UVTAR

Ultraviolet and Temperature Assisted Reproduction of RNA and DNA

It is generally believed that RNA preceded DNA in life’s evolutionary history (RNA World hypothesis; Gilbert, 1986). This belief is based in part on the fact that, because it is less stable, RNA exists more often in single strand and shorter length segments than DNA, and can, therefore, fold in on itself or pack together to form three dimensional structures
akin to proteins, which, under certain conditions, can catalyze chemical reactions. For example, the active surfaces of ribosomes, the molecular machinery of the cell where proteins are made, consist of RNA known as ribosomal RNA (rRNA). An important catalytic activity of rRNA, which points to RNA as the first molecule of life, is its demonstrated ability to catalyze peptide bonds between amino acids to form proteins (Chang, 2000). In fact, it is becoming apparent that RNA has many extraordinary characteristics pointing to its pioneering status (Spirin, 2002).

DNA, on the other hand, is less poly-faceted and lacks a hydroxol group on its ribose sugar, allowing it to obtain its full three-dimensional conformation and to coil up to fit within
the nucleus of more modern eukaryote organisms, suggesting relevance to life at a later date. It has, therefore, been reasonable to presume that RNA preceded DNA. However, both molecules are produced with similar abiogenic yields in vitro and both appear to have similar ultraviolet absorbing and dissipating characteristics. Therefore, within the present framework, there is no overwhelming reason why DNA could not have replicated con-temporarily alongside RNA, performing the same function of catalyzing the water cycle and entropy production through UV light absorption and dissipation. The two molecules eventually forming a symbiosis allowing new possibilities for more efficient reproduction and evolution, and correspondingly, greater entropy production.

The two naturally occurring molecules RNA and DNA will, thus, be treated here on equal footing by denoting both inclusive possibilities as “RNA/DNA”, while acknowledging
that future data may favor one over the other as the first molecule of life in the context of the proposed theory. Simpler synthetic molecules, postulated as pre-RNA candidates,
such as PNA, TNA and GNA (Egholm et al., 1993), do not occur naturally and, therefore, probably have little to do with photon absorption and dissipation in the biosphere.
At temperatures above 90 C (at one atmosphere and pH 7), almost all of double strand RNA or DNA is denatured into flexible single strands (Haggis, 1974). At lower
temperatures, the amount of denaturing depends on the relative proportion of G−C base pairs, the length of the strand, the pH of the solvent (very low and very high pH correlates
with more denaturing; Williams et al., 2001), and the salt concentration (higher salt concentration correlates with less denaturing). RNA has generally lower denaturing temperature than similar length DNA. Random nucleotide sequences and smaller length segments also have lower denaturing temperature. For example, random RNA formed from equal concentrations of A, G, C, and U has a melting temperature (de- fined as that temperature at which half of the double strands are denatured) of 50 C, while calf thymus DNA has a melting temperature of 87 C (Haggis, 1974). At the higher atmospheric pressures thought to have existed at the beginning of life (up to twice the present value) these denaturing temperatures may have been somewhat higher.

At the high temperatures of the surface of the seas existing
before the beginnings of life on Earth, the nucleotides
probably floated independently, unable to stack through Van
der Waals and hydrophobic interactions, or pair conjugate
through hydrogen bonding, because of their large Brownian
motion. However, the Earth’s surface gradually began to
cool, and when the sea-surface temperature cooled to below
that of the melting temperature of RNA or DNA (relevant to
the local prevailing ambient pressure, pH, and salinity) a phenomenon,
which may be called “ultraviolet and temperature
assisted RNA/DNA reproduction” (UVTAR), could have occurred.
One estimate has the surface temperature of the Earth descending
below 100 C about 4.4 billion years ago (Schwartz
and Chang, 2002). Giant impacts, extending into the “late lunar
bombardment era” of ca. 3.9 Ga, may have periodically
reset ocean temperatures to above the boiling point (Zahnle
et al., 2007). There is geochemical evidence in the form of
18O/16O ratios found in cherts of the Barberton greenstone
belt of South Africa indicating that the Earth’s surface temperature
was around 80 C at 3.8 Ga (Knauth, 1992; Knauth and Lowe, 2003), falling to 70±15 C during the 3.5–3.2 Ga
era (Lowe and Tice, 2004). These surface temperatures, existing
at the beginnings of life (ca. 3.8 Ga), are suggestively
close to the denaturing temperatures of RNA/DNA.

