Synthetic Biology, Part B: Computer Aided Design and DNA by Chris Voigt

By Chris Voigt

Synthetic biology features a number of diverse techniques, methodologies and disciplines, and lots of diversified definitions exist. This quantity of tools in Enzymology has been break up into 2 components and covers issues corresponding to Measuring and Engineering important Dogma procedures, Mathematical and Computational equipment and Next-Generation DNA meeting and Manipulation.

  • Encompasses a number of varied methods, methodologies and disciplines
  • Split into 2 components and covers themes equivalent to measuring and engineering valuable dogma strategies, mathematical and computational tools and next-generation DNA meeting and manipulation

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Additional resources for Synthetic Biology, Part B: Computer Aided Design and DNA Assembly

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DNA mutation 3. 1. Prediction of DNA-binding profiles using FoldX 4. Changing Binding Capabilities 5. Designing New Specificities 6. 1. 2. 3. 4. Clashes 7. Conclusions and Future Outlook Acknowledgments References 4 5 6 6 6 8 8 8 9 9 12 13 14 15 15 15 15 16 16 17 Abstract With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. 00001-2 # 2011 Elsevier Inc.

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Additionally, it is useful to consider the van der Waals intramolecular clashes of the DNA molecule that could appear upon base mutation. This extra term penalizes those DNA variants that may have a good binding energy, but are forced into the DNA structure. Considering these energy terms, one can derive a DNA sequence profile by doing a partition function for each position. This procedure requires the following steps (Fig. 1): 1. The first step is to look for the best template in a database. Look at the RCSB-PDB Web site for crystal structures of the candidate bound to DNA (structures solved by NMR can also be used but usually crystal structures give better results).

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