Steven A. Benner
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View article: Interstep compatibility of a model for the prebiotic synthesis of RNA consistent with Hadean natural history
Interstep compatibility of a model for the prebiotic synthesis of RNA consistent with Hadean natural history Open
Models for prebiotic syntheses often have many steps, each separately validated by laboratory experiments. The challenge then asks whether these steps work together in natural geological environments, absent human intervention. Here, we an…
View article: CryoEM structures of evolved Family B DNA polymerase bound to template-primer substrates
CryoEM structures of evolved Family B DNA polymerase bound to template-primer substrates Open
The cryoEM revolution has made it possible to determine structures of many macromolecules of interest that have remained intractable to crystallographic analysis. But, despite the many advances in instrumentation and software, complexes wi…
View article: Sequencing a DNA analog composed of artificial bases
Sequencing a DNA analog composed of artificial bases Open
"ALternative Isoinformational ENgineered" (ALIEN) DNA is a biomimetic polymer composed of four entirely anthropogenic nucleotides. These alternative nucleosides form base pairs orthogonal to canonical bases and fold into the familiar B-for…
View article: Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets
Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets Open
Anthropogenic evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built …
View article: Six-Letter DNA Nanotechnology: Incorporation of <b>Z</b>-<b>P</b> Base Pairs into Self-Assembling 3D Crystals
Six-Letter DNA Nanotechnology: Incorporation of <b>Z</b>-<b>P</b> Base Pairs into Self-Assembling 3D Crystals Open
Artificially expanded genetic information systems (AEGIS) were developed to expand the diversity and functionality of biological systems. Recent experiments have shown that these expanded DNA molecular systems are robust platforms for info…
View article: Template-Independent Enzymatic RNA Synthesis
Template-Independent Enzymatic RNA Synthesis Open
A route to prepare ribonucleoside triphosphates featuring a 3’-aminoxy (3’-O-NH 2 ) removable blocking group is reported here. We then show that versions of two DNA polymerases, human DNA polymerase theta (Polθ) and mimiviral PrimPol, acce…
View article: Harnessing non-standard nucleic acids for highly sensitive icosaplex (20-plex) detection of microbial threats
Harnessing non-standard nucleic acids for highly sensitive icosaplex (20-plex) detection of microbial threats Open
Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific,…
View article: Draft genome of <i>Thermoanaerobacter thermohydrosulfuricus</i> strain AK152, a novel thermophilic and anaerobic bacterium isolated from a hot spring in Iceland
Draft genome of <i>Thermoanaerobacter thermohydrosulfuricus</i> strain AK152, a novel thermophilic and anaerobic bacterium isolated from a hot spring in Iceland Open
We present the draft genome of the bacterium Thermoanaerobacter thermohydrosulfuricus strain AK152, a thermophilic, endospore–spore-forming, anaerobe isolated from a hot spring in Grensdalur, in Southwestern Iceland. This assembled genome …
View article: Nanopores map the acid-base properties of a single site in a single DNA molecule
Nanopores map the acid-base properties of a single site in a single DNA molecule Open
Nanopores are increasingly powerful tools for single molecule sensing, in particular, for sequencing DNA, RNA and peptides. This success has spurred efforts to sequence non-canonical nucleic acid bases and amino acids. While canonical DNA …
View article: A folding motif formed with an expanded genetic alphabet
A folding motif formed with an expanded genetic alphabet Open
Adding synthetic nucleotides to DNA increases the linear information density of DNA molecules. Here we report that it also can increase the diversity of their three-dimensional folds. Specifically, an additional nucleotide (dZ, with a 5-ni…
View article: Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution
Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution Open
With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve recep…
View article: Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development
Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development Open
Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10–100 nucleotides in length. Their targets, often with specificity and high affinity, range f…
View article: Functional Selection of Tau Oligomerization‐Inhibiting Aptamers
Functional Selection of Tau Oligomerization‐Inhibiting Aptamers Open
