Chemistry Reference
In-Depth Information
these structural features of DNA (and to a lesser extent RNA) are discussed in
Section 9.1.3. Before that, however, we shall discuss the biological function of DNA and
then see how the highly developed properties of oligonucleotides may find application in
bio-inspired artificial systems and materials.
9.1.2 Biological Functions and Beyond
The main biological functions of DNA are the storage and propagation of genetic infor-
mation. All the information encoding the physical manifestation and life of an organism is
stored in the form of a DNA-based library in each cell. DNA therefore makes use of a
four-letter code of the bases, adenine (A), thymine (T), guanine (G) and cytosine (C).
Triplet sequences of these bases encode for the natural 20 amino acids that are built into
the polypeptide programmed by the DNA sequence via an RNA transcript as the informa-
tion mediator [2]. In double-stranded DNA, each nucleobase of the sequence pairs with its
counter part (A with T and G with C), making the double-strand containing the same
sequence twice (once in a “sense” and once in an “antisense” fashion). This feature is not
only the fundamental basis for the processes of DNA replication and transcription but also
ensures the integrity of the code in the common case where one side of the redundant
double sequence suffers physical damage and the remaining copy serves as a template for
the repair process. A crucial parameter for an efficient and error-free copy process per-
formed by the corresponding DNA replication, transcription and repair enzymes is the
fidelity of correct base pairing. Nature has evolved the base pairs A-T and G-C (termed
“Watson-Crick” base pairs named after the discoverers of the DNA double helical struc-
ture) in a way that A pairs exclusively with T and G exclusively with C in order to con-
serve the integrity of the genetic code. Interestingly, this high degree of orthogonality of
base pairing is not only manifested on the level of (sequential) single base pair formation
events as it is the case in the processes of DNA replication, transcription and repair, but
also leads to a very high sequence specificity for the formation of longer double strands
from pairs of single strands with matching sequences [6]. In practice this means that even
a larger number (hundreds) of individual single-stranded sequences mixed with their
matching counterstrands in the same (aqueous) solution leads to the “self-sorting” of the
system to give a product mixture containing only double-strands composed of matching,
error-free sequences. A prerequisite to the success of this experiment, however, is that the
sequences are not too similar, not too short and that the system is given enough time and
thermal energy to equilibrate from an initial chaos of kinetically formed, mispaired struc-
tures to the thermodynamic minimum being the sum of all perfectly paired combinations.
This is usually best achieved by heating the mixture of single-strands in a buffered, aque-
ous solution containing a rather high concentration of NaCl (and sometimes MgCl 2 and
other salts) to a temperature above which all oligonucleotides should exist as unpaired
single strands (see the discussion of the DNA melting temperature in Section 9.4.2) and
subsequently allowing the system to slowly cool down to (usually) room temperature,
thereby allowing all possible combinations
to find their
thermodynamic sink
(“hybridization”).
Although this experiment surely describes a process of utmost biological significance,
we may already have noticed that this self-assembling puzzle game in which all pieces
find their designated counter parts just depending on their intrinsic, preprogrammed
Search WWH ::




Custom Search