Pending Patent-Rapid Selection and Production of DNA

Summary of Invention

The present invention relates to compositions and methods for making and using DNA capture elements (DCEs). In one embodiment, methods relate to making and amplifying target DCEs. In certain embodiments methods for making DCEs concern using a signal producing moiety and an agent to reduce or eliminate the signal prior to amplifying a target-specific DCE. In some embodiments, methods disclosed herein may be used to rapidly generate large quantities of DCEs directed to a particular target agent. Some embodiments of the present invention relate to systems for performing automated generation of DCEs. (Page 47 of Provisional Patent Application.)


Research and use of fluorescent semiconductor nanocrystals (also known as quantum dots or qdots) have evolved over the past several years from electronic materials science to biological applications. Current approaches to the synthesis, solubilization, and functionalization of qdots and their applications to cell and animal biology has grown. Qdots have far-reaching potential for the study of intracellular processes at the single-molecule level, such as high-resolution cellular imaging, long-term in vivo observation of cell trafficking, tumor targeting, and diagnostics. (0003 on Page 2 of provisional application.)

Aptamers are single-stranded nucleic acids isolated from random-sequence nucleic acid libraries by selection such as in vitro selection. Many DNA or RNA sequences have been isolated that bind a diverse range of targets, including metal ions, small organic compounds, biological cofactors, metabolites, proteins and nucleic acids. The target versatility and the high binding affinity of both DNA and RNA aptamers, their properties of precise molecular recognition, along with the simplicity of in vitro selection, make aptamers attractive as molecular receptors and sensing elements. (0004 on Page 2of provisional application.)

Current methods, techniques and devices that have been applied to identification of chemical and biological analytes typically involve capturing the analyte through the use of a non-specific solid surface or through capture deoxyribonucleic acids (DNA) or antibodies. A number of known binding agents must then be applied, particularly in the case of biological analytes, until a binding agent with a high degree of affinity for the analyte is identified such as an aptamer. A labeled aptamer (e.g., labeled DNA or labeled antibodies) must be applied, where the aptamer causes, for example, the color or fluorescence of the analyte to change if the binding agent exhibits affinity for the analyte (i.e., the binding agent binds with the analyte). The aptamer may be identified by studying which of the various binding agents exhibited the greatest degree of affinity for the analytes. (0005 on Page 3 of patent application.)

There are a number of problems associated with current methods of chemical and biological agent identification. It takes a great deal of time and effort to repetitiously generate and apply each of the known labeled aptamers, until an aptamer exhibiting a high degree of affinity is found. In addition, once the identification of a high affinity aptamer is made the synthesis of multiple copies for use becomes a challenge. Accordingly, these techniques are not conducive to easy automation. Current methods are also not sufficiently robust to work in the heat, dust, humidity or other environmental conditions that might be encountered, for example, on a battlefield or in a food processing plant. Portability and ease of use are also problems seen with current methods for chemical and biological agent identification. (0006 on Page 3 of patent application.)

For practical applications, there remains a need for a method of immobilizing nucleic acid aptamers directed to bind a target and for rapidly generating multiple copies of the immobilized aptamer for use in identifying the presence or levels of a target agent recognized by the aptamer. (0007 on Page 3 of patent application.)

Inventors: Johnathan Kiel, Eric Holwitt, Michael Fan (Fan, Maomian) and Shelly D. Roper. (Inventors bolded and italicized were CMI employees as of the date of filing.)

Addendum and updated application filed on December 27, 2007. Application No. 11/965,039 (37 Claims).

Electronically published Jan 1, 2009 – US 2009/0004644 A1 (37 Claims).

Office Action by the USPO for application No. 11/965,039, Examiner: Woolwine, Samuel. C., 2 November 2009 (Claims 1-12 and 31).

In the Restriction Requirement, the Examiner has restricted the invention into four groups, namely:

Group I drawn to compositions comprising double-stranded nucleic acids wherein a signal reducing moiety (e.g. quenching agent) is bound to one strand thereof (claim 31) and a reporter moiety is bound to the other strand thereof (claims 1-12);

Group II drawn to methods of making and/or using Group I (claims 13-24);

Group III drawn to a system for making Group I using Group IV (claims 25-30); and Group IV drawn to materials including a reporter moiety (e.g. “quantum dot”), signal reducing moiety (e.g. “quenching agent”), nucleic acids, and solid substrates (e.g. “magnetic beads”) (claims 32-37).

Response to Restriction Requirement was filed on November 17, 2009. The Patent examiner is Samuel C. Woolwine. CMI provisionally elected Group I, Claims 1-12 and 31.

Office Action by USPO for application No. 11/965,039, Examiner: Woolwine, Samuel C., February 5, 2010.

Office action filed in November 2010. Went back with evidence that double stranded is one of our key issues; and that Gold published info that said that will never work. Overcame all objections and back to the examiner. New Recipe docs from Bev Schaffer sent to Bert in early Dec 2010. Holding for response from USPO and the newly assigned examiner.

Maomian (Michael) Fan was employed by CMI from 20 February 2003 through 29 February 2008. Subsequent to 1 March 2008 Dr. Fan is employed as a government civilian currently working at Wright-Patterson AFB, OH.

This Patent is attributable to work performed by CMI under USAF Contract: F41624-03-D-7000-001.

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