Kinked DNA in crystalline complex with EcoRI endonuclease

Frederick, Christin; Grable, John; Melia, Michele; Samudzi, Cleopas T.; Jen‐Jacobson, Linda; Wang, Bi-Cheng; Greene, Patricia J.; Boyer, Herbert W.; Rosenberg, John M.

doi:10.1038/309327a0

Cited by 305 publications

(107 citation statements)

References 47 publications

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“…(0) respectively (14,15). The role of unwinding is uncertain, although it may be a mechanism for recognition of specific sequences (15). For RNA polymerase, the unwinding angle measured has varied between 2400 (7 bases) to 5800 (17 bases) and has been suggested to be a part of the mechanism for the formation of the 'open complex' required for initiation of RNA synthesis (16,17).…”

Section: Methodsmentioning

confidence: 99%

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The effect ofEscherichia coliUvr protein binding on the topology of supercoiled DNA

Grossman

1986

Nucl Acids Res

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The effects of the binding of the E. coli UvrA and UvrB proteins on the linking number (AL) of superhelical DNA has been measured. The effects of cofactor ATP structure on UvrAB-nucleoprotein complex formation revealed that nucleotide binding, not hydrolysis; is sufficient to locally unwind the DNA helix of both ultraviolet light-damaged as well as undamaged DNAs. The extent of this unwinding is of the same order of magnitude as the nucleotide distances of the double incision sites generated by the UvrABC endonucleolytic reaction. INTRODUCTIONThe E. coli uvr repair system is unique in that its specificity is sufficiently broad to accommodate a wide spectrum of seemingly different kinds of DNA damaging agents. As a consequence, organisms possessing such a system can respond to a plethora of environmental hazards without having to evolve new enzyme systems as new types of agents are introduced into its environment. Parenthetically, the spectrum of agents to which E. coli uvr mutants are sensitive is remarkably similar to the damage sensitivity of human repair-deficient skin fibroblasts derived from xeroderma pigmentosum patients (1). These findings suggest that the enzyme mechanisms may be similar and point to the significance of studying the E. coli uvr system as a model for a DNA repair deficiency amongst patients predisposed to skin cancer The incision components of the E. coli uvr repair system responsible for the initial recognition of damaged DNA consists of the UvrA protein which in the presence of ATP binds to the damaged DNA, as well as to undamaged DNA duplexes (2). The UvrA protein requires thesimultaneous presence of the UvrB and UvrC proteins to initiate a dual incision event in DNAs containing ultraviolet light induced pyrimidine dimers (3,4) and 6,4-pyrimidine-pyrimidone adducts (3), photoactivated psoralen mono-and diadducts (5), acetylaminofluorine-guanine adducts (5), cis-platinum-guanine adducts (6) and benzo[a]pyrene-guanine adducts (7). In almost all of those experiments carried out with DNA substrates of defined sequences, the dual incision events were shown to involve a 5'-incision event 7 nucleotides to a damaged site and 3-4 nucleotides 3'-to the same site. In spite of the fact that the primary chemical events are dissimilar and the extent to which these agents distort DNA, the sites of incision are

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Section: Methodsmentioning

confidence: 99%

“…The gels were stained 6 hrs in 2 Mg/ml ethidium bromide (with gentle shaking), destained for 0. (0) respectively (14,15). The role of unwinding is uncertain, although it may be a mechanism for recognition of specific sequences (15).…”

Section: Methodsmentioning

confidence: 99%

The effect ofEscherichia coliUvr protein binding on the topology of supercoiled DNA

