Team:Cooper Union/TdT project

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Cooper Union 2014 iGEM

De novo synthesis is a way of creating DNA oligonucleotides without the need of a template strand. Since the conventional method is expensive, time consuming, and inefficient, our team wants to focus on the ways to minimize the time and money required for DNA synthesis and to allow the labs to produce oligonucleotides easily without ordering. Terminal Deoxynucleotidyl Transferase, also referred as TdT, is an enzyme that has the ability to add nucleotides to single stranded oligos, while other DNA enzymes can only add a nucleotide to double stranded ones. Our improved system is based on a theoretical model for template-free synthesis of DNA that proposed deoxynucletotiode triphospate substrates containing a reversible protective group on the 3' hydroxy group. In that system, the 3' protective group was an Acetyl group, with reversibility being achieved by a altering pH and thereby activating a Our system simplifies this novel approach by proposing heat and ultraviolet light labile reversible 3' protective groups. We first tested our system with commercially available heat labile Our eventual goal will be to a novel microfluidic de novo synthesizer that will allow laboratories, from academia and commercial biotech, to DIYBio community labs to rapidly and economically synthesize any strand of DNA. We hope that this system will become the key platform that bridges the ''in silico'' to ''in vitro'' gap in the design-test-build cycle of DNA synthesis and experimentation. References

Minhaz Ud-Dean, S.M. (2008) A Theoretical Model for Template-Free Synthesis of Long DNA Sequence. Syst. Synth. Biol. 2:67-73 Kuan, W.L., Joy, J. (2010) Generation of Active Bovine Terminal Deoxynucleotidyl Transferase (TdT) in E. coli. Biochemistry Insights. 3: 41-46.

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-De novo synthesis is a way of creating DNA oligonucleotides without the need of a template strand. Since the conventional method is expensive, time consuming, and inefficient, our team wants to focus on the ways to minimize the time and money required for DNA synthesis and to allow the labs to produce oligonucleotides easily without ordering. Terminal Deoxynucleotidyl Transferase, also referred as TdT, is an enzyme that has the ability to add nucleotides to single stranded oligos, while other DNA enzymes can only add a nucleotide to double stranded ones.
+De novo synthesis is a way of creating DNA oligonucleotides without the need of a template strand. Since the conventional method is expensive, time consuming, and inefficient, our team wants to focus on the ways to minimize the time and money required for DNA synthesis and to allow the labs to produce oligonucleotides easily without ordering.
+Terminal Deoxynucleotidyl Transferase, also referred as TdT, is an enzyme that has the ability to add nucleotides to single stranded oligos, while other DNA enzymes can only add a nucleotide to double stranded ones.
@@ Line 56: / Line 60: @@
 We hope that this system will become the key platform that bridges the ''in silico'' to ''in vitro'' gap in the design-test-build cycle of DNA synthesis and experimentation.
+References
+<BR><BR>
+Minhaz Ud-Dean, S.M. (2008) A Theoretical Model for Template-Free Synthesis of Long DNA Sequence. Syst. Synth. Biol. 2:67-73
+Kuan, W.L., Joy, J. (2010) Generation of Active Bovine Terminal Deoxynucleotidyl Transferase (TdT) in E. coli. Biochemistry Insights. 3: 41-46.
-To understand how TdT works, one has to understand the enzymes and its activities.
-Enzyme is a biological catalyst that aids chemical reaction and are mostly made of proteins. While it is specific to act on either forward or reverse reaction, it decreases the activation energy of a reaction to influence on rate of the reaction, without altering any other conditions or equilibrium constants.