A tRNA world

Knowledge about the kinetics of chemical reactions in cells is
important for an understanding of signaling pathways and
regulation. Even though there are many kinetic measurements of in
vitro reactions in literature, methods for in vivo measurements are
sparse. With help of Temperature Oscillation Optical Lock-in (TOOL)
microscopy we measure the kinetics of DNA hybridization inside
cells and detect signicant acceleration or deceleration compared to
in vitro measurements, dependent on the DNA sample. The dierences
can not be explained by molecular crowding eects. Only models that
take the background interactions with genomic DNA and RNA as well
as the activity of single stranded and double stranded binding
proteins into account, can be tted to data. The results imply that
the biological relevance of kinetic rates measured in vitro has to
be rejudged carefully. The RNA world hypothesis predicts catalytic
molecules based on RNA, as for example early replicators, as
precursor of modern biology. But how can a pool of appropriate RNA
molecules arise under early earth conditions? In a Gillespie-model,
we observe the length distribution, secondary structure and
sequences of a pool of RNA molecules in porous rocks like they
appear near sites of volcanic activity. We assume a monomer in ux,
a length dependent out ux, a random, non-templated polymerisation
and a degradation that is much stronger for single stranded than
for double stranded RNA. After equilibrium is reached, the pool is
populated with many hairpin-like structures due to the selection
pressure for hybridized strands that can be bricks for RNA
machines. Once sequence motifs and their complements appear in the
reactor, they protect each other and are present longer than
statistically expected. This "protection by hybridization" has the
same ngerprint as a weak replication. As a consequence, the pool
does not cover the full sequence space but includes more similar
sequences, which is an important condition for chemical reactions.
Replication of genetic information by RNA molecules is considered
to be a key process in the beginning of evolution. It is so crucial
that traces of this early replication are expected to be present in
key processes of modern biology. We present a replication scheme
based on hairpins derived from the sequence of tRNA that replicates
the genetic information about a succession of sequence snippets.
The replication is driven by temperature oscillations as they occur
naturally inside of porous rocks in presence of temperature
gradients, and independent on external chemical energy sources. It
is selective for correct information and shows exponential growth
rates with doubling times in the range of seconds to minutes and is
thereby the fastest early replicator in the literature. The
replication scheme can naturally be expanded to longer successions
by using double hairpins derived from full tRNA sequences by only
few mutations. By charging double hairpins with amino acids or
peptides, the proposed replication bridges the gap from the RNA
world to modern biology by oering a rudimentary translation
mechanism, that sorts amino acids to chains according to genetic
information.