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| Description
PharmaSeq is a gene analysis company with proprietary technologies for performing nucleic acid-based assays using unique light-powered microtransponders. It is a privately held start-up biotechnology company with research and development facilities located in Monmouth Junction, NJ, near Princeton. The company has eight patents from the U.S. Patent and Trademark Office covering microtransponder-based assays. PharmaSeq's strategy is to apply microtransponder technology initially to DNA diagnostic assays, and then move forward in genomics, forensics, pharmaceutical drug discovery, communications and other areas. Methods for the detection of nucleic acids and proteins will be among the most rapidly growing techniques used in medical diagnostics laboratories in the early twenty-first century. While our understanding of the underlying genetic and biochemical mechanisms has rapidly grown due to the progress of the human genome program, our ability to rapidly and inexpensively determine relevant DNA sequence information for any given individual is lacking. The potential benefit of applicable technology to the U.S. economy is enormous. The market size for DNA probe diagnostic assays is estimated at $1 billion in 2002 in the U.S. alone, and close to twice as much worldwide.
Microtransponders like the one shown in the figure to the right are used in a novel DNA detection system to quickly and accurately detect and differentiate large numbers of unique DNA sequences in a single assay. Each microtransponder is an integrated circuit composed of photocells, memory, clock and antenna. The microtransponder stores information identifying the sequence of an attached oligonucleotide probe in its electronic memory. Microtransponders coated with DNA probes are stable for long periods of time, making them ideal for use in medical research and commercial assays. Complementary DNA sequences in a biological specimen bind to DNA probes on microtransponders using proprietary chemistry.
A scanner then detects two signals: 1) the fluorescent signal generated by the labeled specimen nucleic acid hybridized to the probe on the microtransponder, and; 2) the unique identification number of the microtransponder. The scanner shown is a high-speed flow fluorometer modified to detect radio frequency. When many probes (and thus, many microtransponders) are used in an assay, the scanner very rapidly identifies which microtransponder(s) are involved in the reaction by activating the transponder's memory by laser. Thus, positive DNA probe hybridizations are identified. This multiplex feature makes the technology ideal for assays in which screening for several genes, gene fragments or mutations is necessary, which are vital requirements in medicine and research. It also allows specimens to be screened for multiple pathogens quickly and accurately. Protein detection assays have also been performed successfully using assay designs such as the one shown below.
Multiplex DNA assays often employ two-dimensional (2D) arrays of DNA molecules on glass surfaces. PharmaSeq's novel microtransponder-based assay offers the advantage of three-dimensional (3D) arrays of DNA probes. The probes are indexed by the unique serial number of the DNA probe encoded in the memory of the microtransponder. This liquid 3D array is disassembled for the fluorescence measurements and analyzed as a linear string of solid-phase particles speeding through the flow chamber of the scanner. PharmaSeq's assay will have superior sensitivity, selectivity and high throughput, and will be upgradeable with new DNA probes. Alternatively, it allows the use of relatively few probes at low cost in an assay that does not require a high multiplex level or expensive and unique equipment. The DNA probe assays are configured in the same manner as current diagnostic assays for ease of use.
