Base-stacking oligonucleotides

In addition to the base-pairing disruption, this melting also destroys the stacking of bases in fixed orientations relative to one another that is observed in the duplex. Later, we will present an argument based upon thermodynamic measurements of the stabilities of synthetic oligonucleotides (small pieces of synthetic nucleic acids) that the next-nearest neighbor interactions observed in the base stacking sequence are a major contributor to the relative stabilities of duplexes. 

Table 16.5 Enthalpy and melting temperature results from calorimetric studies of oligonucleotides used to generate data for nearest-neighbor base-stacking interactions. The poly designates a strand of base-pairs of undetermined length.

C.A. Hunter, X.-J. Lu, DNA Base-stacking interactions A comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265, 603-619 (1997)... 

Sistare, M.F. Codden, S.J. Heimlich, G. Thorp, H.H. Effects of base stacking on guanine electron transfer Rate constants for G and GG sequences of oligonucleotides from catalytic electrochemistry. J. Am. Chem. Soc. 2000, 122, 4742-4749. 

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