- BS in Molecular Biophysics and Biochemistry. Yale University (1976)
- MS in Molecular Biophysics and Biochemistry. Yale University (1976)
- PhD in Chemistry. Harvard University (1979)
The Benner group has:
- Initiated synthetic biology as a field. The Benner group was the first to synthesize a gene for an enzyme, and used organic synthesis to prepare the first artificial genetic systems. These systems have been used to direct the synthesis of artificial proteins having unnatural amino acids, in FDA-approved clinical assays for HIV, hepatitis B and hepatitis C that improves the medical care of over 400,000 patients annually, and to support the first artificial chemical system capable of Darwinian evolution.
- Invented dynamic combinatorial chemistry, combining ideas from molecular evolution, enzymology, analytical chemistry, and organic chemistry to generate a strategy to discover small molecule therapeutic leads. A German company, Alantos, is today using this technology to develop drug leads.
- Established paleomolecular biology, where researchers resurrect ancestral proteins from extinct organisms for study in the laboratory, The strategy allows scientists to connect chemistry to function in biology, which is defined by an organism's fitness in a complex and changing environment.
- Helped found evolutionary bioinformatics, in 1991, launched one of the first web-based bioinformatics servers with Gaston Gonnet, generated the first naturally organized protein sequence databases, and helped develop the MasterCatalog that generated ca. $4 million in sales. This work also supported the first exhaustive matching of a modern protein sequence database, the first convincing tools to predict structure in proteins from sequence data, strategies to detect distant homologs using structure prediction, and "post-genomic" tools to detect changing protein function.
- National Science Foundation Graduate Fellow
- Junior Fellowship, Harvard Society of Fellows
- Dreyfus Award for Young Faculty, 1982
- Searle Scholar, 1984-86
- Sloan Foundation Fellow, 1984-86
- Anniversary Prize, Federation of European Biochemical Societies, 1993
- Nolan Summer Award, 1998
- Arun Gunthikonda Memorial Award, 1998
- Townes R. Leigh Commemorative Professor, 1999
- B. R. Baker Award, 2001
- Sigma Xi Senior Faculty Award 2005
Directed Evolution of Polymerases To Accept Nucleotides with Nonstandard Hydrogen Bond Patterns
Laos R, Shaw R, Leal NA, Gaucher E, Benner S.
(2013) 52, 5288-5294
Artificial genetic systems have been developed
by synthetic biologists over the past two decades to include
additional nucleotides that form additional nucleobase pairs
independent of the standard T:A and C:G pairs. Their use in
various tools to detect and analyze DNA and RNA requires
polymerases that synthesize duplex DNA containing unnatural
base pairs. This is especially true for nested polymerase chain
reaction (PCR), which has been shown to dramatically lower noise in multiplexed nested PCR if nonstandard nucleotides are
used in their external primers. We report here the results of a directed evolution experiment seeking variants of Taq DNA
polymerase that can support the nested PCR amplification with external primers containing two particular nonstandard
nucleotides, 2-amino-8-(1'-B-D-2'-deoxyribofuranosyl)imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (trivially called P) that pairs with
6-amino-5-nitro-3-(1'-B-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (trivially called Z). Variants emerging from the directed
evolution experiments were shown to pause less when challenged in vitro to incorporate dZTP opposite P in a template.
Interestingly, several sites involved in the adaptation of Taq polymerases in the laboratory were also found to have displayed
"heterotachy" (different rates of change) in their natural history, suggesting that these sites were involved in an adaptive change
in natural polymerase evolution. Also remarkably, the polymerases evolved to be less able to incorporate dPTP opposite Z in the
template, something that was not selected. In addition to being useful in certain assay architectures, this result underscores the
general rule in directed evolution that "you get what you select for".
Conversion strategy using an expanded genetic alphabet to assay nucleic acids
Yang, Z., Durante, M., Glushakova, L., Sharma, N., Leal, N., Bradley, K., Chen, F., Benner, S. A.
Methods to detect DNA and RNA (collectively
xNA) are easily plagued by noise, false positives, and false
negatives, especially with increasing levels of multiplexing in
complex assay mixtures. Here, we describe assay architectures
that mitigate these problems by converting standard xNA
analyte sequences into sequences that incorporate nonstandard
nucleotides (Z and P). Z and P are extra DNA building blocks
that form tight nonstandard base pairs without cross-binding
to natural oligonucleotides containing G, A, C, and T
(GACT). The resulting improvements are assessed in an
assay that inverts the standard Luminex xTAG architecture,
placing a biotin on a primer (rather than on a triphosphate).
This primer is extended on the target to create a standard
GACT extension product that is captured by a CTGA oligonucleotide attached to a Luminex bead. By using conversion, a
polymerase incorporates dZTP opposite template dG in the absence of dCTP. This creates a Z-containing extension product that
is captured by a bead-bound oligonucleotide containing P, which binds selectively to Z. The assay with conversion produces
higher signals than the assay without conversion, possibly because the Z/P pair is stronger than the C/G pair. These architectures
improve the ability of the Luminex instruments to detect xNA analytes, producing higher signals without the possibility of
competition from any natural oligonucleotides, even in complex biological samples.
The "strong" RNA world hypothesis. Fifty years old.
Neveu, Mark; Kim, Hyo-Joong; Benner, Steven A
13 (4) (2013) DOI: 10.1089/ast.2012.0868
This year marks the 50th anniversary of a proposal by Alex Rich that RNA, as a single biopolymer acting in two
capacities, might have supported both genetics and catalysis at the origin of life. We review here both published and
previously unreported experimental data that provide new perspectives on this old proposal. The new data include
evidence that, in the presence of borate, small amounts of carbohydrates can fix large amounts of formaldehyde that
are expected in an environment rich in carbon dioxide. Further, we consider other species, including arsenate,
arsenite, phosphite, and germanate, that might replace phosphate as linkers in genetic biopolymers. While linkages
involving these oxyanions are judged to be too unstable to support genetics on Earth, we consider the possibility
that they might do so in colder semi-aqueous environments more exotic than those found on Earth, where cosolvents
such as ammonia might prevent freezing at temperatures well below 273 K. These include the ammonia-water
environments that are possibly present at low temperatures beneath the surface of Titan, Saturn’s largest moon.
Synthesis and Properties of 5-Cyano-Substituted Nucleoside Analog
with a Donor-Donor-Acceptor Hydrogen-Bonding Pattern
Hyo-Joong Kim, Fei Chen, and Steven A. Benner
J. Org. Chem.
6-Aminopyridin-2-ones form Watson-Crick pairs with complementary purine analogues to add a third
nucleobase pair to DNA and RNA, if an electron-withdrawing group at position 5 slows oxidation and epimerization. In previous
work with a nucleoside analogue trivially named dZ, the electron withdrawing unit was a nitro group. Here, we describe an
analogue of dZ (cyano-dZ) having a cyano group instead of a nitro group, including its synthesis, pKa, rates of acid-catalyzed
epimerization, and enzymatic incorporation.
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
Chen, F; Yang, ZY; Yan, M; Alvarado, JB; Wang, G; Benner, SA
Nucl. Acids Res.
39 (9) 3949-3961 (2011)
To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1'-?-d-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-?-d-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells.
(View all publications by Steven Benner)
- Chemical genetics
- Synthetic biology
- Planetary biology
- Systems biology
- The connection of natural history to the physical sciences