Grossman

1986

Nucl Acids Res

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“…In their X-ray crystallographic study of the influence of base sequence on helix structure in the dodecamer [d(CGCGAATTCGCG)],, Dickerson and Drew [6] reported several structural deviations or purine-pyrimidine sequences relative to purine-purine or pyrimidine-pyrimidine sequences. The six internal residues in the Dickerson sequence and in the [7] have performed Xray analysis of the EcoRI endonuclease co-crystallized with the tridecamer [d(TCGCGAATTCGCG)I2 (again, the central six-base sequence is the EcoRI site) and found that at the GAA-TTC junction, there is a kink. Although comparison of the oligonucleotide structure in the co-crystal with that of the dodecamer in the 'pure' crystal lead Frederick et al to suggest that their structure requires the enzyme for stability, they further suggest that this kinked conformation may exist transiently for the oligonucleotide alone in solution [7].…”

Section: Theoretical (Upper Triangle) Andexperimental (Lower Triangmentioning

confidence: 99%

“…The six internal residues in the Dickerson sequence and in the [7] have performed Xray analysis of the EcoRI endonuclease co-crystallized with the tridecamer [d(TCGCGAATTCGCG)I2 (again, the central six-base sequence is the EcoRI site) and found that at the GAA-TTC junction, there is a kink. Although comparison of the oligonucleotide structure in the co-crystal with that of the dodecamer in the 'pure' crystal lead Frederick et al to suggest that their structure requires the enzyme for stability, they further suggest that this kinked conformation may exist transiently for the oligonucleotide alone in solution [7]. In any case, there is evidence for some type of conformational change in this hexamer sequence at the site of transition from purine to pyrimidine.…”

Section: Theoretical (Upper Triangle) Andexperimental (Lower Triangmentioning

confidence: 99%

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]₂ using two‐dimensional nuclear Overhauser enhancement spectroscopy

Broido

James

Zon

et al. 1985

European Journal of Biochemistry

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Proton two-dimensional nuclear Overhauser enhancement (2 D NOE) spectra in the pure absorption phase were obtained at 500 MHz for [d(GGAATTCC)], in aqueous solution at a series of mixing times. The experimental data were analyzed by comparison with theoretical spectra calculated using the complete 70 x 70 relaxation matrix including all proton dipole-dipole interactions and spin diffusion [Keepers, J. W. &James, T. L. (1984) J . M a p . Reson. 57,404-4261. The theoretical spectra at each mixing time were calculated using two structures: a standard B-form DNA structure and an energy-minimized structure based on the similarity of the six internal residues of the title octamer with those of the dodecamer [d(CGCGAATTCGCG)],, for which the crystal structure has been determined. Neither the standard B-form nor the energy-minimized structure will yield theoretical 2 D NOE spectra which accurately reproduce all peak intensities in the experimental spectra. However, many features of the experimental spectra can be represented by both the B-form and the energy-minimized structure. Sequencedependent structural characteristics are manifest in the 2 D NOE spectra, in particular at the purine-pyrimidine junction as noted previously in the crystal structure. On the whole, the energy-minimized structure appears to yield theoretical 2 D NOE spectra which mimic many, if not all, aspects of the experimental spectra. All 2 D NOE data were consistent with nanosecond correction times as implied by proton spin-lattice relaxation time measurements. But better fits of some of the 2 D NOE data using small variations in an effective isotropic correlation time suggest that there may be some local variations in mobility within the octamer duplex structure in solution.With recent advances in DNA synthesis enabling the preparation of DNA oligomers of known, specific sequence [l -41, X-ray crystallographers are examining DNA oligomers of different sequences and reporting details of sequence-dependent crystalline conformations [3, 5 -81. Questions regarding the structure of these DNA fragments in solution are also being addressed. These questions focus on the extent of preservation of the crystal structures in solution and on the manner in which the solution and crystal structures differ. On a more general level, discussion also focusses on whether or not it is accurate to speak of a molecular structure in solution and by what means may such a structure be determined. The continuing development of high-resolution NMR technology has both spurred such questions and been of great use in the quest for answers. Two-dimensional NMR (2D NMR), in particular, has developed to the point that proton spectra of biomolecules, spectra with perhaps hundreds of lines and once thought to be undecipherable, can now, in many cases, be totally assigned [I, 4,9 -111. Following assignment, both oneand two-dimensional NMR techniques enable spectroscopists to start probing in detail the solution conformations of these molecules.Correspondence to T. L. James, Departmen...

