DNA Code Validation Using Experimental Fluorescence Measurements and Thermodynamic Calculations
Final rept. May 2003-Oct 2003
STATE UNIV OF NEW YORK AT ALBANY RESEARCH FOUNDATION
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Initial stages were completed in the development of an enabling technology for DNA computing. The technology focuses on construction of a biomolecular architecture to employ new algorithmic paradigms based on DNA hybridization. The intent is to develop a computing basis so that many discrete math problems can be solved in linear real time. Methods were developed to generate and screen collections of single-stranded DNA sequences called a DNA n,d code. Strands of 16 nucleotides were designed such that a code strand would hybridize only with its reverse- complement and would not cross-hybridize with any other strand in the set. Strands were tested for their potential to mispair by measuring fluorescence for every possible pair of strands over varying temperatures in the presence of SYBR Green I, a dye whose fluorescence increases exponentially when bound to double-stranded DNA. Strands with potential to bind to themselves or to another sequence in the set were identified and removed from the DNA n,d code. Sets of up to six pooled sequences were also tested to show that this method works with sets of multiple strands. In addition, the thermodynamic parameters of binding were examined using the program PairFold. Free energies of binding are reported.
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