The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

The dawn of the RNA World: Toward functionalcomplexity through ligation of random RNA oligomers

ABSTRACT A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. Keywords: RNA folding; structural motif; modular evolution; RNA ligation; hairpin ribozyme; RNA polymerase

Mineral Catalysis and Prebiotic Synthesis: Montmorillonite-Catalyzed Formation of RNA

Mineral Catalysisand Prebiotic Synthesis:Montmorillonite-CatalyzedFormation of RNA

Montmorillonite, a clay mineral formed by the weathering of volcanic ash, may have played a central role in the evolution of life. Because of its structure, montmorillonite tends to adsorb organic compounds and this contributes to its ability to catalyze a variety of organic reactions critical to scenarios of life’s origins. We have shown experimentally that RNA molecules bind efficiently to clays and that montmorillonite can catalyze the formation of longer molecules (oligomers), thus lending support to the RNA world hypothesis. This theory proposes that life based on RNA preceded current life, which is based on DNA and protein.

Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors.

Abstract

How the biochemical machinery evolved from simple precursors is an open question. Here we show that ribonucleotides and amino acids condense to peptidyl RNAs in the absence of enzymes under conditions established for genetic copying. Untemplated formation of RNA strands that can encode genetic information, formation of peptidyl chains linked to RNA, and formation of the cofactors NAD(+), FAD, and ATP all occur under the same conditions. In the peptidyl RNAs, the peptide chains are phosphoramidate-linked to a ribonucleotide. Peptidyl RNAs with long peptide chains were selected from an initial pool when a lipophilic phase simulating the interior of membranes was offered, and free peptides were released upon acidification. Our results show that key molecules of genetics, catalysis, and metabolism can emerge under the same conditions, without a mineral surface, without an enzyme, and without the need for chemical pre-activation.

Surface-Cross-Linked Micelles as Multifunctionalized Organic Nanoparticles for Controlled Release, Light Harvesting, and Catalysis

Abstract

The self-assembly and self-organization of porphyrins and related macrocycles enables the bottom-up fabrication of photonic materials for fundamental studies of the photophysics of these materials and for diverse applications. This rapidly developing field encompasses a broad range of disciplines including molecular design and synthesis, materials formation and characterization, and the design and evaluation of devices. Since the self-assembly of porphyrins by electrostatic interactions in the late 1980s to the present, there has been an ever increasing degree of sophistication in the design of porphyrins that self-assemble into discrete arrays or self-organize into polymeric systems. These strategies exploit ionic interactions, hydrogen bonding, coordination chemistry, and dispersion forces to form supramolecular systems with varying degrees of hierarchical order. This review concentrates on the methods to form supramolecular porphyrinic systems by intermolecular interactions other than coordination chemistry, the characterization and properties of these photonic materials, and the prospects for using these in devices. The review is heuristically organized by the predominant intermolecular interactions used and emphasizes how the organization affects properties and potential performance in devices.

Most efficient base to compute from...

Assume there are V independent states of information, then we can present V/N digits in base N.

The amount of information we can represent: I=NV/N$I=N^{V/N}$

The value of N that makes I the maximum is the most "efficient" base

Natural log both sides: lnI=(V/N)lnN

Take the derivative: (lnI)'=V(1-lnN)/N2$N^2$

When lnI gets to an extreme, (lnI)'=0, i.e. N=e

Take the second derivative: (lnI)''=V(2lnN-3)/N3$N^3$

When N=e, (lnI)''=−1/N3$-1/N^3$, which is negative

Therefore, I reaches its maximum when N=e.

ALSO SEE: https://www.americanscientist.org/issues/pub/2001/6/third-base/1