ribozyme Archives

A) Sequence alignment tree of the 45 biochemically tested RNAs. Clustering of the RNAs by sequence alignment coincided by the RNA’s use of specific DNA cofactors as coded by different colors. Clusters were determined by both RNA sequence distances and the DNA cofactors they recruited. The name of each of the 14 clusters and its most abundant sequence are given on the right. Sequences given in parentheses name the representative RNAs that were tested biochemically. The detailed tree with all 1331 sequences is shown in fig. S4. (B) Network illustrating the edit distances between the biochemically tested 45 RNAs (circles). The size of the circles represents the relative abundance of the RNA in selection round 6. The color of the circles reflects DNA cofactor use and is the same as the 14 clusters in panel A and Fig. 2. The numbers on the lines are the edit distances between the two connected RNAs. -- Science Advances via PubMed

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

Assembly Of Catalytic Complexes From Randomized Oligonucleotides

by Keith CowingMay 3, 2025May 3, 2025

The early evolution of life relied on catalytic RNAs (ribozymes) for central functions.

A diagram of left-handed and right-handed versions of the amino acid isovaline, found in the Murchison meteorite. NASA

Astrochemistry, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Comets and Asteroids, Genomics, Proteomics, Bioinformatics, Imaging & Spectroscopy, Interstellar, Meteorites & Asteroids, Origin & Evolution of Life, Press Release

Astrochemistry: The Mystery of Life’s Handedness Deepens

by Keith CowingNovember 22, 2024November 22, 2024

The mystery of why life uses molecules with specific orientations has deepened with a NASA-funded discovery that RNA — a key molecule thought to have potentially held the instructions for […]

The autocatalytic reaction network. Top: the full network of reactions that were characterized in the autocatalytic P1 Flexizyme assembly network. The assembled, chimeric P1 5 ribozyme is represented in cyan. The arrow thickness corresponds roughly to the relative reaction rates. -- biorxiv.org

Biochemistry & Organic Chemistry, Genomics, Proteomics, Bioinformatics, Status Report

Autocatalytic Assembly Of A Chimeric Aminoacyl-RNA Synthetase Ribozyme

by Keith CowingNovember 8, 2024September 18, 2025

Autocatalytic reactions driving the self-assembly of biological polymers are important for the origin of life, yet few experimental examples of such reactions exist.

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 […]

(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 […]

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 […]

Fitness landscape of the TPR. Average fitness values for a given nucleotide position in TPR secondary structure (A) and tertiary structure (B) (Movie S2). Mean fitness of point mutations is shown by color scale from red to blue. Names of stems and junctions of t1 and 5TU are colored in cyan and orange, respectively. For full map fitness of individual mutations at all positions, see SI Appendix, Fig. S19. - Aarhus University

Biochemistry & Organic Chemistry, Biophysics, Cryobiology, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Origin & Evolution of Life, Press Release

Cryo-microscopy Reveals Nano-sized Copy Machine Implicated In The Origin Of Life

by Keith CowingJanuary 24, 2024January 23, 2024

How the intricate molecular machinery of life arose from simple beginnings has been a long-standing question. Several lines of evidence point towards a primordial “RNA world”, where an “RNA copy […]

Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

RNA-catalyzed RNA Ligation Within Prebiotically Plausible Model Protocells

by Keith CowingFebruary 11, 2023February 11, 2023

Demonstrating RNA catalysis within prebiotically relevant models of primordial cells (protocells) remains a challenge in Origins of life research.

ribozyme

Assembly Of Catalytic Complexes From Randomized Oligonucleotides

Astrochemistry: The Mystery of Life’s Handedness Deepens

Autocatalytic Assembly Of A Chimeric Aminoacyl-RNA Synthetase Ribozyme

Protocell Effects on RNA Folding, Function, and Evolution

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

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

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

Cryo-microscopy Reveals Nano-sized Copy Machine Implicated In The Origin Of Life

RNA-catalyzed RNA Ligation Within Prebiotically Plausible Model Protocells

Impact Crater Hydrothermal Systems Support Rapid Microbial Enrichment and Diverse Metabolic Potential

Photometric and Spectroscopic Observations of Comet 2P/Encke’s Nucleus in the Mid-Infrared Wavelength Region

A New Method Maps An Exoplanet’s True Shape

Wavefront-Conditioned Photon Measurements for Exoplanet Spectroscopy: Contrast Limits and Conditional Gains

ExoPAG 35 – Early Career Talks Invitation