid and sensitive identification of viruses and other biomedical pathogens is essential for the advancement of therapeutic and intervention strategies necessary to protect public health. We have investigated the use of aligned Ag nanorod arrays, prepared by oblique angle vapor deposition (OAD), as surface-enhanced Raman scattering (SERS) substrates for the identification and classification of viral pathogens. The current talk will address aspects of the fundamental nanostructural design of metallic nanorod arrays and their influence on SERS enhancement, as well as the development of a spectroscopic assay for virus detection based on these unique nanostructured SERS probes. We will also present results of multivariate statistical analyses on the SERS spectra of different pathogenic species that indicate that it is possible to identify, differentiate, classify and quantify biomolecules based on their intrinsic SERS spectra.