Skip to main content
SpringerLink
Log in

The Role of Water in the EcoRI-DNA Binding

  • Chapter
Restriction Endonucleases

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 14))

Abstract

In many respects, Type II restriction endonucleases are prototypical DNA-binding proteins. In order to avoid catastrophic consequences for the cell, however, these enzymes must be far more stringent in recogn ition of their target sequences and subsequent DNA cleavage than other specific sequence recognition proteins that regulate gene activity. In contrast to E. Coli Lac and λ Cro repressors, for example, that show gradually decreasing binding energies as the recognition sequence is changed (Frank et al. 1997; Takeda et al. 1992), many restriction nucleases are exquisitely specific. EcoRI will bind to its recognition sequence, GAATTC, with an association equilibrium constant Ka,sp∼1011 M−1 and to a completely nonspecific sequence with Ka,nonsp ∼107M−1. A change of even a single base pair is sufficient to decrease the binding constant at least by 103, bringing it within a factor ∼10 or less of nonspecific binding (Lesser et al. 1990).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Courtenay ES, Capp MW, Anderson CF, Record MT Jr (2000) Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of “osmotic stress” experiments in vitro. Biochemistry 39:4455–4471

    Article  PubMed  CAS  Google Scholar 

  • Davis-Searles PR, Saunders AJ, Erie DA, Winzor DJ, Pielak GJ (2001) Interpreting the effects of small uncharged solutes on protein-folding equilibria. Annu Rev Biophys Biomol Struct 30:271–306

    Article  PubMed  CAS  Google Scholar 

  • Frank DE, Saecker RM, Bond JP, Capp MW, Tsodikov OV, Melcher SE, Levandovski MM, Record MT Jr (1997) Thermodynamic of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a nonspecific site. J Mol Biol 267:1186–1206

    Article  PubMed  CAS  Google Scholar 

  • Fried MG, Stickle DF, Smirnakis KV, Adams C, MacDonald D, Lu P (2002) Role ofhydration in the binding of lac repressor to DNA. J Biol Chem 277:50676–50682

    Article  PubMed  CAS  Google Scholar 

  • Garner MM, Rau DC (1995) Water release associated with specific binding of gal repressor. EMBOJ 14:1257–1263

    CAS  Google Scholar 

  • Ha J-H, Spolar RS, Record MT Jr (1989) Role of the hydrophobic effect in stability of sitespecific protein-DNA complexes. J Mol Biol 209:801–816

    Article  PubMed  CAS  Google Scholar 

  • Janin J (1999) Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. Structure 7:R277–R279

    Article  PubMed  CAS  Google Scholar 

  • Jen-Jacobson L (1997) Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers 44:153–180

    Article  PubMed  CAS  Google Scholar 

  • Jen-Jacobson L, Kurpiewski M, Lesser D, Grable J, Boyer HW, Rosenberg JM, Greene PJ (1983) Coordinate ion pair formation between EcoRI endonuclease and DNA. J Biolchem 258:14638–14646

    CAS  Google Scholar 

  • Jen-Jacobson L, Lesser D, Kupriewski M (1986) The enfolding arms of EcoRI endonuclease: role in DNA binding and cleavage. Cell 45:619–629

    Article  PubMed  CAS  Google Scholar 

  • Khrapunov S, Brenowitz M (2004) Comparison of the effect of water release on the interaction of the Saccharomyces cerevisiae TATA binding protein (TBP) with “TATA box” sequences composed of adenosine or inosine. Biophys J 86:371–383

    Article  PubMed  CAS  Google Scholar 

  • Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM (1990) Refinement of EcoRI endonuclease crystal structure: a revised protein change tracing. Science 249:1307–1309

    Article  PubMed  CAS  Google Scholar 

  • Leikin S, Parsegian VA, Rau DC (1993) Hydration Forces. Annu Rev Phys Chem 44:369–395

    Article  PubMed  CAS  Google Scholar 

  • Lesser DR, Kurpiewski MR, Jen-Jacobson L (1990) The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science 250:776–786

