scholarly journals Kinetic Explanations for the Sequence Biases Observed in the Nonenzymatic Copying of RNA Templates

2021 ◽  
Author(s):  
Dian Ding ◽  
Lijun Zhou ◽  
Constantin Giurgiu ◽  
Jack W. Szostak
Keyword(s):  
Nucleic Acid ◽  
Origin Of Life ◽  
Reaction Rate ◽  
Nearest Neighbor ◽  
Reaction Rates ◽  
Primer Extension ◽  
Extension Rate ◽  
The Origin Of Life ◽  
Noncanonical Nucleotides ◽  
Kinetics Of

ABSTRACTThe identification of nonenzymatic pathways for nucleic acid replication is a key challenge in understanding the origin of life. We have previously shown that nonenzymatic RNA primer extension using 2-aminoimidazole (2AI) activated nucleotides occurs primarily through an imidazolium-bridged dinucleotide intermediate. The reactive nature and preorganized structure of the intermediate increase the efficiency of primer extension but remain insufficient to drive extensive copying of RNA templates containing all four canonical nucleotides. To understand the factors that limit RNA copying, we synthesized all ten 2AI-bridged dinucleotide intermediates and measured the kinetics of primer extension in a model. The affinities of the ten dinucleotides for the primer/template/helper complexes vary by over 7,000-fold, consistent with nearest neighbor energetic predictions. Surprisingly, the reaction rates at saturating intermediate concentrations still vary by over 15-fold, with the most weakly binding dinucleotides exhibiting a lower maximal reaction rate. Certain noncanonical nucleotides can decrease sequence dependent differences in affinity and primer extension rate, while monomers bridged to short oligonucleotides exhibit enhanced binding and reaction rates. We suggest that more uniform binding and reactivity of imidazolium-bridged intermediates may lead to the ability to copy arbitrary template sequences under prebiotically plausible conditions.

A KINETICS AND MECHANISTIC STUDY OF THE OXIDATION OF L-ARGININE BY QDC IN DMF-WATER MEDIUM

2021 ◽  
pp. 11-12
Author(s):  
Deepika Jain ◽  
Shilpa Rathor
Keyword(s):  
Perchloric Acid ◽  
Reaction Rate ◽  
Main Product ◽  
Activation Parameters ◽  
Reaction Rates ◽  
Mechanistic Study ◽  
Water Medium ◽  
Volume Percentage ◽  
Kinetics Of Oxidation ◽  
Kinetics Of

The present paper describes the kinetics of oxidation of l-Arginine by QDC in the presence of perchloric acid in 30% DMF-H O(v/v) medium at 2 + 40⁰C spectrophotometrically at λ =354nm. The reaction is rst order with respect to [QDC], [H ], and [substrate]. The reaction rate increased with max increasing volume percentage of DMF in reaction mixture. Michaelis- Menten type kinetic was observed with l-Arginine. The reaction rates were studied at different temperature and the activation parameters has been computed. The main product was identied as Cr (III) and 4-Guanidino buteraldehyde.

scholarly journals Differential adsorption of nucleic acid bases: Relevance to the origin of life

2001 ◽  
Vol 98 (3) ◽  
pp. 820-822 ◽  
Author(s):  
S. J. Sowerby ◽  
C. A. Cohn ◽  
W. M. Heckl ◽  
N. G. Holm
Keyword(s):  
Nucleic Acid ◽  
Origin Of Life ◽  
Nucleic Acid Bases ◽  
The Origin Of Life

scholarly journals An optimal degree of physical and chemical heterogeneity for the origin of life?

2011 ◽  
Vol 366 (1580) ◽  
pp. 2894-2901 ◽  
Author(s):  
Jack W. Szostak
Keyword(s):  
Nucleic Acid ◽  
Origin Of Life ◽  
Self Assembly ◽  
Building Blocks ◽  
Reaction Products ◽  
Amphiphilic Molecules ◽  
Essential Components ◽  
The Origin Of Life ◽  
Chemical Inputs ◽  
Physical And Chemical

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.

scholarly journals The kinetics of the reduction of the lipophilic quinone avarone by N-alkyl-1,4-dihydronicotinamides of various lipophilicities

1999 ◽  
Vol 64 (11) ◽  
pp. 647-654 ◽  
Author(s):  
Mario Zlatovic ◽  
Dusan Sladic ◽  
Miroslav Gasic
Keyword(s):  
Cationic Surfactants ◽  
Reaction Rate ◽  
Anionic Surfactants ◽  
Reaction Rates ◽  
Biologically Active ◽  
Ionic Surfactants ◽  
Protic Solvent ◽  
Model Compounds ◽  
Kinetics Of ◽  
Long Chain

