SITIS Archives - Topic Details
Program:  SBIR
Topic Num:  AF071-045 (AirForce)
Title:  Rapid Development of DNA Aptamers for Agent Identification, Tracking and Neutralization
Research & Technical Areas:  Chemical/Bio Defense

  Objective:  Develop new methods that will economically and rapidly select and manufacture DNA aptamers that can be deployed to the field to counter biological agents.
  Description:  The intent is to develop new technologies to select and manufacture DNA aptamers. DNA aptamers can replace antibodies used in certain detection and identification systems for biological threat agents. DNA aptamers have the obvious advantage of not requiring animals or cell cultures for production, are generally more stabile than proteins, and because of scalability issues lend themselves to mass production. However the selection of DNA aptamers against targets, even with automation, is time consuming requiring many rounds of selection using the SELEX (Systemic Evolution of Ligands by EXponential enrichment) method. A superior method would select DNA aptamers with high affinity and high selectivity after only one round of selection. Making this difficult is the fact that the starting library of aptamers usually contain more weak and less selective binders than high affinity binders with high selectivity. In other words, the weak less selective binders out compete the strong binders in the early rounds of selection. Complicating this is the fact that the number of target molecules usually are greater than the number of strong high affinity binders. Thus, the law of mass action makes selection of high affinity and selective aptamers after only one round extremely difficult. Several methods have been proposed to defeat this problem (such as capillary electrophoresis); none has been able to select DNA aptamers equal to those from the SELEX method. Successfully overcoming the law of mass action will require considerable scientific cleverness. Any physical, chemical, or computational method will be considered. While DNA aptamers can be synthesized either synthetically or bio-synthetically using plasmid DNA, both methods present several difficulties. For synthetic methods, the current four step per cycle phosphoramidite chemistry is expensive considering the amount of material that will be needed, and for biosynthetic methods the need to separate the aptamer strand from its compliment and then functionalize it for further reactions present problems (unless one is willing to accept chemistry using the terminal phosphate). There are needs to either reduce the cost of current synthetic methods or develop new synthetic methods for DNA oligonucleotides. For biosynthesis, the ability to easily separate the "+" strand from its compliment needs to be improved as well as methods to inexpensively functionalize the DNA strand for any required conjugations.

  PHASE I: Develop an economic and rapid method to select DNA aptamers in a single round.
  
  PHASE II: Demonstrate the method against a target selected by the customer. Compare this rapidly selected aptamer against one selected using the SELEX method for binding specificity and affinity. Develop a method to rapidly and economically manufacture DNA aptamers.

  DUAL USE COMMERCIALIZATION: Military application: DNA aptamers can be used to identify infectious diseases in field situations, hospital clinical laboratories, or research laboratories. Commercial application: DNA aptamers can be used to identify infectious diseases in field situations, hospital clinical laboratories, or research laboratories, and present the possibility of being used as an anti-toxin.

  References:  1. Kiel, J.L., Holwitt, E.A., Parker, J.E., Vivekananda, J.,and Franz, V. Nanoparticle-labeled DNA Capture Elements for Detection and Identification of Biological Agents. In Optically Based Biological and Chemical Sensing for Defence ( J.C. Carrano and A. Zukauskas, eds.), Proceedings of SPIE, vol. 5617, pp. 382-387, 2004. 2. Kiel, J.L., Parker, J.E., Holwitt, E.A., and Vivekananda, J. DNA capture elements for rapid detection and identification of biological agents. In Chemical and Biological Sensing V (P. J. Gardner, ed.), Proceedings of SPIE, vol. 5416, pp. 105-110, 2004.

Keywords:  DNA Aptamers, SELEX, biological agents, detection, identification

Additional Information, Corrections, References, etc:
Ref #1 - 2: Available online through SPIE Digital Library.
Ref #1 - 2: Available online through SPIE Digital Library.

Questions and Answers:
Q: In discussing "failed" methods, the solicitation description directly mentions capillary electrophoresis. Is there a perception of a fundamental barrier to CE's applicability which would particularly disadvantage a proposal employing this technique.
A: No, there is no pre-judgment against using capillary electrophoresis to rapidly select aptamers. Nor do i believe there is a fundamental barrier to using CE. For the purpose of rapid aptamer selection it has not been particularly successful, in my opinion, up till now. It clearly has potential. More work needs to be done as well as comparison studies between SELEX and any method using CE.
Q: In discussing "failed" methods, the solicitation description directly mentions capillary electrophoresis. Is there a perception of a fundamental barrier to CE's applicability which would particularly disadvantage a proposal employing this technique.
A: No, there is no pre-judgment against using capillary electrophoresis to rapidly select aptamers. Nor do i believe there is a fundamental barrier to using CE. For the purpose of rapid aptamer selection it has not been particularly successful, in my opinion, up till now. It clearly has potential. More work needs to be done as well as comparison studies between SELEX and any method using CE.

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