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"Duzdevich, Daniel"
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Freeze-thaw cycles enable a prebiotically plausible and continuous pathway from nucleotide activation to nonenzymatic RNA copying
Nonenzymatic template-directed RNA copying using chemically activated nucleotides is thought to have played a key role in the emergence of genetic information on the early Earth. A longstanding question concerns the number and nature of different environments that might have been necessary to enable all of the steps from nucleotide synthesis to RNA copying. Here we explore three sequential steps from this overall pathway: nucleotide activation, synthesis of imidazolium-bridged dinucleotides, and template-directed RNA copying. We find that all three steps can take place in one reaction mixture undergoing multiple freeze-thaw cycles. Recent experiments have demonstrated a potentially prebiotic methyl isocyanide-based nucleotide activation chemistry. However, the original version of this approach is incompatible with nonenzymatic RNA copying because the high required concentration of the imidazole activating group prevents the accumulation of the essential imidazolium-bridged dinucleotide. Here we report that ice eutectic phase conditions facilitate not only the methyl isocyanide-based activation of ribonucleotide 5′-monophosphates with stoichiometric 2-aminoimidazole, but also the subsequent conversion of these activated mononucleotides into imidazolium-bridged dinucleotides. Furthermore, this one-pot approach is compatible with template-directed RNA copying in the same reaction mixture. Our results suggest that the simple and common environmental fluctuation of freeze-thaw cycles could have played an important role in prebiotic nucleotide activation and nonenzymatic RNA copying.
Journal Article
Darwin's On the Origin of Species
Charles Darwin's most famous book On the Origin of Species is without question, one of the most important books ever written. While even the grandest works of Victorian English can prove difficult to modern readers, Darwin wrote his text in haste and under intense pressure. For an era in which Darwin is more talked about than read, Daniel Duzdevich offers a clear, modern English rendering of Darwin's first edition. Neither an abridgement nor a summary, this version might best be described as a \"translation\" for contemporary English readers. A monument to reasoned insight, the Origin illustrates the value of extensive reflection, carefully gathered evidence, and sound scientific reasoning. By removing the linguistic barriers to understanding and appreciating the Origin, this edition aims to bring 21st-century readers into closer contact with Darwin's revolutionary ideas.
eBook
An Experimental Approach to Inform Venus Astrobiology Mission Design and Science Objectives
Exploring how life is distributed in the universe is an extraordinary interdisciplinary challenge, but increasingly subject to testable hypotheses. Biology has emerged and flourished on at least one planet, and that renders the search for life elsewhere a scientific question. We cannot hope to travel to exoplanets in pursuit of other life even if we identify convincing biosignatures, but we do have direct access to planets and moons in our solar system. It is therefore a matter of deep astrobiological interest to study their histories and environments, whether or not they harbor life, and better understand the constraints that delimit the emergence and persistence of biology in any context. In this perspective, we argue that targeted chemistry- and biology-inspired experiments are informative to the development of instruments for space missions, and essential for interpreting the data they generate. This approach is especially useful for studying Venus because if it were an exoplanet we would categorize it as Earth-like based on its mass and orbital distance, but its atmosphere and surface are decidedly not Earth-like. Here, we present a general justification for exploring the solar system from an astrobiological perspective, even destinations that may not harbor life. We introduce the extreme environments of Venus, and argue that rigorous and observation-driven experiments can guide instrument development for imminent missions to the Venusian clouds. We highlight several specific examples, including the study of organic chemistry under extreme conditions, and harnessing the fluorescent properties of molecules to make a variety of otherwise challenging measurements.
Journal Article
Unusual Structures Are Present in DNA Fragments Containing Super-Long Huntingtin CAG Repeats
In the R6/2 mouse model of Huntington's disease (HD), expansion of the CAG trinucleotide repeat length beyond about 300 repeats induces a novel phenotype associated with a reduction in transcription of the transgene.
We analysed the structure of polymerase chain reaction (PCR)-generated DNA containing up to 585 CAG repeats using atomic force microscopy (AFM). As the number of CAG repeats increased, an increasing proportion of the DNA molecules exhibited unusual structural features, including convolutions and multiple protrusions. At least some of these features are hairpin loops, as judged by cross-sectional analysis and sensitivity to cleavage by mung bean nuclease. Single-molecule force measurements showed that the convoluted DNA was very resistant to untangling. In vitro replication by PCR was markedly reduced, and TseI restriction enzyme digestion was also hindered by the abnormal DNA structures. However, significantly, the DNA gained sensitivity to cleavage by the Type III restriction-modification enzyme, EcoP15I.
\"Super-long\" CAG repeats are found in a number of neurological diseases and may also appear through CAG repeat instability. We suggest that unusual DNA structures associated with super-long CAG repeats decrease transcriptional efficiency in vitro. We also raise the possibility that if these structures occur in vivo, they may play a role in the aetiology of CAG repeat diseases such as HD.
Journal Article
In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole–activated substrates
The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5′-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide–activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3′-5′ phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.
Journal Article
Towards physiological complexity with in vitro single-molecule biophysics
Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena—from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying proteinnucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance.
Journal Article
ESD Ideas: Exoplanet, origins of life and biosphere researchers offer a perspective fundamental to ensuring humanity's future
Studying the origin of life and its prevalence in the universe offers a perspective that compels us to look after our irreplaceable home in the cosmos. An entrenched conception of humans as distinct from Nature prevents us from seeing and embracing our place in space and time, to our catastrophic detriment. We call on our colleagues to harness this unique perspective to connect their research with broader problems facing humanity, while leveraging the trust, credibility, and privilege of the scientific enterprise.
Journal Article
Towards physiological complexity with in vitro single-molecule biophysics
Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena—from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein–nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance.
Journal Article
