Team:Cooper Union/TdT project

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. Here we introduce the De novo Enzyme Mediated Oligonucleotide Synthesizer (DEMOS); a programmblee enzyme based, template-free, synthesizer for nucleic acid polymers. 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

Improvements to the De novo Synthesizer

In our present configuration, full length recombinant bovine TdT was used in the reaction. This particular enzyme denatures in the presence of elevated temperatures, thereby necessitating the repeated addition of enzyme during each step of nucleotide addition after blocking group removal via 95 degrees C heat pulse. Therefore it would be useful to either isolate a naturally occurring variant of TdT or similar enzyme, that is heat tolerant, most likely from a thermophylic organism, or engineer such a variant. Another potential course of improvement would be to construct truncated and other variants of engineered TdT that exhibit faster kinetics of modified nucleotide incorporation. Lastly, our present system used commercially available nucleotides that had heat labile 3' protective groups. By switching to photolabile nucleotides, the system should perform better by exhibiting an overall faster reaction cycle, since temperature ramp up and down cycles are avoided and no extra TdT enzyme would need to be added at the beginning of each cycle, as heat denaturation would also be avoided. We are presently exploring these improved features.

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

Koukhareva, I. and Lebedev, A. (2009) 3'-Protected 2'-Deoxynucleoside 5'-Triphosphates as a Novel Tool for Heat-Triggered Activation of PCR. Anal Chem. 81(12):4955-4962

Kuan, W.L., Joy, J. Mee, N.F., Perlyn, K.Z., Wen, T.S., Nguen, T., James, J., Chai, E., Flotow, H., Crasta, S., Chua, K., Peng, N.S. and Hill, J. (2010) Generation of Active Bovine Terminal Deoxynucleotidyl Transferase (TdT) in E. coli. Biochemistry Insights. 3: 41-46.

Boule, J.B., Rougeon, F.Papanicolaou, C. (2001) Terminal Deoxynucleotidyl Transferase Indiscriminately Incorporates Ribonucleotides and Deoxyribonucleotides. J. Biol. Chem. 276, 33: 31388-31393.

Motea, E.A. and Berdis, A.J. (2010) Terminal Deoxynucleotidyl Transferase: The Story of a Misguided DNA Polymerase. Biochim. Biophys. Acta. 1804, 5: 1151-1166.