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| Patents
Electronically-indexed solid-phase assay for biomolecules Screening of drugs from chemical combinatorial libraries employing transponders U.S. Patent Number: 6,387,623 Materials and methods are disclosed for identifying chemical compounds having desired binding properties towards a binding partner of pharmaceutical interest. The method employs transponders associated with the solid phase material used in the assay and a scanner to encode and decode data stored electronically on the transponder. The data stored on the transponder identifies the monomeric building blocks added during the synthesis. The structural identification of synthesized compounds bound to the solid phase is done by decoding the transponder. Electronically-indexed solid-phase assay for biomolecules U.S. Patent Number: 6,376,187 Abstract: Disclosed are materials and methods for detecting biomolecules in samples employing transponders associated with the bead(s) used as the solid phase in the assay, and information pertinent to the assay is encoded on the transponders memory elements. A dedicated read/write device is used remotely to encode or remotely to read the information. The invention can be used in direct or competitive ELISA-type assays, or in multiplex assays for the simultaneous assay of several analytes. Multiplex assay for nucleic acids employing transponders U.S. Patent Number: 6,361,950 Abstract: Disclosed are materials and methods for performing multiplex assays for nucleic acids, in which a transponder is associated with the bead(s) forming the solid phase used in the assay, nucleic acid probes are bound to the surface of the particles, and data concerning the assay is encoded on the transponder. A dedicated read/write device is used to remotely encode or read the data. Multiplex assay for nucleic acids employing transponders U.S. Patent Number: 6,051,377 Abstract: Disclosed are materials and methods for performing multiplex assays for nucleic acids, in which a transponder is associated with the bead(s) forming the solid phase used in the assay, nucleic acid probes are bound to the surface of the particles, and data concerning the assay is encoded on the transponder. A dedicated read/write device is used to remotely encode or read the data. Method of determining the sequence of nucleic acids employing solid-phase particles carrying transponders U.S. Patent Number: 6,046,003 Abstract: A method is described for determining the sequence of nucleic acids. The method employs small solid phase particles having transponders, with a primary layer of an oligonucleotide of known sequence attached to the outer surface of the particle. A read/write scanner device is used to encode and decode data on the transponder. The stored data includes the sequence of the oligonucleotide immobilized on the transponder. The sequence of sample nucleic acids is determined by detecting annealing to an oligonucleotide bound to a particle, followed by decoding the transponder to determine the sequence of the oligonucleotide. Multiplex assay for nucleic acids employing transponders U.S. Patent Number: 6,001,571 Abstract: Disclosed are materials and methods for performing multiplex assays for nucleic acids, in which a transponder is associated with the bead(s) forming the solid phase used in the assay, nucleic acid probes are bound to the surface of the particles, and data concerning the assay is encoded on the transponder. A dedicated read/write device is used to remotely encode or read the data. Screening of soluble chemical compounds for their pharmacological properties utilizing transponders U.S. Patent Number: 5,981,166 Abstract: The invention provides a method to rapidly screen chemical compounds by delivering the compounds to the assay as a coating on transponders, rather than as powder or solution. The transponder's function is to store data that identify the compound. The data can be decoded in any moment of the assay, and the identity of the desired compound established. Method of determining the sequence of nucleic acids employing solid phase particles carrying transponders U.S. Patent Number: 5,736,332 Abstract: A method is described for determining the sequence of nucleic acids. The method employs small solid phase particles having transponders with a primary layer of an oligonucleotide of known sequence attached to the outer surface of the particle. A read/write scanner device is used to encode and decode data on the transponder. The stored data includes the sequence of the oligonucleotide immobilized on the transponder. The sequence of sample nucleic acids is determined by detecting annealing to an oligonucleotide bound to a particle, followed by decoding the transponder to determine the sequence of the oligonucleotide. Particle for solid phase assay including transponder and specific binding component - particularly for nucleic acid hybridization, allowing multiple assays to be done simultaneously