Team:SDU-Denmark/Tools

=Plasmid ligation helper=

To avoid having to manually calculate how many uL's of DNA and plasmid we should use to achieve optimal ligation circumstances, we created a small Program for the texas instruments calculators. It's simple called Ligation, and you can get it [[Media:Team-SDU-Denmark-LIGATION.8xp.zip|here]].

=A plasmid editor (APE)= APE is a very powerful plasmid and linear DNA editor. It has helped us analyse our data from the very beginning. Among our favorite features are:
 * Restriction site highlighting
 * Expandable feature library with quick discovery. Perfect for analysing sequence results for biobrick inserts.
 * DNA alignment feature. Another tool for analysing sequencing results
 * Creates plasmid maps for easy reviewing

Ape was created by M. Wayne Davis. It runs on Windows, Linux and Mac OS X

Ligation
Q: How much DNA should be used in a ligation using T4 DNA Ligase?

A: The unit definition uses 0.12 μM (300 μg/ml) lambda HindIII fragments. The high DNA concentration can be used for linker ligation. To promote circle formation, useful in transformation, a lower total DNA concentration should be used. The overall concentration of vector + insert should be between 1-10 μg/ml for efficient ligation. Insert:vector molar ratios between 2 and 6 are optimal for single insertions. Ratios below 2:1 result in lower ligation efficiency. Ratios above 6:1 promote multiple inserts. If you are unsure of your DNA concentrations, perform multiple ligations with varying ratios. From T4 DNA Ligase FAQ.