    Article  PubMed  CAS  Google Scholar 

  • Lesser D, Kurpiewski MR, Waters T, Connolly BA, Jen-Jacobson L (1993) Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. Proc Natl Acad Sci USA 90:7548–7552

    Article  PubMed  CAS  Google Scholar 

  • Li L, Matthews KS (1997) Differences in water release with DNAbinding by ultrabithorax and deformed homeodomains. Biochemistry 36:7003–7011

    Article  PubMed  CAS  Google Scholar 

  • Lohman TM (1985) Kinetics of protein-nucleic acid interactions: use of salt effects to probe mechanisms of interaction. CRC Crit Rev Biochem 19:191–245

    Article  Google Scholar 

  • Lundback T, Hansson H, Knapp S, Ladenstein R, Hard T (1998) Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus. J Mol Biol 276:775–786

    Article  PubMed  CAS  Google Scholar 

  • Lynch TW, Sligar SG (2000) Macromolecular hydratoion changes associated with BamHI binding and catalysis. J Biol Chem 275:30561–30565

    Article  PubMed  CAS  Google Scholar 

  • Lynch TW, Sligar SG (2002) Experimental and theoretical high pressure strategies for investigating protein-nucleic acid assemblies. Biochim Biophys Acta 1595:277–282

    Article  PubMed  CAS  Google Scholar 

  • Lynch TW, Kosztin D, McLean MA, Schulten K, Sligar SG (2002) Dissecting the molecular origins of specific protein-nucleic acid recognition: hydrostatic pressure and molecular dynamics. Biophys J 82:93–98

    Article  PubMed  CAS  Google Scholar 

  • McClarin JA, Frederick CA, Wang BC, Greene P, Boyer HW, Grable J, Rosenberg JM (1986) Structure of the DNA-EcoRI endonuclease recognition complex at 3Å resolution. Science 234 (4783):1526–1541

    Article  PubMed  CAS  Google Scholar 

  • Minton AP (1998) Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. Methods Enzymol 295:127–149

    Article  PubMed  CAS  Google Scholar 

  • Newman M., Strzelecka T., Dorner LF, Schildkraut I, Aggarwal AK (1995) Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNAbinding. Science 269:656–663

    Article  PubMed  CAS  Google Scholar 

  • Parsegian VA, Rand RP, Rau DC (1995) Macromolecules and water: probing with osmotic stress. Methods Enzymol 259:43–94

    Article  PubMed  CAS  Google Scholar 

  • Parsegian VA, Rand RP, Rau DC (2000) Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives. Proc Natl Acad Sci USA 97:3987–3992

    Article  PubMed  CAS  Google Scholar 

  • Pingoud A, Jeltsch A (1997) Recognition and cleavage of DNA by Type II restriction endonucleases. Eur J Biochem 246:1–22

    Article  PubMed  CAS  Google Scholar 

  • Pingoud A, Jeltsch A (2001) Structure and function of Type II restriction endonucleases. Nucleic Acids Res 15:3705–3727

    Article  Google Scholar 

  • Poon J, Bailey M, Winzor DJ, Davidson BE, Sawyer WH (1997) Effects of molecular crowding on the interaction between DNA and the Escherichia coli regulatory protein TyrR. Biophys J 73:3257–3264

    Article  PubMed  CAS  Google Scholar 

  • Record MT Jr, Spolar RS(1990) Some thermodynamic principles of nonspecific and sitespecific protein-DNA interactions. In: Revzin A (ed) The biology of nonspecific DNA-protein interactions. CRC Press, Boca Raton, pp 33–69

    Google Scholar 

  • Record MT Jr, Zhang W, Anderson CF (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv Prot Chem 51:281–353

    Article  CAS  Google Scholar 

  • Robinson CR, Sligar SG(1993) Molecular recognition mediated by bound water. Amechanism for star activity of the restriction endonuclease EcoRI. J Mol Biol 234:301–306

    Article  Google Scholar 

  • Robinson CR, Sligar SG (1995a) Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNAinteractions. Method Enzymol 259:395–427

    Article  CAS  Google Scholar 

  • Robinson CR, Sligar SG (1995b) Heterogenity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, PvuII, and EcoRV specificity. Proc Natl Acad Sci USA 92:3444–3448

