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Daniel Hutter

Education

  • MS in Chemistry. Swiss Federal Institute of Technology (ETH), Zurich, Switzerland (1994)
  • PhD in Chemistry. ETH, Zurich, Switzerland (2001)

Research summary

Synthetic biology. I synthesized DNA oligonucleotides containing modified backbone linkers and studied their duplex conformation and stability. The results obtained have significant implications for gene therapy as well as for the search for life beyond Earth. I also synthesized nucleosides exhibiting hydrogen bonding patterns different from those found in natural DNA, giving rise to an artificially expanded genetic information system with more than just two base pairs. The vast variety of possible applications includes many medical diagnostic tools inaccessible through natural DNA alone.

Personalized medicine. Genetically based side effects from drugs could be managed if it would be possible to sequence the entire genome of an individual patient in a short time (a few days at most) and at low cost (a few thousand dollars). This would vastly increase the range of available drugs. Current methods for sequencing DNA are not able to match these goals. I am synthesizing modified nucleoside triphosphates for highly parallel sequencing technologies on micro arrays that would slash price and time of current methods by several orders of magnitude. In a related project I am developing an improved synthetic method for the fast, clean and selective transformation of nucleosides into their respective triphosphates.

Dynamic combinatorial synthesis. This concept should greatly increase the speed for finding leads in drug discovery. Instead of a scientist designing a drug to a particular enzymatic target, the enzyme itself synthesizes its preferred ligand from two combinatorial libraries of small molecules that are in dynamic equilibrium with each other. These libraries have to exhibit several specific properties, however, that render the successful application of this concept non-trivial. I am currently synthesizing different libraries that are promising candidates.

Recent Publications

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High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology
Lyudmyla G. Glushakova, Andrea Bradley, Kevin M. Bradley, Barry W. Alto, Shuichi Hoshika, Daniel Hutter, Nidhi Sharma, Zunyi Yang, Myong-Jung Kim, Steven A. Benner
J Virol Methods 214 , Elsevier 60-74 (2015) doi: 10.1016/j.jviromet.2015.01.003
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Helicase Dependent Isothermal Amplification of DNA and RNA using Self-Avoiding Molecular Recognition Systems
Zunyi Yang, Chris McLendon, Daniel Hutter, Kevin M. Bradley, Shuichi Hoshika, Carole Frye, and Steven A. Benner
ChemBioChem (2015) June 15; 16(9): 1365-1370. doi:10.1002/cbic.201500135.
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Recombinase-Based Isothermal Amplification of Nucleic Acids with Self-Avoiding Molecular Recognition Systems (SAMRS)
Nidhi Sharma, Shuichi Hoshika, Daniel Hutter, Kevin M. Bradley, and Steven A. Benner
ChemBioChem (2014) DOI: 10.1002/cbic.201402250
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Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups
Hutter, D; Kim, MJ; Karalkar, N; Leal, NA; Chen, F; Guggenheim, E; Visalakshi, V; Olejnik, J; Gordon, S; Benner, SA
Nuc. Nuc. Nuc. acids 29 (11) , Taylor & Francis Group 879-895 (2010)
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Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection
Chen, F; Gaucher, EA; Leal, NA; Hutter, D; Havemann, SA; Govindarajan, S; Ortlund, EA; Benner, SA
Proc. Natl. Acad. Sci. USA 107 (5) 1948-1953 (2010)

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Incorporation of Multiple Sequential Pseudothymidines by DNA Polymerases and Their Impact on DNA Duplex Structure
Havemann, SA; Hoshika, S; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 (3) , Taylor & Francis Group 261-278 (2008)
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Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules
Kim, HJ; Kim, MJ; Karalkar, N; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 , Taylor & Francis Group 43-56 (2008)

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Synthetic Biology for Improved Personalized Medicine
Benner, SA; Hoshika, S; Sukeda, M; Hutter, D; Leal, NA; Yang, ZY; Chen, F
Nucleic Acids Symp. Ser. 52 (1) 243-244 (2008) doi: 10.1093/nass/nrn123
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Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Yang, ZY; Hutter, D; Sheng, PP; Sismour, AM; Benner, SA
Nucl. Acids Res. 34 (21) 6095-6101 (2006)
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Expanding the genetic alphabet: Non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern
Hutter, D; Benner, SA
J. Org. Chem. 68 (25) 9839-9842 (2003)
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