DNA structural variations in the E. coli tyrT promoter

Drew, Horace R.; Travers, Andrew

doi:10.1016/0092-8674(84)90379-9

Cited by 476 publications

(385 citation statements)

References 36 publications

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“…The sensitivity of deoxyribonuclease I action to structural variations of DNA which influence the width of the minor groove has been well documented [24][25][26][27][28][29]. Deoxyribonuclease I binding results in an opening of the minor groove to about 150 nm (from an average of I1 0-120 nm) and 20" bending toward the major groove.…”

Section: Discussionmentioning

confidence: 99%

Effects of Minor and Major Groove‐Binding Drugs and Intercalators on the DNA Association of Minor Groove‐Binding Proteins RecA and Deoxyribonuclease I Detected by Flow Linear Dichroism

Tuite

Sehlstedt

Hagmar

et al. 1997

European Journal of Biochemistry

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Linear and circular dichroic spectroscopies have been employed to investigate the effects of small DNA ligands on the interactions of two proteins which bind to the minor groove of DNA, viz. RecA protein from Escherichia coli and deoxyribonuclease 1 (bovine pancreas). Ligands representing three specific non-covalent binding modes were investigated: 4',6-diamidino-2-phenylindole and distamycin A (minor groove binders), methyl green (major groove binder), and methylene blue, ethidium bromide and ethidium dimer (intercalators). Linear dichroism was demonstrated to be an excellent detector, in real time, of DNA double-strand cleavage by deoxyribonuclease I. Ligands bound in all three modes interfered with the deoxyribonuclease I digestion of dsDNA, although the level of interference varied in a manner which could be related to the ligand binding site, the ligand charge appearing to be less important. In particular, the retardation of deoxyribonuclease I cleavage by the major groove binder methyl green demonstrates that accessibility to the minor groove can be affected by occupancy of the opposite groove. Binding of all three types of ligand also had marked effects on the interaction of RecA with dsDNA in the presence of non-hydrolyzable cofactor adenosine 5'-0-3-thiotriphosphate, decreasing the association rate to varying extents but with the strongest effects from ligands having some minor groove occupancy. Finally, each ligand was displaced from its DNA binding site upon completion of RecA association, again demonstrating that modification of either groove can affect the properties and behaviour of the other. The conclusions are discussed against the background of previous work on the use of small DNA ligands to probe DNA-protein intcractions.

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Section: Discussionmentioning

confidence: 99%

Effects of Minor and Major Groove‐Binding Drugs and Intercalators on the DNA Association of Minor Groove‐Binding Proteins RecA and Deoxyribonuclease I Detected by Flow Linear Dichroism

Tuite

Sehlstedt

Hagmar

et al. 1997

European Journal of Biochemistry

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“…DNA cleavage proceeds one strand at a time and the enzyme shows no sequence specificity although it has been suggested that certain variations of groove width of the DNA can be detected (Drew & Travers, 1984). The crystal structure of bovine pancreatic DNAase I has been determined (Suck et al, 1984; (Frederick etal., 1984;McClarin etal., 1986).…”

Section: Beta Proteinsmentioning

confidence: 99%

Structural aspects of protein-DNA recognition

Freemont

Lane

Sanderson

1991

Biochemical Journal

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“…The DNase I cleavage pattern in the MBP-Piv binding region has long tracts of no cleavage due to A-tract repeats that narrow the minor groove, thus inhibiting DNase I binding and cleavage (15). These A-tracts are also appropriately phased along the DNA helix to contribute sequence-directed DNA bending to this region of the DNA (16.).…”

Section: Figmentioning

confidence: 99%

Multiple DNA Binding Activities of the Novel Site-specific Recombinase, Piv, from Moraxella lacunata

Tobiason

Lenich

Glasgow

1999

Journal of Biological Chemistry

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The recombinase, Piv, is essential for site-specific DNA inversion of the type IV pilin DNA segment in Moraxella lacunata and Moraxella bovis. Piv shows significant homology with the transposases of the IS110/ IS492 family of insertion elements, but, surprisingly, Piv contains none of the conserved amino acid motifs of the Int or Hin/Res families of site-specific recombinases. Therefore, Piv may mediate site-specific recombination by a novel mechanism. To begin to determine how Piv may assemble a synaptic nucleoprotein structure for DNA cleavage and strand exchange, we have characterized the interaction of Piv with the DNA inversion region of M. lacunata. Gel shift and nuclease/chemical protection assays, competition and dissociation rate analyses, and cooperativity studies indicate that Piv binds two distinct recognition sequences. One recognition sequence, found at multiple sites within and outside of the invertible segment, is bound by Piv protomers with high affinity. The second recognition sequence is located at the recombination cross-over sites at the ends of the invertible element; Piv interacts with this sequence as an oligomer with apparent low affinity. A model is proposed for the role of the different Piv binding sites of the M. lacunata inversion region in the formation of an active synaptosome.Numerous site-specific DNA recombination systems and DNA transposition systems have been characterized biochemically and have been found to follow two distinct chemical pathways for DNA cleavage and strand transfer in recombination (reviewed in Refs. 1-4). Site-specific recombination, mediated by the recombinases of the -integrase and Hin/resolvase families, involves a two-step transesterification reaction in which the intermediate is a covalent recombinase-DNA linkage. This covalent attachment is the result of nucleophilic attack on the DNA phosphodiester backbone by a hydroxyl group of the conserved serine (Hin/resolvase), or tyrosine (-integrase), of the recombinase. In the second transesterification reaction, the phosphodiester linkages of the exchanged DNA strands are restored (reviewed in Refs. 2 and 3). In contrast, DNA transposition, mediated by transposases containing the catalytic DDE amino acid motif, utilizes a hydrolysis reaction for cleavage at the ends of the transposable element. This first cleavage leaves 3Ј-OH ends to act directly as the attacking nucleophile in a one-step trans-esterification reaction resulting in strand exchange. Resolution of the transposition process involves DNA replication or DNA repair activity to fill in gaps left at the target site due to the staggered cut mediated by the transposase and the 3Ј hydroxyl groups at the element ends (reviewed in Refs. 1 and 4).These features of the recombination reactions mediated by site-specific recombinases and transposases suggest that a group of related recombinases would not mediate both sitespecific recombination and transposition. Therefore, it is surprising that the site-specific recombinase Piv, which directs site-specific DN...

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DNA structural variations in the E. coli tyrT promoter

Cited by 476 publications

References 36 publications

Effects of Minor and Major Groove‐Binding Drugs and Intercalators on the DNA Association of Minor Groove‐Binding Proteins RecA and Deoxyribonuclease I Detected by Flow Linear Dichroism

Effects of Minor and Major Groove‐Binding Drugs and Intercalators on the DNA Association of Minor Groove‐Binding Proteins RecA and Deoxyribonuclease I Detected by Flow Linear Dichroism

Structural aspects of protein-DNA recognition

Multiple DNA Binding Activities of the Novel Site-specific Recombinase, Piv, from Moraxella lacunata

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