Many techniques for investigating order-disorder structural transitions follow changes that occur in a spectroscopic property when the transition is induced thermally. A convenient property to follow for nucleic acids is UV absorption, which results from complex n —► Tt* and Tt —tt* transitions of the bases.53-55 A decrease in UV absorption is observed in nucleic acids upon duplex formation. This decrease is called "hypochromism".55 For short oligonucleotides, 30-40% hypochromicity at 260 or 280 nm is typical.
Hypochromism is largely due to interactions between electrons in different bases.56-61 In particular, the transition dipole moment of the absorbing base interacts with the light-induced dipoles of neighboring bases. For a polymeric array of chromophore residues, such as bases in a nucleic acid, this interaction depends on the relative orientation and separation of bases. If the bases are stacked parallel so that the transition dipole moments of adjacent bases are oriented more or less head-to-head (helical form), the probability of photon absorbance by a base is reduced due to light-induced dipoles in neighboring bases. Because the shape of the UV absorption of nucleotide bases is not significantly affected by these interactions,56 the order-disorder transition of RNA can be followed by monitoring the UV absorption at a single wavelength, typically at 260 nm for AU-rich or 280 nm for GC-rich sequences.62"64
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