Conformation of the OR3 operator of phage λ and its fragment in aqueous and aqueous-trifluoroethanol solutions
DOI:
https://doi.org/10.7124/bc.0001A3Abstract
Circular dichroism method (CD) was used to study conformation of the synthetic deoxy-oligonucleotide of 17 base pairs long, which is an OR3 operator of phage λ, and its 9-base pairs fragment5' TATCCCTT |GCGGTGATA|
3' ATAGGGAA |CGCCACTAT|
The stability regions of the double-stranded state are determined for these duplexes. Conformations of the short DNA fragments in aqueous solutions of different NaCl concentrations are shown to exist within the limits of B-family. A cooperative change in the CD spectra is observed in trifluoroethanol (TFE) solutions with TFE concentration typical of each oligonucleotide, which is supposed to be due to B-A transition. The B-form stabilization by terminal base pairs is evaluated using the B-A transition theory. Each terminal base pair stabilizes the B form by the value of ~1.7 kcal/mol.
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