Biopolym. Cell. 1990; 6(6):52-58.
A computer-aided search for giant DNA-protein complexes
1Lukina N. I., 2Soidla T. R.
  1. Leningrad Polytechnical Institute
    Leningrad, USSR
  2. B. P. Konstantinov Institute of Nuclear Physics, Academy of Sciences of the USSR
    Gatchina, Leningrad distr., USSR

Abstract

Two simple programs to detect extensive spatial asymmetries of DNA were created. The programs were used to study the 2 u,m plasmid of Saccharomyces yeast. A nearly 600 bp. uninterrupted region of special spatial orientation of G-C base pairs was found covering the REP 3 locus. The anomaly was obvious when estimating the helix lead approx. 104.4 (but not at 1 ,10:0 or 10.6). It is supposed that the region corresponds to a giant non-nucleosomal DNA-protein complex supposedly of an «oozing» mechanism according to the classification by Ptashne (19*86). The complex is also indicated by some recent experimental results. The new programs can be used for searching giant DNA-protein complexes.

References

[1] Johnson PF, McKnight SL. Eukaryotic Transcriptional Regulatory Proteins. Annu Rev Biochem. 1989;58(1):799–839.
[2] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[3] Goulet I, Zivanovic Y, Prunell A. Helical repeat of DNA in solution. The V curve method. Nucleic Acids Res. 1987;15(7):2803-21.
[4] Satchwell SC, Drew HR, Travers AA. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986;191(4):659-75.
[5] Hartley JL, Donelson JE. Nucleotide sequence of the yeast plasmid. Nature. 1980;286(5776):860-5.
[6] So?dla TR, Nevzgliadova OV. A 2-um plasmid of Saccharomyces. Mol Biol (Mosk). 1987;21(6):1467-79.
[7] Murray JA, Cesareni G. Functional analysis of the yeast plasmid partition locus STB. EMBO J. 1986;5(12):3391-9.
[8] Fagrelius TJ, Livingston DM. Location of DNAase I sensitive cleavage sites in the yeast 2 micron plasmid DNA chromosome. J Mol Biol. 1984;173(1):1-13.
[9] Veit BE, Fangman WL. Chromatin organization of the Saccharomyces cerevisiae 2 microns plasmid depends on plasmid-encoded products. Mol Cell Biol. 1985;5(9):2190-6.
[10] Ptashne M. Gene regulation by proteins acting nearby and at a distance. Nature. 1986 Aug 21-27;322(6081):697-701.