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  • DNA microarrays or DNA-chips have become a widely used tool both in research and practice. Immobilization of capture probes in an array of spots on a flat surface makes possible a high throughput parallel detection of many DNA fragments present in the sample but represents an important change of the hybridization conditions due to the presence of the surface. Contemporary methods of probe design do not take into account the difference in hybridization between bulk solution and surface and therefore do not predict correctly the properties of capture probes. The aim of the project is modeling of DNA-chip hybridization parameters. Methodologically the project consists of three complementary approaches: study of the influence of the surface on charge distribution in the solution, ab initio calculations of stacking interaction and base-pairing in conditions simulating presence of a charged surface, and, finally molecular dynamics simulations of surface-attached oligonucleotides. The supposed results will bring a better insight into basic principles governing hybridization on an array, and in a longer term, make the design of capture probes and development of DNA chips more accurate, faster and less expensive. (en)
  • Prohloubit poznání o chování DNA ve styku s povrchy především z hlediska hybridizačních parametrů, konkrétně stanovit vliv povrchu na a. rozložení nábojů a elektrického pole v roztoku b. stabilitu duplexu z hlediska párování bazí a patrových interakcí c. dynamiku ukotvených oligonukleotidů
Title
  • Modeling of DNA-chip hybridization in real conditions (en)
  • Modelování hybridizace na DNA čipech v reálných podmínkách
skos:notation
  • GC204/09/J010
http://linked.open...avai/cep/aktivita
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  • DNA-čip; hybridizace; molekulární modelování; vliv povrchu (en)
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  • The project gone according to plan both in terms of expertise and in terms of disbursement of funds. (en)
  • Řešení projektu proběhlo podle plánu jak z hlediska odborného tak i z hlediska čerpání finančních prostředků. (cs)
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http://linked.open.../cep/klicoveSlovo
  • hybridizace
  • molekulární modelování
  • DNA-čip
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