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1H NMR study of the interaction of bacteriophage λ Cro protein with the O R 3 operator

II. Assignment of the non-exchangeable proton resonances of the O R 3 operator

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Abstract

The 17 base pair operator O R 3 oligonucleotide, which is the preferential binding site for the Cro repressor of phage λ, was studied by two-dimensional NMR spectroscopy. A sequential assignment procedure based on two-dimensional Nuclear Overhauser Effect (NOESY) and scalar coupling correlated (COSY) NMR spectroscopy, together with the knowledge of the oligodesoxynucleotide sequence, made it possible to assign the non-exhangeable base protons and the H1′ and the H2′-H2″ sugar protons of the O R 3 operator DNA. The pattern of the observed NOE connectivities is consistent with a right-handed helical DNA structure. The base and sugar proton assignments provide the necessary information for further studies of the O R 3 operator — Cro repressor interaction.

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Abbreviations

COSY:

correlated spectroscopy

FID:

free induction decay

NOE:

nuclear Overhauser effect

NOESY:

nuclear Overhauser effect spectroscopy

RD:

relaxation delay

TSP:

sodium 3-trimethylsilyl-(2,2,3,3-2H4)propionate

EDTA:

sodium ethylendiamine tetraacetate

References

  • Anderson WF, Ohlendorf DH, Takeda Y, Matthews BW (1981) Structure of the cro repressor from bacteriophage λ and its interaction with DNA. Nature 290:754–758

    Google Scholar 

  • Aue WP, Bartholdi E, Ernst RR (1976) Two-dimensional spectroscopy. Application to nuclear magnetic resonance. J Chem Phys 64:2229–2246

    Google Scholar 

  • Bax A, Freeman R (1981) Investigation of complex networks of spin-spin coupling by two-dimensional NMR. J Magn Res 44:542–563

    Google Scholar 

  • Buck F, Hahn K-D, Zemann W, Rüterjans H, Scheek R, Kaptein R, Beyreuther K, Sadler JR, Chernov BK, Kirpichnikov MP (1984) NMR study of repressor — operator interactions. In: Zelinka J, Balan J (eds) Metabolism and enzymology of nucleic acids, vol 5:27–40. Slovac Academy of Sciences, Bratislava

    Google Scholar 

  • Chou S-H, Hare DR, Wemmer DE, Reid BR (1983) Sequencespecific recognition of deoxyribonucleic acid. Chemical synthesis and nuclear magnetic resonance assignment of the imino protons of λ O R 3 operator deoxyribonucleic acid. Biochemistry 22:3037–3041

    Google Scholar 

  • Clore GM, Gronenborn AM (1983) Sequence-dependent structural variations in two right-handed alternating pyrimidine-purine DNA oligomers in solution determined by nuclear Overhauser enhancement measurements. EMBO J 2:2109–2115

    Google Scholar 

  • Clore GM, Gronenborn AM (1984) A nuclear-Overhauser-enhancement study of the solution structure of a double-stranded DNA undecamer comprising a portion of the specific target site for the cyclic-AMP-receptor protein in the gal operon. Eur J Biochem 141:119–129

    Google Scholar 

  • Feigon J, Leupin W, Denny WA, Kearns DR (1983) Two-dimensional proton nuclear magnetic resonance investigation of the synthetic DNA decamer d(ATATCGATAT) 2. Biochemistry 22:5943–5951

    Google Scholar 

  • Gurevich AZ, Barsukov IL, Arseniev AS, Bystrov VF (1984) Combined COSY-NOESY experiment. J Magn Res 56:471–478

    Google Scholar 

  • Hare DR, Wemmer DE, Chou S-H, Drobuy G, Reid BR (1983) Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional NMR methods. J Mol Biol 171:319–336

    Google Scholar 

  • Hilbers CW (1979) Hydrogen-bonded proton exchange and its effect on NMR spectra of nucleic acids. In: Shulman RG (ed) Biological applications of magnetic resonance. Academic Press, New York, pp 1–43

    Google Scholar 

  • Kirpichnikov MP, Hahn K-D, Buck F, Rüterjans H, Chernov BK, Kurochkin AV, Skryabin KG, Bayev AA (1984) 1HNMR study of the interaction of bacteriophage λ Cro protein with the O R 3 operator. Nucl Acids Res 12:3551–3561

