Base stacking of DNA leads to:
Base stacking: stacking of the nucleotide chromophores in helical structures leads to the phenomenon of 'hypochromicity' (diminished ability of the bases to absorb ultraviolet light). The nucleotides may lay in a such a way that the faces of the ring are appositioned. The stacking is most likely to occur near chain termini where the bases move. It gives rigiditiy to the strand. Stacking of the DNA (and RNA) bases is a strong contributor to the overall stabilization of the double helix. It is detected by circular dichroism and optical rotatary dispersion. Hyperchromicity and hypochromicity: DNA maximally absorbs ultraviolet light at a wavelength of 260nm. Bases are principally responsble for absorption. Stacking of DNA diminishes the capacity of bases to absorb light resulting in hypochromicity. Elimination of stacking by denaturation or heating results in hyperchromicity. The explanation for this increase is that duplex DNA absorbs less ultraviolet light by about 40% than do individual DNA chains. Ref: Molecular Biology of the Gene, 5th Edition, Page 110 Images: Image showing the difference in absorbance of ultraviolet light between single stranded and double stranded DNA
Linear dichromicity
Hypochromicity
Hyperchromicity
Electrophoresis