Team:PoznanSoft

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MUFASA: Multiple fragments assembler for scarless cloning of big genetic constructs.

Overlap-based cloning techniques like Gibson Assembly and Circular Polimerase Extension Cloning (CPEC) have been recently becoming more and more popular. While available software allows rapid overlap design for constructs of conventional size, details of its functioning are not always fully transparent. MUFASA aims not only at facilitating the scarless cloning from the oligonucleotide design to putting the tubes into the thermocycler, but also at designing the fragments themselves in parallel with the overlaps for synthesis of big constructs de novo. Use of multiple overlaps pose a risk of non-specific hybridization and overlap “shadowing”. Such “shadowy places” may be eliminated by thermodynamic sequence optimization of both CPEC primers and fragments of the desired construct.

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-<h2 >REColi: Signal amplification and formattable bacterial memory by DNA edition. </h2>
+<h2 >MUFASA: Multiple fragments assembler for scarless cloning of big genetic constructs.</h2>
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-We have designed a synthetic digital device inspired by electronic circuits called multiplexers. Its 3-bit memory allows saving and processing binary inputs in E. coli. Induced expression of serine recombinases, capable of specific DNA editing, enables construction of biological analogues of transistors - transcriptors - and their use as elementary memory units called SR-latches. The fourth, strobe signal resets the system to its original state. We have shown that the system could efficiently store data about previous contact with inducing sugars across hundreds of generations. This memory unit offers high sensitivity in inducer detection and signal amplification, allowing cheap induction or further development and use as a trace contaminants sensor. Eight possible output combinations, reported as RGB fluorescent proteins, may also turn out to be useful for complex coexpression research.
+Overlap-based cloning techniques like Gibson Assembly and Circular Polimerase Extension Cloning (CPEC) have been recently becoming more and more popular. While available software allows rapid overlap design for constructs of conventional size, details of its functioning are not always fully transparent. MUFASA aims not only at facilitating the scarless cloning from the oligonucleotide design to putting the tubes into the thermocycler, but also at designing the fragments themselves in parallel with the overlaps for synthesis of big constructs de novo. Use of multiple overlaps pose a risk of non-specific hybridization and overlap “shadowing”. Such “shadowy places” may be eliminated by thermodynamic sequence optimization of both CPEC primers and fragments of the desired construct.
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