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

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.

Crick and Orgel and molybdenum...

Crick and Orgel proposed their Directed Panspermia theory at a conference on Communication with Extraterrestrial Intelligence, organized by Carl Sagan and held at the Byuraka Observatory in Soviet Armenia in 1971. This theory which they described as an “highly unorthodox proposal” and “bold speculation” was presented as a plausible scientific hypothesis. Two years after the conference they published an article in Icarus on 1973.

Crick and Orgel were careful to point out that Directed Panspermia was not a certainty; but rather a plausible alternative that ought to be taken seriously. In thepaper Crick and Orgel recognised that they “do not have any strong arguments of this kind, but there are two weak facts that could be relevant”. The 1973 paper focuses on the universality of the genetic code and the role that molybdenum plays in living organisms (I am likewise working on a history of molybdenum and the origins of life) which is more than one would expected given the abundance of molybdenum on the earth’s crust.

Francis Crick and Leslie Orgel. (Circa 1993)

Crick and Orgel used the universality of the genetic code to support the theory of directed panspermia because if life had originated multiple times or evolved from a simpler genetic code one could expect living things to use a slew of genetic codes. Further, if there was only one code, Crick and Orgel reasoned that as organisms evolved they should evolve to use the same codons to code for different amino acids.

We can draw a parallel to language: while many human populations use the same symbols (letters), they combine them in different ways. These different languages use the same alphabets but different combinations of the same symbols to denote different objects (French, Italian, Spanish, Portuguese, Catalan) as opposed to different codes (languages which uses different alphabets like Spanish and Mandarin); however, what we find is analog to a single universal language.

Their most convincing argument was the importance of molybdenum in organic processes and its relative scarcity on Earth. They had argued that living organisms should bear the stamp of the environment in which they originated. Organisms, Crick and Orgel held, would be unlikely to develop a dependency on elements that were extremely rare as organisms that relied on elements which were more abundant would be favored by selection.  An organisms that was able to substitute the rare element for one which has similar biochemical properties but is more frequent would have a clear advantage.

http://blogs.scientificamerican.com/guest-blog/2013/01/09/the-origins-of-directed-panspermia/