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“…Since the preference of cleavage is inversely correlated to the thermal stability of the oligodeoxynucleotide substrates, it might also be that in the course of the recognition process, a structural transition of the substrate is induced, as was reported for the EcoRI . DNA complex [30]. The feasability of this transition might depend on the stability of the duplex structure in this region.…”

Section: Discussionmentioning

confidence: 99%

A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI

Wolfes

Fließ

Pingoud

1985

European Journal of Biochemistry

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We have investigated the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI which recognize the sequence -d(GGCC)-. For this purpose decadeoxynucleotides were synthesized by the solid-phase phosphotriester method and purified by high-performance liquid chromatography. The kinetics of cleavage of these oligodeoxynucleotides were determined for the three isoschizomers with the following results.1. The sequence adjacent to the recognition site strongly influences the rate of cleavage. The preference is qualitatively the same for all three enzymes: AGGCCT > TGGCCA > GGGCCC z CGGCCG, and follows the thermal stability of the different decanucleotides. 2. Substitutions within the recognition site, namely d l for dG and dU for dC, affect the rate of cleavage differently for the three enzymes. The results can be rationalized in terms of an interaction of HaeIII with the major and minor groove of the DNA, of BspRI mainly with the minor groove and of BmRI with the major groove of DNA. It is obvious from our data that the mechanism of recognition of the Same site is different for the three isoschizomers.Type I1 restriction endonucleases recognize and cleave specific sequences in double-stranded DNA. Due to their high specificity, their structural simplicity and their ready availability they serve as convenient model systems for the investigation of specific protein/nucleic acid interactions (for review see 111). To date only a few of the approximately 400 known restriction endonucleases have been characterized with respect to their mode of interaction with their substrates. Of particular interest in this context has been the structural aspect of the high specificity of these enzymes. In order to determine which functional groups within the recognition sequence of the DNA substrate interact with the respective enzyme, different approaches have been employed. The most widely used approach has been to measure the interaction between enzymes and substrates containing nucleotide analogs in which base, sugar or phosphate moieties are modified [2 -91.In addition to contacts formed between the enzyme and the nucleotides constituting the recognition site, there is an interaction between the enzyme and nucleotides flanking the recognition site. By investigating the rates of cleavage of substrates with different flanking sequences preferences of the enzyme for particular nucleotides adjacent to the recognition site can be established [lo].We have been interested in a comparison of the structural requirements needed for the recognition of the substrate by entirely different enzymes that, however, recognize the same DNA sequence. Such a comparison provides an excellent opportunity to learn something about the fundamental principles governing specific protein/nucleic acid interactions.Correspondence to A. Pingoud, Zentrum Biochemie, Medizinische Hochschule Hannover, Konstanty-Gutschow-StraRe 8, D-3000 Hannover 61, Federal Republic of Germany Abbreviations. HPLC, high-performance liquid chromatography; M...

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Kinked DNA in crystalline complex with EcoRI endonuclease

Cited by 305 publications

References 47 publications

The effect ofEscherichia coliUvr protein binding on the topology of supercoiled DNA

The effect ofEscherichia coliUvr protein binding on the topology of supercoiled DNA

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]₂ using two‐dimensional nuclear Overhauser enhancement spectroscopy

A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI

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Kinked DNA in crystalline complex with EcoRI endonuclease

Cited by 305 publications

References 47 publications

The effect ofEscherichia coliUvr protein binding on the topology of supercoiled DNA

The effect ofEscherichia coliUvr protein binding on the topology of supercoiled DNA

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two‐dimensional nuclear Overhauser enhancement spectroscopy

A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI

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Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]₂ using two‐dimensional nuclear Overhauser enhancement spectroscopy