RNA world Archives

Astrochemistry, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Protocell Effects on RNA Folding, Function, and Evolution

by Keith CowingSeptember 26, 2024September 26, 2024

Creating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic “RNA […]

Cold RNA misfolding and phase transitions. (A) Illustration of a multi-colored free-energy landscape (FEL) at different temperatures. The temperature arrow indicates the tendency to explore low-lying energy states with the FEL becoming rougher upon cooling: from high (red) to intermediate (green) and low (blue) temperatures. Transition state (TS) distances are typically shorter for M than N, denoting disordered and compact misfolded structures. The encircled schematic folds are for illustration purposes. (B) Temperature-dependent entropy (black) and enthalpy (grey) of N for H1L12A (empty symbols) and H1L4A (full symbols). The results are reported in Table S5 and S6, Supp. Info. Fits to the entropy values in the hot (red) and cold (blue) regimes for H1L12A (solid lines) and H1L4A (dashed lines) are also shown. The transition between the two regimes occurs at TG ⇠ 293K ⇠ 20C (dashed grey band) with a sudden change in Cp. Inset. Stability curves of H1L12A (empty black circles) and H1L4A (solid grey squares). Maximum stability is found at TS ⇠ 278K ⇠ 5C (vertical black line) with melting temperatures at TH ⇠ 370K ⇠ 100C (red lines). Extrapolations of G0(T) in the cold regime predict cold denaturation at TC ⇠ 220K ⇠ 50C for both hairpins (blue lines). -- PNAS

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Cryobiology, Genomics, Proteomics, Bioinformatics, Press Release

A New Biochemistry For RNA At Low Temperatures

by Keith CowingSeptember 11, 2024September 11, 2024

Ribonucleic acid (RNA) is a biological molecule with crucial functions in the genetics of organisms and plays a key role in the origin and evolution of life. With a composition […]

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). -- Wikipedia

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

RNA World: Overcoming Nucleotide Bias In The Nonenzymatic Copying Of RNA Templates

by Keith CowingSeptember 6, 2024September 6, 2024

The RNA World hypothesis posits that RNA was the molecule of both heredity and function during the emergence of life.

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Status Report

RNA-Catalyzed Evolution

by Keith CowingJune 17, 2024

NASA-supported researchers have used a laboratory technique called directed evolution to create an RNA enzyme that is capable of carrying out RNA polymerase activity. In living cells, protein polymerases catalyze […]

A phase-contrast micrograph of a ciliate (Frontonia sp.) digesting blue-green algae (cyanobacteria). The cytostome (the "mouth" of the cell) is seen on the right side down. Image credit: (CC BY-SA 4.0 DEED)

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life

Early Replicators

by Keith CowingMay 12, 2024May 12, 2024

Mathematical models of how ribonucleic acid (RNA)-like molecules make copies of themselves reveal new insights as the origins of life on Earth.

(a) Formation process of the ribose from 10 (Z)-ethene-1,2-diol, 5 formaldehyde, and 5 water under the condition of 10 GPa - 1400 K. (b) Free energy landscape for analyzing the formation process of ribose, as a function of two kinds of C-C distance as the collective variables. To better distinguish the selected carbon atoms, C1 and C2 are marked by yellow and orange colors, respectively. (c) The evolution process of the ribose from the open chain to a five-membered ring (10 GPa - 1400 K). (d) Comparison of the formation ability of five-membered ring and sixmembered ring based on the free energy calculation with the C-O distance as the collective variable. -- physics.bio-ph

Astrogeology, Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Fossils & Paleontology, Habitable Zones, Status Report, Water/Hycean Worlds & Oceanography

Synthesis And Stability Of Biomolecules Under Earth’s Upper Mantle Conditions

by Keith CowingMay 9, 2024

How life started on Earth is a long-time unsolved mystery. There are various hypotheses ranging from outer space to seabed.

(A) Compositions of the R3C ligase ribozyme (73-mer, top) and that of the reduced form, R3C-A (46-mer, bottom). They are shown in black. The 5′-6-FAM-labeled ligation substrate (12-mer) is shown in green. The stem loop regions of the original R3C ligase ribozyme are designated as “Hammer” and “Grip”. (B) Schematic presentation of the evolution process of ribozymes. During the RNA elongation process, a short RNA would have fused with other RNA domains that interacted with specific compounds (effectors), resulting in an RNA whose activity regulation was dependent on the specific effector. Each circle represents a nucleotide comprising RNA.

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Development of Allosteric Ribozymes for ATP and l-Histidine Based on the R3C Ligase Ribozyme

by Keith CowingApril 30, 2024April 30, 2024

During the evolution of the RNA, short RNAs are thought to have joined together to form long RNAs, enhancing their function as ribozymes.

Researchers from Tokyo University of Science have engineered a ribozyme structure which mimics the early RNA world and provides novel insights on the role of RNA in primitive life, to its various real-world applications -- Tokyo University of Science

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Origin & Evolution of Life, Press Release

New Study Unveils RNA’s Role In Early Life And Future Bioengineering

by Keith CowingApril 18, 2024April 18, 2024

The beginning of life on Earth and its evolution over billions of years continue to intrigue researchers worldwide. The central dogma or the directional flow of genetic information from a […]

Grand Prismatic Spring in Yellowstone National Park, seen here from an aerial photo, provides a modern-day glimpse into the types of environments where sulfites may have accumulated and possibly played a role in kick-starting the earliest life on Earth. - USGS

Astrochemistry, Astrogeology, Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Origin & Evolution of Life, Press Release

Sulfur And The Origin Of Life

by Keith CowingMarch 14, 2024March 14, 2024

Many artists have tried to depict what Earth might have looked like billions of years ago, before life made its appearance. Many scenes trade snow-covered mountains for lava-gushing volcanoes and […]

Scatterplots show the evolving populations of hammerheads across multiple rounds of evolution. Hammerheads copied by the lower-fidelity polymerase (52-2) drift away from the original RNA sequence (white contours) and lose their function. Hammerheads copied by the new higher-fidelity polymerase (71-89) retain function, with new functional sequences emerging over time. -- Salk Institute

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Press Release

Modeling The Origins Of Life: New evidence For An RNA World

by Keith CowingMarch 5, 2024March 5, 2024

Charles Darwin described evolution as “descent with modification.” Genetic information in the form of DNA sequences is copied and passed down from one generation to the next. But this process […]