Biopolym. Cell. 1987; 3(6):289-294.
Structure and Function of Biopolymers
Preference of BspRI restrictase as to the proper sites on DNA
1Sagitov V. R., 1Metlitskaya A. Z., 1Aleksandrov A. A.
  1. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR


Relative hydrolysis rates are measured for 15 BspRI sites (GGCC) on pBR322 and pUC19 plasmids and for 4 sites on pAO3 plasmid. Some features of nucleotide sequences in 5'-direction from the site have been found: the sequence CPuT or its part PuT adjacent to the site with high hydrolysis rate; PuPu pair in —1-2 position and/or A in —3 position relative to the boundary of sites with low hydrolysis rate; some combinations of these features, but T always in —1 position for sites with intermediate rates. Relative hydrolysis rates of sites are the same for supercoiled and linear DNAs. An attempt is made to explain these results in terms of peculiarities of local DNA structure near the restriction site.


[1] Drew HR, Travers AA. Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities. Nucleic Acids Res. 1985;13(12):4445-67.
[2] Thomas M, Davis RW. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975;91(3):315-28.
[3] Forsblom S, Rigler R, Ehrenberg M, Philipson L. Kinetic studies on the cleavage of adenovirus DNA by restriction endonuclease Eco RI. Nucleic Acids Res. 1976;3(12):3255-69.
[4] Armstrong K, Bauer WR. Preferential site-dependent cleavage by restriction endonuclease PstI. Nucleic Acids Res. 1982;10(3):993-1007.
[5] Armstrong KA, Bauer WR. Site-dependent cleavage of pBR322 DNA by restriction endonuclease HinfI. Nucleic Acids Res. 1983;11(12):4109-26.
[6] Nath K, Azzolina BA. Cleavage properties of site-specific restriction endonucleases. Gene Amplif Anal. 1981;1:113-30.
[7] Gingeras TR, Brooks JE. Cloned restriction/modification system from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 1983;80(2):402-6.
[8] Wolfes H, Fliess A, Pingoud A. A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI. Eur J Biochem. 1985;150(1):105-10.
[9] Parker RC, Watson RM, Vinograd J. Mapping of closed circular DNAs by cleavage with restriction endonucleases and calibration by agarose gel electrophoresis. Proc Natl Acad Sci U S A. 1977;74(3):851-5.
[10] Fersht A. Structure and mechanism of action of enzymes. Moscow, Mir, 1980; 432 p.
[11] Koncz C, Kiss A, Venetianer P. Biochemical characterization of the restriction-modification system of Bacillus sphaericus. Eur J Biochem. 1978;89(2):523-9.
[12] Maniatis T., Fritsch E. F., Sambrook J. Molecular cloning: a laboratory manual New York: Cold Spring Harbor Lab. publ., 1982 545 p.
[13] Sutcliffe JG. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43 Pt 1:77-90.
[14] 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.
[15] 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.
[16] Lu AL, Jack WE, Modrich P. DNA determinants important in sequence recognition by Eco RI endonuclease. J Biol Chem. 1981;256(24):13200-6.
[17] Frederick CA, Grable J, Melia M, Samudzi C, Jen-Jacobson L, Wang BC, Greene P, Boyer HW, Rosenberg JM. Kinked DNA in crystalline complex with EcoRI endonuclease. Nature. 1984 May 24-30;309(5966):327-31.
[18] Calladine CR. Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol. 1982;161(2):343-52.