Ensemble Publications

"Macrocycles for Drug Discovery – An Underexploited Structural Class". E.M. Driggers, S.P. Hale, J. Lee and N.K. Terrett. Nature Reviews Drug Discovery, 7, 608-624 (2008). http://www.nature.com/nrd/journal/v7/n7/abs/nrd2590.html

"Diamine Catalyzed Hemicyanine Dye Formation from Nonfluorescent Precursors through DNA Programmed Chemistry". Y. Huang, J. Coull. J. Am. Chem. Soc., 130 (11), pp 3238–3239. (2008). http://pubs.acs.org/doi/abs/10.1021/ja0753602

"DNA-Programmed Chemistry in Rapid Homogeneous Assays for DNA and Protein Targets" Haff, Lawrence A.; Wilson, Christopher G.M.; Huang, Yumei; Benton, Benjamin K.; Bond, Julian F.; Stern, Andrew M.; Begley, Richard F.; and Coull, James M. Clinical Chemistry, 52, 2147-2148 (2006). PDF (1.1 MB)

"Statistical Analysis of Chemical Libraries Before and After Affinity Selections"

Bio-Organic Gordon Research Conference, Andover, NH, June 11, 2007, Josh Bittker, Nathan Walsh, Stephen Hale, Ed Driggers, Ben Benton, Chris Wilson, Julian Bond, Xiaoyu Li, Frank Favaloro, Andrew Fraley, Shukui Guan, John Furr, Jinbo Lee, Nick Terrett PDF (400 KB)

 

"DNA Programmed Macrocycles for Challenging Therapeutic Targets"

Society for Biomolecular Sciences Conference & Exhibition, April 15-19, 2007, Stephen Hale PDF (2.3 MB)

 

"Statistical Analysis of Chemical Libraries Both Before and After Affinity Selections"

BioIT World Conference & Expo" April 30-May 2, 2007, Nathan Walsh PDF (756 KB)

David Liu Laboratory Publications

For a description of DNA-Templated Organic Synthesis (DTS) and a full publication list with downloadable papers, go to the Liu Harvard University Laboratory website, http://evolve.harvard.edu/

"The Generality of DNA-Templated Synthesis as a Basis for Evolving Non-Natural Small Molecules" Gartner, Z. J. and Liu, D. R. J. Am. Chem. Soc. 123, 6961-6963 (2001). PDF (252 KB) | Supplemental info A Highlight describing this work appears in Angew. Chem. Int. Ed. 41, 89-90 (2002). PDF (80 KB)

This work reports the generality of DNA-templated synthesis, its distance independence, and a model translation of multiple DNA sequences into corresponding synthetic products in a manner suitable for in vitro selection and PCR amplification of templates encoding desired synthetic molecules.

 

"Expanding the Reaction Scope of DNA-Templated Synthesis" Gartner, Z, J.; Kanan, M. W.; Liu, D. R. Angew. Chem. Int. Ed., 41, 1796-1800 (2002). PDF (136 KB)

This paper reveals the potential of DNA to direct a wide range of synthetic organic reactions by reporting many new DNA-templated chemistries, including the first general carbon-carbon bond forming reactions (nitro-aldol, nitro-Michael, dipolar cycloadditions, Wittig olefinations, and Pd-mediated cross-couplings) templated by nucleic acids.

 

"Multistep Small-Molecule Synthesis Programmed by DNA Templates" Gartner, Z. J.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc., 124, 10304-10306 (2002). PDF (272 KB) | Supplemental info News stories describing this work appear in Chem. & Eng. News 80 [34] 12 (2002) PDF (1.9 MB), and in Science, 300, 242 (2003).

This paper describes the development of linker and purification strategies that enable the products of DNA-templated reactions to serve as starting materials for subsequent DNA-templated transformations. These findings enable DNA sequences to be translated into structures of useful complexity.

 

"Two Enabling Architectures for DNA-Templated Organic Synthesis" Gartner, Z. J.; Grubina, R.; Calderone, C. T.; Liu, D. R. Angew. Chem. Int. Ed. 42, 1370-1375 (2003).  PDF (224 KB) A Science and Technology Concentrate describing this work appears in Chem. & Eng. News 81 [13] 24 (2003). PDF (3.4MB)

This paper reports the development of two template architectures (omega and T) that expand the types of reactions that can be performed in a DNA-templated format.

 

"Highly Sensitive In Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding Affinity and Specificity" Doyon, J. B.; Snyder, T. M.; Liu, D. R. J. Am. Chem. Soc. 125, 12372-12373 (2003). PDF (100 KB) | Supplemental info

This work describes the development of affinity and specificity selections for DNA-linked synthetic molecules such as those emerging from DNA-templated small molecule library synthesis.

 

"DNA-Templated Organic Synthesis: Nature's Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules" Li, X.; Liu, D. R. Angew. Chem. Int. Ed. 43, 4848-4870 (2004). PDF (1.2 MB)

This article reviews the growth of DNA-templated synthesis from its origins as a model system for self-replication to its recent development into a general way to control the reactivity of synthetic molecules using effective molarity.

 

"DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles" Gartner, Z. J.; Tse, B. N.; Grubina, R.; Doyon, J. B.; Snyder, T. M.; Liu, D. R. Science 305, 1601-1605 (2004). PDF (512 KB) | Supplemental info This work is featured as a Research Highlight in Nature Biotechnology 22, 1247 (2004).

This paper describes the translation of a single-solution library of DNA templates into a library of corresponding synthetic small-molecule macrocycles, the in vitro selection of a single member of the DNA-templated library for its protein binding activity, and the amplification by PCR of the DNA encoding the active macrocycle.

 

"Ordered Multistep Synthesis in a Single Solution Directed by DNA Templates" Snyder, T. M. and Liu, D. R. Angew. Chem. Int. Ed. 44, 7379-7382 (2005). PDF (576 KB) | Supplemental info

 

"Small-Molecule Diversification From Iterated Branching Reaction Pathways Enabled by DNA-Templated Synthesis" Calderone, C. T. and Liu, D. R. Angew. Chem. Int. Ed. 44, 7383-7386 (2005). PDF (488 KB) | Supplemental info

 

"Translation of DNA into a Library of 13,000 Synthetic Small-Molecule Macrocycles Suitable for In Vitro Selection" Tse, B. N.; Snyder, T. M.; Shen, Y.; Liu, D. R. J. Am. Chem. Soc. 130, 15611-15626 (2008).  PDF (4.2 MB) | Supplemental info

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