During daylight hours, the water at the Archean seasurface
absorbed some solar infrared light, and the aromatic
bases of RNA/DNA and amino acids absorbed solar ultraviolet
light, while other organic molecules absorbed visible
light. It is then probable that the sea-surface skin temperature
in the local neighborhood of the RNA/DNA would heat up
beyond the denaturing temperature and these would separate
into single strands by breaking the hydrogen bonds between
conjugate base pairs.

RNA/DNA strongly absorb ultraviolet radiation at around
260 nm at 1 atmosphere pressure (Haggis, 1974; Chang,
2000) due to the 1 electronic excitation of the bases
(Voet et al., 1963; Callis, 1983). The relaxation to the ground
state of UV excited DNA has been studied in detail by Middleton
et al. (2009, and references therein). An ultra-fast,
sub-picosecond, decay of the 1 excited state is observed
for the unstacked bases in single strand RNA/DNA through
vibrational cooling to the ground state by coupling to the
high frequency modes of the water solvent (Pecourt et al.,
2000, 2001). Water appears to be the most efficient of many
tested solvents (Middleton et al., 2009). Such ultra-fast deexcitation
does not appear to exist for stacked bases in double
strand RNA/DNA, which normally form long-lived, 100-
picosecond, exciton states. This may be partly due to the fact
that hydrophobic interactions exclude water from the interior
of stacked double strand RNA/DNA (Pecourt et al., 2000,
2001).

It has been suggested that these surprising characteristics
are not fortuitous, but rather remnants from earlier days
when life was exposed to significantly higher doses of UV
radiation. The argument is that these characteristics would
have been favored by natural selection since such a highly
efficient non-radiative decay significantly lowers the rate of
RNA/DNA damage through photo-reactions, thereby reducing
the need for frequent repair (Crespo-Hern´andez et al.,
2004; Middleton et al., 2009).

Sagan (1973) pointed out that the rapid UV photon dissipation
characteristics of nucleic acid bases would provide an
important selective advantage to RNA and DNA over other
more easily synthesized organic molecules under the harsh
UV conditions of prebiotic Earth. Mulkidjanian et al. (2003)
have confirmed this using simple Monte Carlo simulations.
However, the interpretation given here of these surprising absorption
and relaxation characteristics of RNA/DNA is more
profound; apart from conferring stability to these molecules
under intense UV radiation, these characteristics confer remarkable
entropy producing potential to these molecules due
to the efficient absorption of UV light and its rapid dissipation
into heat.

As night came, with no light to absorb, the surface
of the sea would cool through evaporation, radiation, and
conduction of heat to the atmosphere, to a temperature below
which the single strands of RNA/DNA could begin to
act as templates and hydrogen bond through their bases with
conjugate nucleotides or oligonucleotide segments floating
nearby. New, complementary double-strand RNA/DNA
would thus be formed at the sea surface during the cool periods
overnight. An alternative form of cooling of the ocean
surface may have been provided by hurricanes which are
known to have an important effect on reducing the surface
temperatures of seas (Manzello et al., 2007). Given the high
sea-surface temperatures existing on early Earth, and a cold
upper atmosphere (Tian et al., 2005), hurricanes would have
been much more prevalent than at present.

As the Sun rose, about 7 h after setting (the rotation of the
Earth was more rapid 3.8 billion years ago) the sea-surface
skin layer would again heat up through the absorption of ultraviolet
and visible light on the organic material, and the
absorption on water of some infrared light that could penetrate
the clouds and water vapor in the atmosphere. Using the
Archean solar intensity spectrum at the Earth’s surface as determined
by Cnossen et al. (2007) and the absorption coeffi-
cient for UV light between 200 nm and 300 nm of 0.78 cm−1
determined from estimated prebiotic concentrations of the
nucleic acids (Miller, 1998; see Sect. 3), while assuming
similar absorption in the visible as that of today’s oceans of
8.0×10−3 cm−1, and that the diffuse downward and upward
long-wave energy flux approximately cancel (Webster, 1994)
it can be estimated that diurnal temperature cycling at the
Archean sea-surface skin layer could have had an amplitude
as large as 4K (Michaelian, 2010a). Schlüssel et al. (1990)
have measured a diurnal temperature variation at the skin surface
of today’s oceans as large as 5 K.

