- 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
- Fellow of the American Association for the Advancement of Science (Biology) 2015
- Honoris Causa, University of Croatia, Romania 2016
- Fellow of the International Society for the Study of the Origin of Life (ISSOL) 2017
When Did Life Likely Emerge on Earth in an RNA-First Process?
S. A. Benner, E. A. Bell, E. Biondi, R. Brasser, T. Carell, H.-J. Kim, S. J. Mojzsis, A. Omran, M. A. Pasek, D. Trail
2 , Chemistry Europe (2020) e1900035
The widespread presence of ribonucleic acid (RNA) catalysts and cofactors in the Earth's biosphere today suggests that RNA was the first biopolymer to support Darwinian evolution. However, most "path-hypotheses" to generate building blocks for RNA require reduced nitrogen-containing compounds not made in useful amounts in the CO2-N2-H2O atmospheres of the Hadean. We review models for Earth's impact history that invoke a single ~1023 kg impactor (Moneta) to account for measured amounts of platinum, gold, and other siderophilic ("iron-loving") elements on the Earth and Moon. If it were the last sterilizing impactor, by reducing the atmosphere but not the mantle Moneta, would have opened a "window of opportunity" for RNA synthesis, a period when RNA precursors rained from the atmosphere onto land holding oxidized minerals that stabilize advanced RNA precursors and RNA. Surprisingly, this combination of physics, geology, and chemistry suggests a time when RNA formation was most probable, ~120±100 million years after Moneta's impact, or ~4.36±0.1 billion years ago. Uncertainties in this time are driven by uncertainties in rates of productive atmosphere loss and amounts of sub-aerial land.
Hachimoji DNA and RNA: A genetic system with eight building blocks
Hoshika H, Leal N, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins Jr. NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr. J, Georgiadis MM, Benner SA
(2019) 22 Feb 2019: Vol. 363, Issue 6429, pp. 884-887. DOI: 10.1126/science.aat0971
We report DNA- and RNA-like systems built from eight nucleotide "letters" (hence the name "hachimoji") that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.
The surprising pairing of 2-aminoimidazo[1,2-a]-
[1,3,5]triazin-4-one, a component of an expanded
Roberto Laos, Christos Lampropoulos, and Steven A. Benner
, Acta Crystallographica (2019) C75, 22-28, https://doi.org/10.1107/S2053229618016923
Synthetic biologists demonstrate their command over natural biology by
reproducing the behaviors of natural living systems on synthetic biomolecular
platforms. For nucleic acids, this is being done stepwise, first by adding replicable
nucleotides to DNA, and then removing its standard nucleotides. This challenge
has been met in vitro with 'six-letter' DNA and RNA, where the Watson-Crick
pairing 'concept' is recruited to increase the number of independently replicable
nucleotides from four to six. The two nucleobases most successfully added so far
are Z and P, which present a donor-donor-acceptor and an acceptor-acceptor-
donor pattern, respectively. This pair of nucleobases are part of an 'artificially
expanded genetic information system' (AEGIS). The Z nucleobase has been
already crystallized, characterized, and published in this journal [Matsuura et al.
(2016). Acta Cryst. C72, 952-959]. More recently, variants of Taq polymerase
have been crystallized with the pair P:Z trapped in the active site. Here we
report the crystal structure of the nucleobase 2-aminoimidazo[1,2-a][1,3,5]-
triazin-4-one (trivially named P) as the monohydrate, C5H5N5O-H2O. The
nucleobase P was crystallized from water and characterized by X-ray diffraction.
Interestingly, the crystal structure shows two tautomers of P packed in a
Watson-Crick fashion that cocrystallized in a 1:1 ratio.
Prebiotic Chemistry that Could Not Not Have Happened
Benner S.A., Kim H.-J., and Biondi E.
