Accelerating chemical replication steps of RNA involving activated ribonucleotides and downstream-binding elements

Vogel, Stephanie R.; Deck, Christopher; Richert, Clemens

doi:10.1039/b510775j

Cited by 79 publications

(115 citation statements)

References 20 publications

Supporting

Mentioning

109

Contrasting

Unclassified

Order By: Relevance

“…Recent work from the Richert lab addresses this problem [39,40]. Downstream helper oligos, designed to leave a single-nucleotide gap between primer and helper oligo, into which the incoming U monomer could fit, were found to contribute significantly to the rate and extent of primer extension.…”

Section: Rate Of Template Copying Chemistrymentioning

confidence: 99%

The eightfold path to non-enzymatic RNA replication

2012

View full text Add to dashboard Cite

The first RNA World models were based on the concept of an RNA replicase -a ribozyme that was a good enough RNA polymerase that it could catalyze its own replication. Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge. At first glance the alternative, in which RNA replication is driven purely by chemical and physical processes, seems even more challenging, given that so many unsolved problems appear to stand in the way of repeated cycles of nonenzymatic RNA replication. Nevertheless the idea of non-enzymatic RNA replication is attractive, because it implies that the first heritable functional RNA need not have improved replication, but could have been a metabolic ribozyme or structural RNA that conferred any function that enhanced protocell reproduction or survival. In this review, I discuss recent findings that suggest that chemically driven RNA replication may not be completely impossible.

show abstract

Section: Rate Of Template Copying Chemistrymentioning

confidence: 99%

The eightfold path to non-enzymatic RNA replication

2012

View full text Add to dashboard Cite

show abstract

“…Hydrolysis of OAt esters, despite their reactivity towards amino and ribo primers, [21] is sufficiently slow. An exploratory study of the hydrolysis of 2 t-OAt in the assay buffer in D 2 O by NMR spectroscopy shows a half-life of 16.2 h (see Supporting Information).…”

mentioning

confidence: 99%

Chemical Primer Extension: Efficiently Determining Single Nucleotides in DNA

et al. 2005

Self Cite

View full text Add to dashboard Cite

Rapid replication: Non‐enzymatic primer extension has previously been studied in the context of prebiotic chemistry, but not for practical applications. Reactions with primers featuring a 3′‐amino‐2′,3′‐dideoxynucleotide can be rapid and selective for all four templating nucleobases (see scheme). On a chip with immobilized capture strands, 500 fmol of template suffice for single‐nucleotide determinations within 2.7 h.

show abstract

“…At the beginning of life, without any use of enzymes, RNA strands bound to longer template strands of RNA could grow in single nucleotide steps according to the base pairing rules of Watson and Crick. These duplication steps could take place on the timescale of hours (Vogel et al 2005) giving support to the theory that RNA spontaneously replicated during prebiotic evolution. Let us suppose now that the initial RNA template strands polymerized by chance in the prebiotic RNA world were circular with nucleotidic sequences similar to those of a remarkable RNA ring called Archetypal Loop AL and studied in (Demongeot and Moreira 2007): this RNA ring offers weak interaction sites (electrostatic at short distance and van der Waals at mean distance) for any polar (hydrophilic) or unpolar (hydrophobic) aminoacid present in the prebiotic medium.…”

Section: Proto-cell Boundarymentioning

confidence: 71%

Biological Boundaries and Biological Age

Demongeot

2009

Acta Biotheor

View full text Add to dashboard Cite

The chronologic age classically used in demography is often unable to give useful information about which exact stage in development or aging processes has reached an organism. Hence, we propose here to explain in some applications for what reason the chronologic age fails in explaining totally the observed state of an organism, which leads to propose a new notion, the biological age. This biological age is essentially determined by the number of divisions before the Hayflick's limit the tissue or mitochondrion in a critical organ (in the sense where its loss causes the death of the whole organism) has already used for its development and adult phases. We give a precise definition of the biological age of an organ based on the Hayflick's limit of its cells and we introduce a desynchronization index (the cell entropy) for some critical tissues or membranes, which are mainly skin, intestinal endothelium, alveoli epithelium and mitochondrial inner membrane. In these actively metabolising interface tissues or membranes, there is a rapid turnover of cells, of their cytoplasmic constituents such as proteins, and of membrane lipids. The boundaries corresponding to these tissues, cells or membranes have vital functions of interface with the environment (protection, homeothermy, nutrition and respiration) and have a rapid turnover (the total cell renewal time is in mice equal to 3 weeks for the skin, 1.5 day for the intestine, 4 months for the alveolae and 11 days for mitochondrial inner membrane) conditioning their biological age. The biological age of a tissue is made of two major components: (1) first, its embryonic age based on the distance (in number of divisions) between the birth date of its first differentiated cell and the time until it reaches its final boundary at the end of its development and (2) second, its adult age whose complement until its death is just the lapse of time made of the sum of remaining cell cycle durations authorized by its Hayflick's limit. From this definition, we calculate the global biological lifespan of an organism and revisit notions like demographic survival curves, duration and synchrony of cell cycles, living boundaries from proto-cells to organs, and embryonic and adult phases duration.

show abstract

Accelerating chemical replication steps of RNA involving activated ribonucleotides and downstream-binding elements

Abstract: Template-directed single nucleotide extension of an RNA primer with oxyazabenzotriazolides of ribonucleotides is shown to be fast and sequence-selective; downstream-binding RNA strands contribute to the acceleration of the reaction.

Cited by 79 publications

References 20 publications

The eightfold path to non-enzymatic RNA replication

The eightfold path to non-enzymatic RNA replication

Chemical Primer Extension: Efficiently Determining Single Nucleotides in DNA

Biological Boundaries and Biological Age

Contact Info

Product

Resources

About