Conformation of the OR3 operator of phage λ and its fragment in aqueous and aqueous-trifluoroethanol solutions

Ivanov, V. I.; Minchenkova, L. E.; Shchelkina, A. K.; Chernov, B. K.; Yartsev, A. P.; Kirpichnikov, M. P.

doi:10.7124/bc.0001A3

Biopolym. Cell. 1986; 2(2):101-106.

http://dx.doi.org/10.7124/bc.0001A3

Cell Biology

Conformation of the O_R3 operator of phage λ and its fragment in aqueous and aqueous-trifluoroethanol solutions

1Ivanov V. I., 1Minchenkova L. E., 1Shchelkina A. K., 1Chernov B. K., 1Yartsev A. P., 1Kirpichnikov M. P.

Institute of Molecular Biology, Academy of Sciences of the USSR
Moscow, USSR

Abstract

Circular dichroism method (CD) was used to study conformation of the synthetic deoxy-oligonucleotide of 17 base pairs long, which is an O_R3 operator of phage λ, and its 9-base pairs fragment
5' 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.

Full text: (PDF, in Russian)

References

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