9 (4) , MDPI 84 (2019) https://doi.org/10.3390/life9040084
We present a direct route by which RNA might have emerged in the Hadean from a fayalite-magnetite mantle, volcanic SO2 gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In chemistry that could not not have happened, these would have generated stable bisulfite addition products that must have rained to the surface, where they unavoidably would have slowly released reactive species that generated higher carbohydrates. The formation of higher carbohydrates is self-limited by bisulfite formation, while borate minerals may have controlled aldol reactions that occurred on any semi-arid surface to capture that precipitation. All of these processes have well-studied laboratory correlates. Further, any semi-arid land with phosphate should have had phosphate anhydrides that, with NH3, gave carbohydrate derivatives that directly react with nucleobases to form the canonical nucleosides. These are phosphorylated by magnesium borophosphate minerals (e.g., luneburgite) and/or trimetaphosphate-borate with Ni2+ catalysis to give nucleoside 5'-diphosphates, which oligomerize to RNA via a variety of mechanisms. The reduced precursors that are required to form the nucleobases came, in this path-hypothesis, from one or more mid-sized (1023-1020 kg) impactors that almost certainly arrived after the Moon-forming event. Their iron metal content almost certainly generated ammonia, nucleobase precursors, and other reduced species in the Hadean atmosphere after it transiently placed the atmosphere out of redox equilibrium with the mantle. In addition to the inevitability of steps in this path-hypothesis on a Hadean Earth if it had semi-arid land, these processes may also have occurred on Mars. Adapted from a lecture by the Corresponding Author at the All-Russia Science Festival at the Lomonosov Moscow State University on 12 October 2019, and is an outcome of a three year project supported by the John Templeton Foundation and the NASA Astrobiology program. Dedicated to David Deamer, on the occasion of his 80th Birthday.
Affinity maturation of a portable Fab-RNA module for
chaperone-assisted RNA crystallography
Deepak Koirala, Sandip A. Shelke, Marcel Dupont, Stormy Ruiz, Saurja DasGupta, Lucas J. Bailey, Steven A. Benner and Joseph A. Piccirilli
Nucl. Acids Res.
1-12 (2018) doi: 10.1093/nar/gkx1292
Antibody fragments such as Fabs possess properties
that can enhance protein and RNA crystallization
and therefore can facilitate macromolecular structure
determination. In particular, Fab BL3-6 binds to
an AAACA RNA pentaloop closed by a GC pair with
~100 nM affinity. The Fab and hairpin have served
as a portable module for RNA crystallization. The potential
for general application make it desirable to
adjust the properties of this crystallization module
in a manner that facilitates its use for RNA structure
determination, such as ease of purification, surface
entropy or binding affinity. In this work, we used both
in vitro RNA selection and phage display selection to
alter the epitope and paratope sides of the binding
interface, respectively, for improved binding affinity.
We identified a 5'-GNGACCC-3' consensus motif in
the RNA and S97N mutation in complimentarity determining
region L3 of the Fab that independently impart
about an order of magnitude improvement in affinity,
resulting from new hydrogen bonding interactions.
Using a model RNA, these modifications facilitated
crystallization under a wider range of conditions and
improved diffraction. The improved features of the
Fab-RNA module may facilitate its use as an affinity
tag for RNA purification and imaging and as a chaperone
for RNA crystallography.
A Direct Prebiotic Synthesis of Nicotinamide Nucleotide
Hyo-Joong Kim, Steven A. Benner
, Wiley-VCH (2018) Jan 12;24(3):581-584. doi: 10.1002/chem.201705394
Under the "RNA World" hypothesis, an early episode of
natural history on Earth used RNA as the only genetically encoded
molecule to catalyze steps in its metabolism catalysis. This, according
to the hypothesis, included RNA catalysts that used RNA cofactors.
However, the RNA World hypothesis places special demands on
prebiotic chemistry, which must now deliver not only four
ribonucleosides, but also must deliver the "functional" portion of these
RNA cofactors. While some (e.g. methionine) present no particular
challenges, nicotinamide ribose is special. Essential to its role in
biological oxidations and reductions, its glycosidic bond that holds a
positively charged heterocycle is especially unstable with respect to
cleavage. Nevertheless, we are able to report here a prebiotic
synthesis of phosphorylated nicotinamide ribose under conditions that
also conveniently lead to the adenosine phosphate components of
this and other RNA cofactors.
Artificially Expanded Genetic Information Systems
for New Aptamer Technologies
Elisa Biondi and Steven A. Benner
, MDPI (2018) 6, 53; doi:10.3390/biomedicines6020053
Directed evolution was first applied to diverse libraries of DNA and RNA molecules a
quarter century ago in the hope of gaining technology that would allow the creation of receptors,
ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been
somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have
too little functionality to have versatile binding properties, and offer too little information density
to fold unambiguously. This review covers the recent literature that seeks to create an improved
platform to support laboratory Darwinism, one based on an artificially expanded genetic information
system (AEGIS) that adds independently replicating nucleotide "letters" to the evolving "alphabet".