Several NADH model compounds, N-alkyl-1,4-dihydronicotinamides, some of them possessing amphiphilic properties, have been synthesized, and the kinetics of their reaction with a biologically active liphophilic quinone, avarone, has been studied in a protic solvent both in the presence and absence of cationic, anionic or non-ionic surfactants. In the absence of micellar agents, the medium- and long-chain N-dodecyl (3) and N-heptadecyl (4) derivatives show a significant increase in the reaction rates compared to other model compounds, due to the stabilization of the semiquinone intermediate. Anionic surfactants retard the reaction, non-ionic surfactants slightly accelerate the reaction with the short-chain derivatives, and retard the reaction with the medium- and long-chain derivatives, and the cationic surfactants increase the reaction rate with all derivatives except the long-chain 4. The results support the e-p-e mechanism of the reduction of lipophilic quinones byNADHmodels in protic medium.

Protective effect of clay minerals on adsorbed nucleic acid against UV radiation: possible role in the origin of life

2004 ◽  
Vol 3 (1) ◽  
pp. 17-19 ◽  
Author(s):  
F. Scappini ◽  
F. Casadei ◽  
R. Zamboni ◽  
M. Franchi ◽  
E. Gallori ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Protective Effect ◽  
Origin Of Life ◽  
Clay Minerals ◽  
Uv Radiation ◽  
Laboratory Experiments ◽  
Biological Evolution ◽  
The Earth ◽  
The Origin Of Life ◽  
Uv Photons

The effect of UV radiation on solutions of free and clay-adsorbed DNA has been investigated. It turns out that clay (montmorillonite/kaolinite) adsorbed nucleic acid undergoes less radiation damage than free nucleic acid. Our laboratory experiments have an astronomical counterpart in terms of solar irradiance on the Earth. An origin of life scenario is proposed where ubiquitous clay minerals lead the surface chemistry of the molecules relevant to the biological evolution and at the same time protect them from the deadly rainfall of UV photons.

scholarly journals The Dissipative Photochemical Origin of Life: UVC Abiogenesis of Adenine

2021 ◽  
Author(s):  
Karo Michaelian
Keyword(s):  
Origin Of Life ◽  
Kinetic Equations ◽  
Reaction Rates ◽  
Photon Flux ◽  
Common Precursor ◽  
Wavelength Absorption ◽  
The Common ◽  
The Origin Of Life ◽  
Precursor Molecules ◽  
Non Equilibrium

I describe the non-equilibrium thermodynamics and the photochemical mechanisms which may have been involved in the dissipative synthesis, proliferation, and evolution of the fundamental molecules at the origin of life from simpler and more common precursor molecules such as HCN, H2O and CO2 under the impressed UVC photon flux of the Archean. The fundamental molecules absorb strongly in this UVC region and exhibit strong coupling between their electronic excited and ground states which endows them with efficient photon disipative capacity (broad wavelength absorption and rapid radiationless dexcitation) suggestive of dissipative structuring. The autocatalytic nature of the synthesized molecules in dissipating the same photochemical potential that directed their synthesis leads to their proliferation. The non-linearity in the photochemical and chemical reaction rates provides numerous stationary states which can be reached by amplification of a molecular concentration fluctuation near a bifurcation, promoting the system into states of generally higher photon disspative efficacy. An example is given of the UV photochemical dissipative structuring, proliferation, and evolution of molecules on route to the nucleobase adenine from the common precursor molecules HCN and H2O occurring within a fatty acid vesicle. The kinetic equations are resolved under different environmental conditions, providing a non-equilibrium thermodynamic analysis of the appearance of an early important molecule for the origin of life.

XIV.—Abiogenic Information Coupling between Nucleic Acid and Protein, or, how Protein and DNA were married

1969 ◽  
Vol 70 (4) ◽  
pp. 273-294 ◽  
Author(s):  
Melvin Calvin
Keyword(s):  
Nucleic Acid ◽  
Origin Of Life ◽  
Chemical Evolution ◽  
The Earth ◽  
Evolution Of Life ◽  
The Origin Of Life

The title to the talk this afternoon, “Abiogenic Information Coupling, or, How protein and DNA were married”, is, indeed, an excerpt from the much broader subject to which your President referred, namely chemical evolution of life on the surface of the earth, with some speculation about elsewhere as well. Actually, the “elsewhere” portion is more than a hopeful addition because it may provide a check on the speculations on the origin of life on the surface of the earth, which is very difficult to obtain inany other way.

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