Biopolym. Cell. 1986; 2(2):101-106.
Cell Biology
Conformation of the OR3 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.
  1. Institute of Molecular Biology, Academy of Sciences of the USSR
    Moscow, USSR


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 fragment
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.


[1] Ivanov VI, Minchenkova LE, Schyolkina AK, Poletayev AI. Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 1973;12(1):89-110.
[2] Minchenkova LE, Zimmer Ch. Reversion of theB toA transition of DNA induced by specific interaction with the oligopeptide distamycin A. Biopolymers. 1980; 19(4):823-31.
[3] Ivanov VI, Krylov DYu, Minyat EE, Minchenkova LE. B-A transition in DNA. J Biomol Struct Dyn. 1983;1(2):453-60.
[4] Seth AK, Jay E. A study of the efficiency and the problem of sulfonation of several condensing reagents and their mechanisms for the chemical synthesis of deoxyoligoribonucleotides. Nucleic Acids Res. 1980;8(22):5445-59.
[5] Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977;74(2):560-4.
[6] Vedenov A, Dykhne A, Frank-Kamenetskii M. The helix -coil transition in DNA. Uspekhi fizicheskikh nauk. 1971; 105(3):479-519.
[7] Malenkov G, Minchenkova L, Minyat E, Schyolkina A, Ivanov V. The nature of the B-A transition of DNA in solution. FEBS Lett. 1975;51(1):38-42.
[8] Ivanov VI, Minchenkova LE, Minyat EE, Frank-Kamenetskii MD, Schyolkina AK. The B to A transition of DNA in solution. J Mol Biol. 1974;87(4):817-33.