Observance of Equilibria Between Two Oligonucleotide Conformations

Reactions (16.24) and (16.25) show the two possible duplex structures associated with the oligonucleotide, d(CGCGAATTCGCG). Optical and calorimetric studies of the melting of this duplex were conducted at various salt (NaCl) and oligonucleotide concentrations to gain information about the relative stabilities of the two structures. The results of these studies are summarized in Table 16.3. 

The calorimetric studies required strand concentrations in the range of 10-3 mol-dm-3 to achieve acceptable signal-to-noise levels. At these high strand concentrations, only one concentration-independent transition was observed. 

The optical results at low salt concentration have been interpreted in terms of the presence of the two conformations given by reactions (16.24) and (16.25). The latter structure is only partially double-stranded and incorporates the hairpin loop region in which four bases are not paired. The lower transition temperature, which is concentration-dependent, with the larger melting enthalpy is ascribed to the disruption of the full duplex structure, which is a bimolecular process. The higher temperature transition (with a lower transition enthalpy) is attributed to the disruption of the hairpin structure, which is a 

Obtained from absorption methods Obtained from calorimetric methods  

The first four oligonucleotides given in the table are self-complementary, and they form full duplex structures in biomolecular processes that are the reverse of melting. The last two oligonucleotides are only partially self-complementary. However, they share a common self-complementary core with the previous two entries in the table. The common core of these four oligonucleotides is given in bold letters in the table. 

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