Direct absorption of a UV photon of 260 nm on
RNA/DNA (which occurs preferentially on one or two of
the nucleic acid bases; Middleton et al., 2009) would leave
4.8 eV of energy locally which, given the heat capacity of
water, would be sufficient energy to raise the temperature by
an additional 3K of a local volume of water that could contain
up to 50 base pairs (Michaelian, 2010a). Given that the
full width of the denaturing curve for RNA/DNA is between
4 and 10K (depending on the G−C content) the sea-surface
temperature in the neighborhood of the segment which absorbed
the UV photon would be raised again beyond the
denaturing temperature of RNA/DNA and the double strand
would separate, providing, in this way, a new generation of
single strand RNA/DNA that could serve as new template for
complementary strand polymerization during the subsequent
cool period. Experimental evidence (Hagen et al., 1965;
Roth and London, 1977) indicates that UV irradiation does
indeed induce denaturation of DNA held in water baths at a
fixed temperature, and that the denaturing effect of UV light
increases as the temperature of the bath approaches DNA
melting temperature.

A temperature assisted mechanism for RNA/DNA reproduction
is not hypothetical; the procedure of repetitive heating and cooling is a process known as polymerase chain
reaction (Mullis, 1990) that is used today in the laboratory
to amplify exponentially a particular DNA or RNA segment
of interest. The enzyme polymerase is used to speed up the
polymerization of nucleotides on the single strand templates
during the low temperature period.

Ultraviolet and temperature assisted RNA/DNA reproduction
would have been enhanced by a number of natural phenomenon.
First, single strand RNA/DNA absorbs from 20%
to 40% more ultraviolet light than does double strand. This
effect, known as hypochromism (Bolton and Weiss, 1962;
Chang, 2000), is related to the orientation of the electric
dipoles of the bases, stacked in fixed relation one above
the other in the double helix. On denaturation, the orientation
of the dipoles is random and the absorption intensity
increases. Double strand RNA/DNA is also less efficient
(rapid) at transforming the electronic excitation energy into
heat than single strand randomly stacked DNA (Middleton et
al., 2009). Both these effects would provide positive feedback
for augmenting entropy production by stimulating denaturation
under solar UV light and by reducing the possibility
of recombination of the separated strands.

A second class of phenomena that could have enhanced
UVTAR is the diurnal variation of the chemical properties
of the sea-surface microlayer. Both the pH and formaldehyde
concentration of the microlayer peak in late afternoon
due, in part, to causes predicted to be more relevant during
the Archean; lower CO2 dissolution in warmer water (Wootton
et al., 2008) and increased UV photochemical reaction
rates (Zhou and Mopper, 1997), respectively. Both high pH
and formaldehyde concentration promote lower DNA/RNA
denaturing temperatures (Williams et al., 2001; Traganos et
al., 1975). Salinity also reaches a maximum at late afternoon
due to increased water evaporation in the microlayer (Zhang
et al., 2003), but this would produce a lesser effect opposing
denaturation.

Since experimental determinations with the PCR technique
give optimal (specificity and rate) annealing temperatures
of primers of about 5K below DNA melting temperatures,
these thermal and chemical diurnal variations, as well
as the longer denaturation and annealing times allowed for
by the UVTAR mechanism (hours instead of minutes for
PCR), suggest that an effective UV and temperature assisted
RNA/DNA replication mechanism could have been operating
at the Archean sea-surface. RNA/DNA at the beginning
of life did not require enzymes for its replication, reproduction
was instead promoted by the day/night fluctuation of the
sea-surface skin temperature about the denaturing temperature
of RNA/DNA.

For more on the UVTAR mechanism, please consult; K. Michaelian, Thermodynamic Dissipation Theory of the Origin of Life, Earth Syst. Dynam., 2, 37–51, 2011
www.earth-syst-dynam.net/2/37/2011/  doi:10.5194/esd-2-37-2011

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