New building blocks for improved therapeutics
Our novel DNA base pair creates an expanded genetic alphabet
The ‘genetic alphabet’ of DNA constitutes two base pairs (A–T and G–C). In a major breakthrough in synthetic biology, Synthorx’ scientific founder Dr. Romesberg and his team have crafted new base pairs, including d5SICSTP and dNaMTP (abbreviated X–Y), that can be replicated, maintained, transcribed, and subsequently translated in vivo. The expansion of the genetic alphabet with X and Y allows for the increased storage of information and the incorporation of novel amino acids into new, unique proteins.
Why it matters
Protein therapeutics have delivered tremendous value to patients, but some have limitations which cannot be corrected utilizing the twenty natural amino acids. Many proteins in the cell have dual and often opposing functions owing to interaction with different receptors. With a native protein, it is impossible to tune the binding to only one receptor type. Synthorx deploys its novel building block technology to create therapeutically useful proteins that are capable of specific receptor interactions to treat disease. Furthermore, the half-life of the protein can also be modulated through site-specific bioconjugation such as incorporation of PEGs. These improved pharmacological properties can make drugs that are more efficacious, safer, and more convenient for patients.
How we accomplish this
A semi-synthetic organism was created that incorporates all the necessary building blocks for scalable synthesis Synthorin™ proteins
Our proprietary bacterial strain, based on a well-established E. coli protein manufacturing strain, expresses a nucleotide transporter (A) that allows controllable maintenance of X–Y genetic information. Supplementing cultures of this strain with X and Y nucleotides leads to their intracellular accumulation to support replication of the DNA encoding genes containing X–Y (B). Induction of transcription stimulates the cell to express the Synthorin messenger RNA harboring non-canonical codons, and the orthogonal tRNAs that decode them (C). Engineered tRNA synthetase enzymes recognize and specifically charge the Synthorx tRNAs with corresponding novel amino acids (nAA) added to the medium (D). Finally, the cell’s natural translation machinery uses these components to decode X–Y codons, site-specifically introducing nAAs into the desired Synthorin product (E).
A semi-synthetic organism that stores and retrieves increased genetic information.
Y. Zhang, J.L. Ptacin, E.C. Fischer, H.R. Aerni, C.E. Caffaro, K. San Jose, A.W. Feldman, C.R. Turner, F.E. Romesberg. Nature (2017) 551:644-647.
A semisynthetic organism engineered for the stable expansion of the genetic alphabet.
Y. Zhang, B.M. Lamb, A.W. Feldman, A.X. Zhou, T. Lavergne, L. Li, F.E. Romesberg. Proc Natl Acad Sci U S A (2017) 114:1317-1322.
The expanded genetic alphabet. (Review)
D.A. Malyshev, F.E. Romesberg. Angew Chem Int Ed Engl (2015) 54:11930-11944.
A semi-synthetic organism with an expanded genetic alphabet
D.A. Malyshev, K. Dhami, T. Lavergne, T. Chen, N. Dai, J.M. Foster, I.R. Corrêa, F.E. Romesberg. Nature (2014) 509:385-388.
Natural-like Replication of an Unnatural Base Pair for the Expansion of the Genetic Alphabet and Biotechnology Applications
L. Li, M. Degardin, T. Lavergne, D. Malyshev, K. Dhami, P. Ordoukhanian, F.E. Romesberg. J Am Chem Soc (2014) 136:826–829.
Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet
D.A. Malyshev, K. Dhami, H.T. Quach, T. Laveryne, P. Ordoukhanian, A. Torkamani, F.E. Romesberg. Proc Natl Acad Sci USA (2012) 109:12005-12010.
KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry
K. Betz, D.A. Malyshev, T. Lavergne, W. Welte, K. Diederichs, T.J. Dwyer, P. Ordoukhanian, F.E. Romesberg. A. Marx, Nat Chem Biol (2012) 8:612-614.
Site-specific labeling of DNA and RNA using an efficiently replicated and transcribed class of unnatural base pairs
Y.J. Seo, D.A. Malyshev, T. Lavergne, P. Ordoukhanian, F.E. Romesberg. J Am Chem Soc (2011) 133:19878-19888.
Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet
A.M. Leconte, G.T. Hwang, S. Matsuda, P. Capek, Y. Hari, F.E. Romesberg. J Am Chem Soc (2008) 130:2336-2343.
DNA research: the path to improved therapeutics