    Google Scholar 

  • Kurochkin AV, Chernov BK, Skryabin KG, Kirpichnikov MP, Bayev AA (1984) Interaction between Cro repressor and the model specific binding site. Dokl Akad Nauk SSSR 275:1213–1216 and unpublished results

    Google Scholar 

  • Macura S, Huang Y, Suter D, Ernst RR (1981) Two-dimensional chemical exchange and cross-relaxation spectroscopy of coupled nuclear spins. J Magn Res 43:259–281

    Google Scholar 

  • Matthews BW, Ohlendorf DH, Anderson WF, Takeda Y (1982) Structure of the DNA-binding region of lac repressor inferred from its homology with Cro repressor. Proc Natl Acad Sci USA 79:1428–1432

    Google Scholar 

  • McKay DB, Steitz TA (1981) Structure of catabolite gene activator protein at 2.3 Å resolution suggests binding to lefthanded B-DNA. Nature 290:744–749

    Google Scholar 

  • Noggle J, Schirmer RE (1971) The nuclear Overhauser effect-Chemical applications. Academic Press, New York

    Google Scholar 

  • Ohlendorf DH, Anderson WF, Fisher RG, Takeda Y, Matthews BW (1982) The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature 298:718–723

    Google Scholar 

  • Pabo CO, Lewis M (1982) The operator-binding domains of repressor: structure and DNA recognition. Nature 298:443–447

    Google Scholar 

  • Ptitsyn OB, Finkelstein AV, Kirpichnikov MP, Skryabin KG (1982) cI and lex A repressors consist of three cro-like domains. FEBS Lett 147:11–15

    Google Scholar 

  • Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO (1982) Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298:447–451

    Google Scholar 

  • Scheek RM, Russo N, Boelens R, Kaptein R (1983) Sequential resonance assignment in DNA 1H NMR spectra by two-dimensional NOE spectroscopy. J Am Chem Soc 105:2914–2916

    Google Scholar 

  • Scheek R, Boelens R, Russo N, van Boom JH, Kaptein R (1984) Sequential resonance assignments in 1H NMR spectra of oligo nucleotides by two-dimensional NMR spectroscopy. Biochemistry 23:1317–1376

    Google Scholar 

  • Takeda Y, Ohlendorf DH, Anderson WF, Matthews BW (1983) DNA-binding proteins. Science 221:1020–1026

    Google Scholar 

  • Tran-Dinh T, Taboury J, Huynh-Dinh T, Renous S, Genissel B, Igolen J (1983) DNA fragment conformations. 1H NMR comparative studies of helix-coil transition and conformation of d(CACGTG) and d(GTGCAC). Eur J Biochem 133:579–589

    Google Scholar 

  • Weiss MA, Patel DJ, Sauer RT, Karplus M (1984a) Two-dimensional 1H NMR study of the λ operator site O L 1: a sequential assignment strategy and its application. Proc Natl Acad Sci USA 81:130–134

    Google Scholar 

  • Weiss MA, Patel DJ, Sauer RT, Karplus M (1984b) 1H NMR study of the λ operator site O L 1: assignment of the imino and adenine H2 resonances. Nucl Acids Res 12:4035–4047

    Google Scholar 

  • Wider G, Macura S, Anil Kumar, Ernst RR, Wüthrich K (1984) Homonuclear two-dimensional 1H NMR of proteins. Experimental procedures. J Magn Res 56:207–234

    Google Scholar 

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Authors and Affiliations

  1. Institute of Biophysical Chemistry, University of Frankfurt, D-6000, Frankfurt/Main 70, Federal Republic of Germany

    K. D. Hahn, F. Buck & H. Rüterjans

  2. Institute of Molecular Biology, USSR Academy of Sciences, Vavilov Street 32, B-334, Moscow, USSR

    B. K. Chernov, K. G. Skryabin & M. P. Kirpichnikov

Authors
  1. K. D. Hahn
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  2. F. Buck
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  3. H. Rüterjans
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  4. B. K. Chernov
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  5. K. G. Skryabin
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  6. M. P. Kirpichnikov
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Hahn, K.D., Buck, F., Rüterjans, H. et al. 1H NMR study of the interaction of bacteriophage λ Cro protein with the O R 3 operator. Eur Biophys J 12, 87–95 (1985). https://doi.org/10.1007/BF00260431

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  • DOI: https://doi.org/10.1007/BF00260431

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