Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII

Gromova, E. S.; Кубарева, Е. А.; Vinogradova, M N; Oretskaya, T. S.; Shabarova, Zoe A.

doi:10.1002/jmr.300040405

Cited by 21 publications

(40 citation statements)

References 34 publications

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“…Those that have are commonly directed towards answering specific questions about particular enzymes, for example, the use of phosphorothioate-substituted substrates to determine the stereochemistry of phosphodiester bond hydrolysis (11,12) or assessing the different effects of various modified bases and backbone architectures on the hydrolytic reactions catalyzed by a pair of neoschizomeric enzymes (13). Notable exceptions include testing the activity of fourteen different Type II enzymes on substrates that include mismatched bases within their recognition sites (14) and a systematic in vitro analysis of the effects of adenine and cytosine methylation on the activities of a large number of REases [Stickel, S. K. and Roberts, R. J., unpublished results available in REBASE (4)].…”

Section: Introductionmentioning

confidence: 99%

Sequence-specific cleavage of RNA by Type II restriction enzymes

Murray¹,

Stickel²,

Roberts³

2010

Nucleic Acids Research

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The ability of 223 Type II restriction endonucleases to hydrolyze RNA–DNA heteroduplex oligonucleotide substrates was assessed. Despite the significant topological and sequence asymmetry introduced when one strand of a DNA duplex is substituted by RNA we find that six restriction enzymes (AvaII, AvrII, BanI, HaeIII, HinfI and TaqI), exclusively of the Type IIP class that recognize palindromic or interrupted-palindromic DNA sequences, catalyze robust and specific cleavage of both RNA and DNA strands of such a substrate. Time-course analyses indicate that some endonucleases hydrolyze phosphodiester bonds in both strands simultaneously whereas others appear to catalyze sequential reactions in which either the DNA or RNA product accumulates more rapidly. Such strand-specific variation in cleavage susceptibility is both significant (up to orders of magnitude difference) and somewhat sequence dependent, notably in relation to the presence or absence of uracil residues in the RNA strand. Hybridization to DNA oligonucleotides that contain endonuclease recognition sites can be used to achieve targeted hydrolysis of extended RNA substrates produced by in vitro transcription. The ability to ‘restrict’ an RNA–DNA hybrid, albeit with a limited number of restriction endonucleases, provides a method whereby individual RNA molecules can be targeted for site-specific cleavage in vitro.

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Section: Introductionmentioning

confidence: 99%

Sequence-specific cleavage of RNA by Type II restriction enzymes

Murray¹,

Stickel²,

Roberts³

2010

Nucleic Acids Research

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“…(c) The cleavage rates of the two strands are significantly different (9). (d) Unlike the prototype EcoRII REase, MvaI is very tolerant of modifications in synthetic substrates (10). The enzyme completes the cleavage of substrates with a nick in one strand, irrespective of whether or not a phosphate is present at the nicking site (8).…”

Section: Introductionmentioning

confidence: 99%

“…The enzyme completes the cleavage of substrates with a nick in one strand, irrespective of whether or not a phosphate is present at the nicking site (8). Moreover, selective modification of one DNA strand typically affects the cleavage of either the modified or the unmodified strand, depending on the nature of the modification, but only very drastic modifications impair cleavage of both strands (7,10). …”

Section: Introductionmentioning

confidence: 99%

Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically

Kaus-Drobek¹,

Czapinska²,

Sokolowska³

et al. 2007

Nucleic Acids Research

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Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, ‘/’ designates the cleavage site) and generates products with single nucleotide 5′-overhangs. The enzyme has been noted for its tolerance towards DNA modifications. Here, we report a biochemical characterization and crystal structures of MvaI in an apo-form and in a complex with target DNA at 1.5 Å resolution. Our results show that MvaI is a monomer and recognizes its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the bases from the minor grove side. The recognition lobe mediates all major grove interactions with the bases. The enzyme in the crystal is bound to the strand with T at the center of the recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand instead of making a double-strand break.

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“…In the case of MvaI, it has been shown experimentally that N6-methylation of the central adenine interferes with cleavage of the methylated strand, but not with cleavage of the unmethylated strand [15]. Similar effects have been observed with N4-methylation of the outer cytosine residue, which also protects the methylated strand, but not the unmethylated strand, from cleavage [15]. Hence, MvaI acts as a nickase at least on some substrates.…”

Section: Differences Between Bcni/mvai and Muthmentioning

confidence: 65%

Restriction endonucleases that resemble a component of the bacterial DNA repair machinery

Sokolowska

Kaus-Drobek

Czapinska

et al. 2007

Cell. Mol. Life Sci.

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It has long been known that most Type II restriction endonucleases share a conserved core fold and similar active-sites. The same core folding motif is also present in the MutH protein, a component of the bacterial DNA mismatch repair machinery. In contrast to most Type II restriction endonucleases, which assemble into functional dimers and catalyze double-strand breaks, MutH is a monomer and nicks hemimethylated DNA. Recent biochemical and crystallographic studies demonstrate that the restriction enzymes BcnI and MvaI share many additional features with MutH-like proteins, but not with most other restriction endonucleases. The structurally similar monomers all recognize approximately symmetric target sequences asymmetrically. Differential sensitivities to slight substrate asymmetries, which could be altered by protein engineering, determine whether the enzymes catalyze only single-strand nicks or double-strand breaks.

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Peculiarities of recognition of CC^A/_TGG sequences in DNA by restriction endonucleases MvaI and EcoRII

Cited by 21 publications

References 34 publications

Sequence-specific cleavage of RNA by Type II restriction enzymes

Sequence-specific cleavage of RNA by Type II restriction enzymes

Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically

Restriction endonucleases that resemble a component of the bacterial DNA repair machinery

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