When a cell divides, it passes on genetic information by producing
copies of its DNA. Chemists have also learned to copy DNA. In the
journal Angewandte Chemie, a German team has now introduced a new
copying technique that uses a single strand of DNA as the “master copy”,
like a cell, but does not require enzymes. Unlike earlier methods, it
allows for stepwise growth of the chain in both the direction preferred
by nature and the opposite direction typical of current DNA synthesis
techniques.
Within a cell, the DNA double strand is separated in segments during the
copying process. One of the single strands serves as the “master copy”
or template. Polymerase enzymes snap together the corresponding
nucleotides stepwise to form the new complementary strand, beginning
with a “starting segment” known as a primer. The backbone of a DNA
strand is an alternating chain of five-membered sugar rings and
phosphate groups. The chain links are formed at the 3’ and 5’ oxygen
atoms of the sugars; natural growth occurs in the 3’ direction.
One question relating to the origin of life is: How was nature able to
copy DNA or RNA strands before polymerases existed? Since the 1980s, DNA
synthesizers have allowed chemists to produce DNA strands, but without a
template or primer; the sequence is determined by the order of addition
of the reagents. Only the use of protective groups that inhibit
uncontrolled reactions and the programmed addition of the reagents
ensure that the sequence of bases is correct. This is clearly not how
nature does it. But how could template-directed primer extension
function purely chemically, with no enzymes?
More recently, different approaches have been used to develop a method
called chemical primer extension, which involves the reaction of
activated nucleotides with the end of a slightly modified DNA primer.
Clemens Richert, Andreas Kaiser, and Sebastian Spies of the University
of Stuttgart (Germany) have now developed this method further. They
found a protective group that can be removed under gentle conditions so
that the DNA duplexes made from the primer and template do not fall
apart. This allows the reactivity of the nucleotides and the terminus of
the primer to be switched on and off as desired, and the sequence
information in the template strand can be read out nucleotide by
nucleotide. For this method to work, the template and primer are both
attached to tiny spheres. As in an automated synthesizer, the reagents
and building blocks can flow over the spheres. The primer is bound to
the template through base pairing. A suitable nucleotide from the
surrounding solution docks at the next vacant binding site of the
template. The nucleotide then binds to the reactive end of the primer
through activated phosphate units. The sites that are supposed to react
are chemically altered to become more reactive than in natural DNA. The
special thing about this method is that the chain extension can be
controlled to occur in either the 3’ or the 5’ direction. This is not
known to take place in nature.
So far, this process has remained quite slow and is limited to short
sequences. Improvement should be possible through optimization of the
reaction conditions and better automation.
