Everything you ever wanted to know about AarI

From 2008.igem.org

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Revision as of 05:14, 22 October 2008

This a multi-part/combinatorial cloning technique that is particularly well suited to shuffling protein domains. The key to this approach is the Type IIS restriction enzyme, AarI, a rare (7-cutter) that cuts 4bp offset from its binding site. Thus, AarI can generate four base overhangs of any sequence.

Since the user can specify the overhangs, this method can be used to "stitch-together" fragments without a scar, which is sometimes necessary to preserve protein function. More importantly, these overhangs can be non-palindromic, which solves the biggest problem faced when trying to do multipart ligations using standard restriction enzymes, the self ligation of a part, blocking it's incorporation into the construct. This problem is illustrated here:

By contrast, AarI cloning allows high efficiency ligations using up to 4 parts (vector plus 3 inserts). While parts can be made with any 4 base overhang (end), we chose a standard set, termed A, B, C, and D. This allows parts to be traded between researchers. We are building a lab database of parts.

These ends yield 3 possible parts: AB, BC and CD. For two part ligations, we use AB and BD parts. Parts could be promoters, protein domains, or terminators, and are typically generated by PCR from a genomic DNA or plasmid template, then TOPO cloned and sequenced. These donor vectors, once validated, can be shuffled with other validated parts, into acceptor vectors, creating large combinatorial libraries of constructs that do not require further sequencing.

While any vector can be adapted to be an acceptor for AarI cloning, we have been working with the yeast pRS__ series of vectors ([1]), and we provide to the registry several types of acceptor vectors built in the pRS315 or 305 backbone. When necessary, markers exchanged by one-piece subclones of the completed cassettes into alternative pRS vectors, using the Kpn1/PspOMI and SacI sites.

For more information on how to clone with the UCSF AarI parts, or better yet, to design your own AarI parts, check out the following protocols.

1. Media:Design AarI primers.pdf

2. Media:How to AarI clone.pdf

AarI Shuttle Vector To facilitate exchange of parts between AarI users and the biobricks community, we are offering a Shuttle Vector. This vector accepts AarI parts in the AB or BD format (as were used in our 2008 project). These parts can then be cut out of the vector, with in-frame biobrick ends.

The cloning sites are depicted below. The AB shuttle receives...IN PROGRESS

These vectors should be used exactly as any other AarI acceptor vector, but note that efficiencies will be ridiculously high (lawn) for a two piece ligation, so it may be help to plate a small fraction of the transformation on a second plate.

Home	The Team	The Project	Parts Submitted to the Registry	Modeling	Human Practices	Notebooks

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-Since the user can specify the overhangs, this method can be used to "stitch-together" fragments '''without a scar''', which is sometimes necessary to preserve protein function. More importantly, these overhangs can be '''non-palindromic''', which solves the biggest problem faced when trying to do multipart ligations using standard restriction enzymes, illustrated here:
+Since the user can specify the overhangs, this method can be used to "stitch-together" fragments '''without a scar''', which is sometimes necessary to preserve protein function. More importantly, these overhangs can be '''non-palindromic''', which solves the biggest problem faced when trying to do multipart ligations using standard restriction enzymes, the self ligation of a part, blocking it's incorporation into the construct. This problem is illustrated here:
 [[Image:AarI fig2b.png]]
@@ Line 30: / Line 30: @@
 '''AarI Shuttle Vector'''
 To facilitate exchange of parts between AarI users and the biobricks community, we are offering a Shuttle Vector. This vector accepts AarI parts in the AB or BD format (as were used in our 2008 project). These parts can then be cut out of the vector, with in-frame biobrick ends.
+The cloning sites are depicted below. The AB shuttle receives...IN PROGRESS
+These vectors should be used exactly as any other AarI acceptor vector, but note that efficiencies will be ridiculously high (lawn) for a two piece ligation, so it may be help to plate a small fraction of the transformation on a second plate.