International Patent Number WO 9720074 Abstract: A novel particle for use in solid phase assays of biomolecules (I) comprises: (a) transponder associated with a solid particle; and (b) one member of a binding pair (BP) attached to the particle surface. Also new are assay kits containing these particles. USE - The particles are used to detect members of BP, specifically a target nucleic acid but also proteins, antibodies (particularly viral) or cells (claimed). ADVANTAGE - The particles allow assays of several analytes to be performed simultaneously, and information stored in the transponder can be retrieved at any time during the process. Information encoded in the transponder means that the particles can be removed from vessels, mixed with other particles, processed etc. without losing track of them. Sequence determination of nucleic acid - using transponder with oligonucleotide probes attached International Patent Number WO 9720073 Abstract: A novel method for determining the sequence of a target nucleic acid (I) comprises: (a) treating the test sample with solid particles having (i) an oligonucleotide probe attached to the surface and (ii) transponder which includes memory elements in which an index number indicating the sequence of the probe is encoded; (b) denaturing the nucleic acid in the sample; (c) hybridizing this to the probe; (d) analysing particles to detect a label indicative of binding to the probe; and (e) decoding data in the transponders with a dedicated read/write scanner to identify the sequence of probes that have bound to (I). Also new are kits for this process comprising an assay vessel containing the particles and a label reagent. USE - The method is used to sequence RNA, DNA or their modifications such as protein-nucleic acids. ADVANTAGE - Compared with conventional sequencing methods this process is much faster since readings are taken from digitally stored data, not from physical/chemical properties of DNA or from positions of DNA in an array. Solid phase chemical synthesis on particles including a transponder - can be encoded to identify the compound synthesised on it, particularly for peptide libraries used to screen for pharmaceutical activity International Patent Number WO 9719958 Abstract: A novel method of solid phase chemical synthesis uses solid particles that include transponders having memories in which an index number, indicating the structure of the synthesised compound, is encoded. USE - The method is especially used for solid phase synthesis of combinatorial peptide libraries which are used to screen for the ability of a particle to bind to a labelled target molecule, i.e. for identification of potential pharmaceuticals. ADVANTAGE - Each particle can be given a unique code and this retrieved from memory at any time during or after synthesis or during assays. | |||||||||
| Publications
Mandecki W, Ardelt B, Coradetti T, Davidowitz H, Flint J, Huang Z, Kopacka W, Lin X, Wang Z, and Darzynkiewicz Z (2006) Microtransponders, the miniature RFID electronic chips, as platforms for cell growth in cytotoxicity assays. Cytometry Part A 69A:1097-1105 Lin X, Flint J, Azaro M, Coradetti T, Kopacka W, Streck D, Wang Z, Dermody J, and Mandecki W (2007) Microtransponder-based multiplex assay for genotyping cystic fibrosis (accepted to Clinical Chemistry) W. Mandecki, M.G. Pappas, N. Kogan, Z. Wang and B. Zamlynny (2002) Light-powered microtransponders for high multiplex level analyses of nucleic acids. In: Microfabricated Sensors: Application of Optical Technology for DNA Analysis. Eds.: R.Kordal, A. Usmani and W.T. Law. American Chemical Society Symposium Series, Washington, DC, vol. 815, pp. 57-69. J.T. Cain, W.C. Clark, L. Schaefer, W. Mandecki, D. Ulinski and M.H. Mickle (2001) Energy Harvesting for DNA Gene Sifting and Sorting. International Journal of Parallel and Distributed Systems and Networks, Vol. 4, No. 3, pp. 140-149. K. Miller (2002) Downsizing DNA assays. The Scientist, 16(1), 52 (news article about PharmaSeq). M. McKnight (2000) The benefits of thinking really small. Business News New Jersey, issue of October 31, 2000 (news article about PharmaSeq). H. Hogan (2000) Microchips offer faster, less expensive sequencing. Biophotonics International, November 2000 (news article about PharmaSeq). H. Hogan (2000) Laser-powered chips sample DNA. Photonics Spectra 34 (9), 44 (news article about PharmaSeq). Pappas, M.G et al. (2000) Light-powered microchip for diagnostics, genomics and drug discovery. Luminescence Forum 6 (3), 4. R. Service (2000) Chemists unveil molecular wizardry in San Francisco. Science 288, 425-427 (news article about PharmaSeq). W. Mandecki (1999) Three-dimensional arrays of microtransponders derivatized with oligonucleotides. Proceedings from the IBC Biochip Technologies Conference, San Francisco, June 1998. D&MD Library Series publication #1941. Drug & Market Development Publications, Southborough, MA 01772, pp. 179-187. | |||||||||
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