    Article  PubMed  CAS  Google Scholar 

  • Robinson CR, Sligar SG (1996) Participation of water in Hin recombinase-DNA recognition. Protein Sci 5:2119–2124

    Article  PubMed  CAS  Google Scholar 

  • Robinson CR, Sligar SG (1998) Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Proc Natl Acad Sci USA 95:2186–2191

    Article  PubMed  CAS  Google Scholar 

  • Sidorova N, Rau DC (1996) Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences. Proc Natl Acad Sci USA 93:12272–12277

    Article  PubMed  CAS  Google Scholar 

  • Sidorova N, Rau DC (1999) Removing water from and EcoRI-noncognate DNA complex with osmotic stress. J Biomol Struct Dynam 17:19–31

    Article  CAS  Google Scholar 

  • Sidorova N, Rau DC (2000) The dissociation rate of the EcoRI-DNA specific complex is linked to water activity. Biopolymers 53:363–368

    Article  PubMed  CAS  Google Scholar 

  • Sidorova N, Rau DC (2001) Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding. J Mol Biol 310:801–816

    Article  PubMed  CAS  Google Scholar 

  • Silva JL, Fougel D, Royer CA (2001) Presure provides new insights into protein folding, dynamics and structure. Trends Biochem Sci 26:612–618

    Article  PubMed  CAS  Google Scholar 

  • Spolar RS, Record MT, Jr, (1994) Coupling of local folding to site-specific binding of proteins to DNA. Science 263:777–784

    Article  PubMed  CAS  Google Scholar 

  • Stanford NP, Szczelkun MD, Marko JF, Halford SE (2000) One-and three-dimensional pathways for proteins to reach specific DNAsites. EMBO J 19:6546–6557

    Article  PubMed  CAS  Google Scholar 

  • Takeda Y, Ross PD, Mudd CP (1992) Thermodynamics of Cro protein-DNA interactions. Proc Natl Acad Sci USA 89:8180–8184

    Article  PubMed  CAS  Google Scholar 

  • Timasheff SN (1993) The control of protein stability and association by weak interactions with water: how do solvents affect these processes. Annu Rev Biophys Biomol Struct 22: 27–65

    Article  Google Scholar 

  • Timasheff SN (1998) Control of protein stability and reactions by weakly interacting cosolvents: the simplicity of the complicated. Adv Protein Chem 51:355–432

    Article  PubMed  CAS  Google Scholar 

  • Viadiu H, Aggarwal AK (2000) Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Mol Cell 5:889–895

    Article  PubMed  CAS  Google Scholar 

  • Vossen KM, Wolz R, Daugherty MA, Fried MG (1997) Role of macromolecular hydration in the binding of the Escherichia coli cyclic AMP receptor to DNA. Biochemistry 36:11640–647

    Article  PubMed  CAS  Google Scholar 

  • Wenner JR, Bloomfield VA (1999) Osmotic pressure effects on EcoRV cleavage and binding. J Biomol Struct Dynam 17:461–471

    Article  CAS  Google Scholar 

  • Wright DJ, Jack WE, Modrich P (1999) The kinetic mechanism of EcoRI endonuclease. J Biol Chem 274:31896–31902

    Article  PubMed  CAS  Google Scholar 

  • Wu J, Parhurst KM, Powell RM, Brenowitz M, Parkhurst LJ (2001) DNA bends in TATA-binding protein-TATA complexes in solution are DNAsequence-dependent.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bld. 9, Room 1E108, Bethesda, Maryland, 20892, USA

    N. Sidorova & D. C. Rau

Authors
  1. N. Sidorova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. C. Rau
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute for Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35392, Giessen, Germany

    Alfred M. Pingoud

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Sidorova, N., Rau, D.C. (2004). The Role of Water in the EcoRI-DNA Binding. In: Pingoud, A.M. (eds) Restriction Endonucleases. Nucleic Acids and Molecular Biology, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18851-0_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-18851-0_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-62324-0

  • Online ISBN: 978-3-642-18851-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation