In Silico Estimation of Annealing Specificity of Query Searches in DNA Databases (小特集 DNAコンピューティングの応用とシミュレーション) In Silico Estimation of Annealing Specificity of Query Searches in DNA Databases

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Abstract

We consider DNA implementations of databases for digital signals with retrieval and mining capabilities. Digital signals are encoded in DNA sequences and retrieved through annealing between query DNA primers and data carrying DNA target sequences. The hybridization between query and target can be non-specific containing multiple mismatches thus implementing similarity-based searches. In this paper we examine theoretically and by simulation the efficiency of such a system by estimating the concentrations of query-target duplex formations at equilibrium. A coupled kinetic model is used to estimate the concentrations. We offer a derivation that results in an equation that is guaranteed to have a solution and can be easily and accurately solved computationally with bi-section root-finding methods. Finally, we also provide an approximate solution at dilute query concentrations that results in a closed form expression. This expression is used to improve the speed of the bi-section algorithm and also to find a closed form expression for the specificity ratios.

Journal

  • Journal of the Japan Society for Simulation Technology

    Journal of the Japan Society for Simulation Technology 24(4), 268-276, 2005-12-15

    日鉄技術情報センタ-

References:  16

Codes

  • NII Article ID (NAID)
    110004059524
  • NII NACSIS-CAT ID (NCID)
    AN00329524
  • Text Lang
    ENG
  • Article Type
    REV
  • ISSN
    02859947
  • NDL Article ID
    7815776
  • NDL Source Classification
    ZM13(科学技術--科学技術一般--データ処理・計算機)
  • NDL Call No.
    Z14-893
  • Data Source
    CJP  NDL  NII-ELS  NDL-Digital 
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