Team:Queens Canada/Guide/DNA

From 2012.igem.org

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Cloning Method
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<p>When cloning parts into our construct, we chose to use PCR overlap extension and digestion/ligation
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+
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When cloning parts into our construct, we chose to use PCR overlap extension and digestion/ligation
+
techniques. In order to perform PCR Overlap extension (our preferred method of cloning) we were
techniques. In order to perform PCR Overlap extension (our preferred method of cloning) we were
required to fabricate a set of primers that were ligated onto the insert. These primer extensions served
required to fabricate a set of primers that were ligated onto the insert. These primer extensions served
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the part onto another part with a matching overlap site; with the primers on either end of the inserts
the part onto another part with a matching overlap site; with the primers on either end of the inserts
acting as the site of initiation for Taq polymerase. Our primary resource was this paper. A picture
acting as the site of initiation for Taq polymerase. Our primary resource was this paper. A picture
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representation of PCR-Overlap Extension can be seen below:
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representation of PCR-Overlap Extension can be seen below:</p>
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<img src="">PCROE</img>
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The other method of cloning made use of the cut sites found in our insert and a few restriction enzymes.
+
<p>The other method of cloning made use of the cut sites found in our insert and a few restriction enzymes.
Early on we noted the BioBrick standard caused a very problematic frame-shifts within the scar when
Early on we noted the BioBrick standard caused a very problematic frame-shifts within the scar when
ligating 2 or more parts. We tried to circumvent the problem by adding 1 or 2 nucleotides onto our DNA
ligating 2 or more parts. We tried to circumvent the problem by adding 1 or 2 nucleotides onto our DNA
sequence to fix the frame but found this to be tedious due to the fact that this varied based on the part
sequence to fix the frame but found this to be tedious due to the fact that this varied based on the part
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we wanted to ligate.
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we wanted to ligate.</p>
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Therefore we started doing research into other assembly standards to see if any of them alleviated
+
<p>Therefore we started doing research into other assembly standards to see if any of them alleviated
the problem. We judged the merits and flaws of each one (a list of the assembly standards considered
the problem. We judged the merits and flaws of each one (a list of the assembly standards considered
can be found here). What we searched for was a standard that would avoid frame-shifts and nonsense
can be found here). What we searched for was a standard that would avoid frame-shifts and nonsense
mutations when doing protein fusion, avoid N-terminal destabilization signals and dam methylation sites
mutations when doing protein fusion, avoid N-terminal destabilization signals and dam methylation sites
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and preserve most of the restriction enzymes from the original BBa standard.
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and preserve most of the restriction enzymes from the original BBa standard.</p>
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Considering these reasons, we chose to switch our prefixes and suffixes to Tom Knight’s BBa 2 standard
+
<p>Considering these reasons, we chose to switch our prefixes and suffixes to Tom Knight’s BBa 2 standard
that allowed seamless in-frame ligations between multiple sequences of successive DNA. This change
that allowed seamless in-frame ligations between multiple sequences of successive DNA. This change
resulted in only 1 restriction enzyme (Xba1 to Nhe1) that differed from original BBa standard therefore
resulted in only 1 restriction enzyme (Xba1 to Nhe1) that differed from original BBa standard therefore
providing the flexibility we needed to simultaneously work with both standards. For ligation, we used T4
providing the flexibility we needed to simultaneously work with both standards. For ligation, we used T4
-
ligase. A pictorial representation of the BBa 2 standard can be seen below:
+
ligase. A pictorial representation of the BBa 2 standard can be seen below:</p>
Prefix
Prefix

Revision as of 00:52, 25 October 2012

Control

ChimeriQ - Description

Cut Sites
Cloning Methods

When cloning parts into our construct, we chose to use PCR overlap extension and digestion/ligation techniques. In order to perform PCR Overlap extension (our preferred method of cloning) we were required to fabricate a set of primers that were ligated onto the insert. These primer extensions served to add overlap sites that match those of the parts we were adding. This allowed for PCR to extend the part onto another part with a matching overlap site; with the primers on either end of the inserts acting as the site of initiation for Taq polymerase. Our primary resource was this paper. A picture representation of PCR-Overlap Extension can be seen below:

PCROE

The other method of cloning made use of the cut sites found in our insert and a few restriction enzymes. Early on we noted the BioBrick standard caused a very problematic frame-shifts within the scar when ligating 2 or more parts. We tried to circumvent the problem by adding 1 or 2 nucleotides onto our DNA sequence to fix the frame but found this to be tedious due to the fact that this varied based on the part we wanted to ligate.

Therefore we started doing research into other assembly standards to see if any of them alleviated the problem. We judged the merits and flaws of each one (a list of the assembly standards considered can be found here). What we searched for was a standard that would avoid frame-shifts and nonsense mutations when doing protein fusion, avoid N-terminal destabilization signals and dam methylation sites and preserve most of the restriction enzymes from the original BBa standard.

Considering these reasons, we chose to switch our prefixes and suffixes to Tom Knight’s BBa 2 standard that allowed seamless in-frame ligations between multiple sequences of successive DNA. This change resulted in only 1 restriction enzyme (Xba1 to Nhe1) that differed from original BBa standard therefore providing the flexibility we needed to simultaneously work with both standards. For ligation, we used T4 ligase. A pictorial representation of the BBa 2 standard can be seen below:

Prefix 5' GAATTC...ACTAGT GCTAGC...CTGCAG 3' EcoRI SpeI ...part... NheI PstI Fusing two parts would then leave the following scar: 5' ...part A... A We also considered making our own artificial restriction enzymes in order to cut DNA off-site. To do so, we would have made zinc fingers to bind DNA and combined them with enzymes capable of cutting away from the binding site. This would allow us to cut as close to the gene as possible. Suffix GCTAGT S ...part B... 3'
Parts for protein expression












































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