Pathological hyperphosphorylation and aggregation of microtubule‐associated Tau protein contribute to Alzheimer's Disease (AD) and other related tauopathies. Currently, no cure exists for Alzheimer's Disease. Aptamers offer significant pot…
View article: Rapid detection of West Nile and Dengue viruses from mosquito saliva by loop-mediated isothermal amplification and displaced probes
Rapid detection of West Nile and Dengue viruses from mosquito saliva by loop-mediated isothermal amplification and displaced probes Open
Arthropod-borne viruses are major causes of human and animal disease, especially in endemic low- and middle-income countries. Mosquito-borne pathogen surveillance is essential for risk assessment and vector control responses. Sentinel chic…
View article: Overcoming resolution attenuation during tilted cryo-EM data collection
Overcoming resolution attenuation during tilted cryo-EM data collection Open
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “preferred orientations” on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen…
View article: Production and Reactions of Organic Molecules in Clouds of Venus
Production and Reactions of Organic Molecules in Clouds of Venus Open
For half a century, the possibility of organic molecules in sulfuric acid droplets in the clouds above Venus has been largely discounted. Here, we report the first results from an experimental exploration of this possibility, of primary in…
View article: Enzyme-Assisted High Throughput Sequencing of an Expanded Genetic Alphabet at Single Base Resolution
Enzyme-Assisted High Throughput Sequencing of an Expanded Genetic Alphabet at Single Base Resolution Open
Many efforts have sought to apply laboratory in vitro evolution (LIVE) to natural nucleic acid (NA) scaffolds to directly evolve functional molecules. However, synthetic biology can move beyond natural NA scaffolds to create molecular syst…
View article: DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters Open
We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one a…
View article: Nicotinamide Riboside, a Promising Vitamin B3 Derivative for Healthy Aging and Longevity: Current Research and Perspectives
Nicotinamide Riboside, a Promising Vitamin B3 Derivative for Healthy Aging and Longevity: Current Research and Perspectives Open
Many studies have suggested that the oxidized form of nicotinamide adenine dinucleotide (NAD+) is involved in an extensive spectrum of human pathologies, including neurodegenerative disorders, cardiomyopathy, obesity, and diabetes. Further…
View article: Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection
Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection Open
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “preferred orientations” on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen…
View article: Nicotinamide Riboside, a Promising Vitamin B<sub>3</sub> Derivative for Healthy Aging and Longevity: Current Research and Perspectives
Nicotinamide Riboside, a Promising Vitamin B<sub>3</sub> Derivative for Healthy Aging and Longevity: Current Research and Perspectives Open
NAD+ is known classically as a metabolite that participates in catabolic and anabolic pathways throughout the metabolism that is taught to students in introductory biochemistry courses. However, non-classical studies starting over a decade…
View article: DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters Open
We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1’-β-D-2’-deoxyribofuranosyl)-imidazo-[1,2- a ]-1,3,5-triazin-(8 H )-4-o…
View article: Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets
Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets Open
One horizon in synthetic biology seeks alternative forms of DNA that store, transcribe, and support the evolution of biological information. Here, hydrogen bond donor and acceptor groups are rearranged within a Watson-Crick geometry to get…
View article: Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores
Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores Open
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today…
View article: Rethinking nucleic acids from their origins to their applications
Rethinking nucleic acids from their origins to their applications Open
Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand thei…
View article: Crystal structures of ‘ALternative Isoinformational ENgineered’ DNA in B-form
Crystal structures of ‘ALternative Isoinformational ENgineered’ DNA in B-form Open
The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA sho…
View article: A Unified Watson-Crick Geometry Drives Transcription of Six-Letter Expanded DNA Alphabets by Cellular RNA Polymerase
A Unified Watson-Crick Geometry Drives Transcription of Six-Letter Expanded DNA Alphabets by Cellular RNA Polymerase Open
Manuscript and Validation Reports