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In this work, we employ atomistic molecular simulations to design experiments for studying the binding of the Cas9-sgRNA complex to its target DNA. We aim to create a robust method for probing the affinity and specificity of Cas9-sgRNA complexes to allow future optimization of Cas-based target DNA detection systems. We simulate various attachment positions of Cy3 and Cy5 fluorescent labels to specific DNA and RNA sites for maximal Forster resonance energy transfer and optimal experimental designs.