DNA Chemical Modifications

By Dr Ananya Mandal, MD

DNA is the basic building block of the genes that form the instructions to the cells on their birth, maturity, functions and eventually death.

Understanding the chemistry of DNA is possibly the most important discovery of the last century. DNA not only helps in understanding hereditary ailments, diagnosis of those at risk and some aspects of genetic therapy, it also helps in manufacture of drugs to treat several genetic diseases.

Chemistry of DNA

  • The DNA molecule is negatively charged. It has a phosphate backbone that gives it the negative charge. This property is important when samples with DNA are subjected to tests like electrophoresis.
  • DNA is soluble in water.  It is generally stored in a buffered solution in the laboratory. A buffer contains chemical buffer Tris (to control pH) and the chelating agent EDTA that helps trap cofactors for enzymes that can attack DNA.
  • DNA is insoluble in ethanol or purified alcohol

Denaturation and renaturation of DNA

DNA can be denatured and renatured. Denaturation is essentially opening up of the strands of the DNA with heat. With renaturation the strands cool off and rebind with each other.

What happens on the molecular level is breakage or “melting” of the hydrogen bonds between bases on different strands giving rise to two single polynucleotide strands.  This process is called denaturation. 

If conditions are favourable the process can be reversed and DNA strands can reanneal. Renaturation of two strands occurs efficiently only when the sequences of base pairs are complementary for example A to T and G to C.

DNA absorption of ultraviolet light

DNA absorbs ultraviolet light. The bases of the DNA called purine and pyrimidine bases absorb light strongly in the ultraviolet range with most absorption at 260 nm. 

Since absorption of light is fixed for fixed amount of DNA the amount of light absorbed when passed through a DNA solution can be analysed and this gives the concentration of DNA in the solution.

DNA staining with ethidium bromide

DNA can be stained with chemical ethidium bromide.  Ethidium bromide (EtBr) is a molecule that can insert between base pairs of the double helix. This leads to better visualization of DNA because the chemical is fluorescent when exposed to ultraviolet light. 

Normal DNA is invisible and can be photographed after it is stained with EtBr. The amount of fluorescence in a DNA solution can be measured and this gives an idea regarding the total mass of DNA in a solution.

Exposure to DNA altering chemicals and human cancers

There are several human cancers that are associated with exposure to DNA altering or genotoxic chemicals. There is typically a long period of time (over years) between early events that include initial chemical exposure, the onset of DNA damage and the fixation of mutations or changes in the DNA, and the subsequent appearance of a tumour.

DNA damage is an important first step in this carcinogenic or cancer causing process. Chemical carcinogens can cause the formation of carcinogen–DNA adducts or may modify the DNA with alterations in its ultrastructure.

The cell attempts to repair many types of DNA damage or may die as the protective measure. But these efforts may fail and residual DNA damage can lead to the insertion of an incorrect base during DNA replication and alter protein formations. The best known example is lung cancer and oral cancer caused by tobacco.

Reviewed by , BA Hons (Cantab)

Further Reading

Last Updated: Oct 14, 2012

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