User:Jarle Pahr/Restriction: Difference between revisions
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{| class="wikitable" border="1" cellpadding="5" cellspacing="0" | {| class="wikitable" border="1" cellpadding="5" cellspacing="0" | ||
|- | |- | ||
! Enzyme combination !! | ! Enzyme combination !! Buffer recommendation !! Experience !! | ||
|- | |- | ||
| AgeI+PciI || NEBuffer 4||Have used NEBuffer 1. Seems to work reasonably well, but may lead to lower CIP activity if dephosphorylating. | | AgeI+PciI || NEBuffer 4||Have used NEBuffer 1. Seems to work reasonably well, but may lead to lower CIP activity if dephosphorylating. | ||
|- | |- | ||
|BsrGI+BamHI-HF||NEBuffer 4|| | |BsrGI+BamHI-HF||NEBuffer 4|| | ||
|- | |||
|XhoI + EcoRI||NEBuffer 2-4|| | |||
|- | |||
|XhoI + BamH||NEBuffer 3|| | |||
|- | |||
|XhoI + PciI||NEBuffer 3|| | |||
|} | |} | ||
Revision as of 06:37, 1 April 2013
Notes on procedures and issues relating to restriction digests:
http://en.wikipedia.org/wiki/Restriction_digest
About star activity: https://www.neb.com/tools-and-resources/usage-guidelines/star-activity
Enzyme volume should not exceed 10 % of total reaction volume, due to glycerol content.
http://utminers.utep.edu/rwebb/html/restriction_digestion.html
http://www.molecularstation.com/dna/restriction-enzyme-digestion/
iGEM - restriction digest protocol: http://partsregistry.org/Help:Protocols/Restriction_Digest
http://www.methods.info/Methods/RNA_DNA/restr_analysis.html
Supercoiled plasmid DNA migrates faster than linear (ex cut plasmid) DNA: http://www.researchgate.net/post/Does_supercoiled_dna_migrate_faster_in_agarose_gel_electrophoresis_than_linear_form_of_dna
https://www.neb.com/tools-and-resources/usage-guidelines/cleavage-close-to-the-end-of-dna-fragments
Enzyme | Recognition site | Supplied buffer(s) | Time saver? | Heat inactivation |
---|---|---|---|---|
AgeI | ACCGGT | Example | ||
PciI | ACATGT | Example | ||
EcoRI | Example | |||
BsrGI | T^GTACvA | NEBuffer 2, BSA | Yes | |
SacII | CCGCGG | Nebuffer 4 | No | |
NdeI | CATATG | |||
BamHI | GGATCC |
Double digests
NEB Double Digest finder: https://www.neb.com/tools-and-resources/interactive-tools/double-digest-finder
Double Digest tool: http://www.thermoscientificbio.com/webtools/doubledigest/
Enzyme combination | Buffer recommendation | Experience | |
---|---|---|---|
AgeI+PciI | NEBuffer 4 | Have used NEBuffer 1. Seems to work reasonably well, but may lead to lower CIP activity if dephosphorylating. | |
BsrGI+BamHI-HF | NEBuffer 4 | ||
XhoI + EcoRI | NEBuffer 2-4 | ||
XhoI + BamH | NEBuffer 3 | ||
XhoI + PciI | NEBuffer 3 |
Software:
http://tools.neb.com/NEBcutter2/
http://rebase.neb.com/rebase/rebase.html
https://www.neb.com/tools-and-resources/interactive-tools/double-digest-finder
http://insilico.ehu.es/restriction/
Sequence Manipulation Suite:
Restriction Digest: http://www.bioinformatics.org/sms2/rest_digest.html