Mineral-Organic Interactions in Prebiotic
Synthesis. The Discontinuous Synthesis Model for the Formation of RNA in Naturally Complex Geological Environments.
Steven A. Benner, Hyo-Joong Kim, and Elisa Biondi
Nucl. Acids & Mol. Bio.
35 , Springer 31-83 (2018) https://doi.org/10.1007/978-3-319-93584-3_3
A common criticism of "prebiotic chemistry research" is that it is done
with starting materials that are too pure, in experiments that are too directed, to get
results that are too scripted, under conditions that could never have existed on Earth.
Planetary scientists in particular remark that these experiments often arise simply
because a chemist has a "cool idea" and then pursues it without considering external
factors, especially geological and planetary context. A growing literature addresses
this criticism and is reviewed here. We assume a model where RNA emerged
spontaneously from a prebiotic environment on early Earth, giving the planet its
first access to Darwinism. This "RNA First Hypothesis" is not driven by the intrinsic
prebiotic accessibility; quite the contrary, RNA is a "prebiotic chemist's nightmare."
However, by assuming models for the accretion of the Earth, the formation of the
Moon, and the acquisition of Earth's "late veneer," a reasonable geological model
can be envisioned to deliver the organic precursors needed to form the nucleobases
and ribose of RNA. A geological model having an environment with dry arid land
under a carbon dioxide atmosphere receiving effluent from serpentinizing igneous
rocks allows their conversion to nucleosides and nucleoside phosphates. Mineral
elements including boron and molybdenum prevent organic material from devolving
to form "tars" along the way. And dehydration and activation allows the formation of
oligomeric RNA that can be stabilized by adsorption on available minerals.
"Skinny" and "Fat" DNA: Two New Double Helices
Hoshika S, Singh I, Switzer C, Molt RW Jr, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA
J. Am. Chem. Soc.
(2018) Sep 19;140(37):11655-11660. doi: 10.1021/jacs.8b05042. Epub 2018 Sep 10
According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our understanding of alternative ways that genetic information might be stored and transmitted.
Snapshots of an evolved DNA polymerase pre- and
post-incorporation of an unnatural nucleotide
Isha Singh, Roberto Laos, Shuichi Hoshika, Steven A. Benner, and Millie M. Georgiadis
Nucl. Acids Res.
46 (15) 7977-7988 (2018) doi: 10.1093/nar/gky552
The next challenge in synthetic biology is
to be able to replicate synthetic nucleic acid
sequences efficiently. The synthetic pair, 2-
amino-8-(1-beta-D-2'- deoxyribofuranosyl) imidazo
[1,2-a]-1,3,5-triazin-[8H]-4-one (trivially designated
P) with 6-amino-3-(2'-deoxyribofuranosyl)-5-nitro-
1H-pyridin-2-one (trivially designated Z), is replicated
by certain Family A polymerases, albeit with lower efficiency.
Through directed evolution, we identified a
variant KlenTaq polymerase (M444V, P527A, D551E,
E832V) that incorporates dZTP opposite P more efficiently
than the wild-type enzyme. Here, we report
two crystal structures of this variant KlenTaq, a
post-incorporation complex that includes a template-primer
with P:Z trapped in the active site (binary
complex) and a pre-incorporation complex with dZTP
paired to template P in the active site (ternary complex).
In forming the ternary complex, the fingers domain
exhibits a larger closure angle than in natural
complexes but engages the template-primer and
incoming dNTP through similar interactions. In the
binary complex, although many of the interactions
found in the natural complexes are retained, there
is increased relative motion of the thumb domain.
Collectively, our analyses suggest that it is the post-incorporation
complex for unnatural substrates that
presents a challenge to the natural enzyme and that
more efficient replication of P:Z pairs requires a more
(View publication page for Steven Benner)
- Chemical genetics
- Synthetic biology
- Planetary biology
- Systems biology
- The connection of natural history to the physical sciences
With cartoons by Jake Fuller, Steven Benner explains how scientists tackle big questions: What is life? How did it begin? If we encounter life in our galactic travels, how would we know it? Learn more.