Cellular and Molecular Biology Topics
Double stranded nucleic acids are stabilized mainly by hydrogen bonding between base pairs, although hydrophobic and Van der Waals interactions also play a role. DNA is more stable at lower temperatures and higher salt concentrations.
DNA can be denatured by heating over a long range of temperatures above normal physiological temperature, a process known as "melting". As the temperature starts to rise, a few base pairs are separated, and if cooled down the pairs will quickly reform. At this point, since the molecule still keeps most of its structure, the unlinked bases are near each other and can reform hydrogen bonds quickly.
But
as the temperature keeps increasing and more base pairs are separated, the
molecule starts loosing structure, complimentary bases are not near each other
any more, and the strands completely separate. This is a cooperative process:
the more base pairs are separated, the easier it is for others to separate. This
is illustrated by the "S" shape of the DNA melting curve.
The melting temperature (Tm) of a DNA molecule depends on the solution (high salt favors stability, formamide reduces stability) and the percent of G-C pairs.
The rate limiting step in the renaturation of DNA is the coming together of complementary bases of about a dozen nucleotides, a step known as nucleation. Once nucleation has occurred, the pairing of the remaining bases is fast.
Two denatured DNA strands can renature only if they can form a complimentary double helix. However, some mismatches are tolerated depending on the conditions of hybridization. High stringency conditions include low salt and high temperature (just below Tm), or the presence of formamide. Under such conditions, duplexes that mismatch by more than a few percent will not renature. Under low stringency conditions (high salt, low temperature) duplexes form and remain stable with 10-40% mismatching.
Solution and temperature can be adjusted experimentally to set the criteria for the % mismatching that will allow stable hybrids to form. The ability of DNA to renature as a hybrid can be used to identify specific fragments of DNA that are complimentary to known DNA strands. This can be used to relate sequences and homologous genes in different species.
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