Biopolym. Cell. 1988; 4(1):20-27.
http://dx.doi.org/10.7124/bc.00020D
Structure and Function of Biopolymers
Measurement ob DNA-protein binding constants by means of chromatograph «Milichrom» —computer complex
1Kalambet Yu. A., 1Burova E. I., 1Juchkov A. A., 1Knorre V. L., 1Alexandrov A. A.
  1. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR

Abstract

The method of gel-chromatography is used to determine the constants of DNA-protein binding. The complex consisting of multiwave scanning chromatograph «Milichrom» and computer «Iskra-226» is used as a registering device. The software for this complex allows determining DNA and protein concentrations at any moment. Information on time dependence of DNA and protein concentrations is used to determine the constants of DNA-protein binding. The method is applied to investigate the interaction of RNA-polymerase of E. coli by a number of plasmids and four one-stranded oligodesoxyribonucleotides — ihe fragments of E. coli promoters.
Full text: (PDF, in Russian)

References

[1] Raju EV, Davidson N. Bindings of RNAse to denatured and native deoxyribonucleic acids. Biopolymers. 1969; 8(6):743-55.
[2] Frankel AD, Ackers GK, Smith HO. Measurement of DNA-protein equilibria using gel chromatography: application to the HinfI restriction endonuclease. Biochemistry. 1985;24(12):3049-54.
[3] Volodin AA, Shepelev VA, Kosaganov YN. Stoichiometry and kinetics of complex formation by the recA protein and a double-stranded DNA. FEBS Lett. 1982;145(1):53-6.
[4] Shepelev VA, Kosaganov YuN, Lazurkin YuS. Interaction of the HMG1 protein with nucleic acids. FEBS Lett. 1984;172(2):172-6.
[5] Baram GI, Grachev MA, Komarova NI, Perelroyzen MP, Bolvanov YuA, Kuzmin SV, Kargaltsev VV, Kuper EA. Micro-column liquid chromatography with multi-wave-length photometric detection. J Chromatogr. 1983; 264(1):69-90.
[6] Oka A, Nomura N, Morita M, Sugisaki H, Sugimoto K, Takanami M. Nucleotide sequence of small ColE1 derivatives: structure of the regions essential for autonomous replication and colicin E1 immunity. Mol Gen Genet. 1979;172(2):151-9.
[7] Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103-19.
[8] Burgess RR, Jendrisak JJ. A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry. 1975;14(21):4634-8.
[9] Chamberlin MJ, Nierman WC, Wiggs J, Neff N. A quantitative assay for bacterial RNA polymerases. J Biol Chem. 1979;254(20):10061-9.
[10] Cherny DI, Aleksandrov AA, Zarudnaya MI, Kosaganov YN, Lazurkin YS, Beabealashvilli RS, Svochkina LP. Investigation of the binding of Escherichia coli RNA polymerase to DNA from bacteriophages T2 and T7 by kinetic formaldehyde method and electron microscopy. Eur J Biochem. 1977;79(1):309-17.
[11] McGhee JD, von Hippel PH. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 1974;86(2):469-89.
[12] deHaseth PL, Lohman TM, Burgess RR, Record MT Jr. Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: differences in the binding behavior of core and holoenzyme. Biochemistry. 1978;17(9):1612-22.
[13] Revzin A, Woychik RP. Quantitation of the interaction of EScherichia coli RNA polymerase holoenzyme with double-helical DNA using a thermodynamically rigorous centrifugation method. Biochemistry. 1981;20(2):250-6.
[14] Giacomoni PU, Delain E, Le Pecq JB. Electron microscopy analysis of the interaction between Escherichia coli DNA-dependent RNA polymerase and the replicative form of phage fd DNA. 1. Mapping of the binding sites. Eur J Biochem. 1977;78(1):205-13.
[15] Giacomoni PU, Delain E, Le Pecq JB. Electron microscopy analysis of the interaction between Escherichia coli DNA-dependent RNA polymerase and the replicative form of phage fd DNA. 2. Analysis of the dissociation kinetics. Eur J Biochem. 1977;78(1):215-20.
[16] Seeburg PH, Nüsslein C, Schaller H. Interaction of RNA polymerase with promoters from bacteriophage fd. Eur J Biochem. 1977;74(1):107-13.
[17] Knorre VL, Savinkova LK, Salganik RI. Oligonucleotide sequences selectively bound by Escherichia coli RNA polymerase. Biopolym. Cell. 1985; 1(6):283-92.
[18] Chamberlin MJ. The selectivity of transcription. Annu Rev Biochem. 1974;43(0):721-75.
[19] Melançon P, Burgess RR, Record MT Jr. Direct evidence for the preferential binding of Escherichia coli RNA polymerase holoenzyme to the ends of deoxyribonucleic acid restriction fragments. Biochemistry. 1983;22(22):5169-76.