DNA site recognition and reduced specificity of the Eco RI endonuclease

Type II restriction endonucleases--a historical perspective and more

This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.

Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism

Accurate analysis of DNA sequence variation in not only humans and animals but also other organisms has played a significant role in expanding our knowledge about genetic variety and diversity in a number of different biological areas. The search for an understanding of the causes of genetic variants and mutations has resulted in the development of a simple laboratory technique, known as the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, for the detection of single nucleotide polymorphisms (SNPs). PCR-RFLP allows rapid detection of point mutations after the genomic sequences are amplified by PCR. The mutation is discriminated by digestion with specific restriction endonucleases and is identified by gel electrophoresis after staining with ethidium bromide (EtBr). This convenient and simple method is inexpensive and accurate for SNP genotyping and especially useful in small basic research studies of complex genetic diseases. The whole protocol takes only a day to carry out.

Fnr-, NarP- and NarL-dependent regulation of transcription initiation from the Haemophilus influenzae Rd napF (periplasmic nitrate reductase) promoter in Escherichia coli K-12

Periplasmic nitrate reductase (napFDAGHBC operon product) functions in anaerobic respiration. Transcription initiation from the Escherichia coli napF operon control region is activated by the Fnr protein in response to anaerobiosis and by the NarQ-NarP two-component regulatory system in response to nitrate or nitrite. The binding sites for the Fnr and phospho-NarP proteins are centered at positions -64.5 and -44.5, respectively, with respect to the major transcription initiation point. The E. coli napF operon is a rare example of a class I Fnr-activated transcriptional control region, in which the Fnr protein binding site is located upstream of position -60. To broaden our understanding of napF operon transcriptional control, we studied the Haemophilus influenzae Rd napF operon control region, expressed as a napF-lacZ operon fusion in the surrogate host E. coli. Mutational analysis demonstrated that expression required binding sites for the Fnr and phospho-NarP proteins centered at positions -81.5 and -42.5, respectively. Transcription from the E. coli napF operon control region is activated by phospho-NarP but antagonized by the orthologous protein, phospho-NarL. By contrast, expression from the H. influenzae napF-lacZ operon fusion in E. coli was stimulated equally well by nitrate in both narP and narL null mutants, indicating that phospho-NarL and -NarP are equally effective regulators of this promoter. Overall, the H. influenzae napF operon control region provides a relatively simple model for studying synergistic transcription by the Fnr and phospho-NarP proteins acting from class I and class II locations, respectively.

Effect of mercury substitution of DNA on its susceptibility to cleavage by restriction endonucleases

Mercurated DNA was synthesized in vitro by substituting Hg-dCTP or Hg-dUMP for dCTP in one strand of M13mp8DNA in a DNA polymerase I reaction. Restriction enzymes, including Sma I, Pst I, Bam HI, Hind III, and Hinc II, were completely inactive when their recognition sites were fully substituted with Hg-dCMP, while Hg-dUMP containing DNA was hydroxlyzed to some extent. Under conditions favoring star activities, or when DNA was substituted with a low level of mercury-nucleotide, DNA was cleaved by restriction enzymes. Susceptibility to degrading and synthesizing enzymes and insensitivity to restriction endonucleases of fully mercurated DNA makes mercuration an attractive molecular "tag" for in vitro manipulation and selective isolation of Hg-DNA.

Substitution of a single bacteriophage T3 residue in bacteriophage T7 RNA polymerase at position 748 results in a switch in promoter specificity

The bacteriophage T3 and T7 RNA polymerases (RNAP) are closely related, yet exhibit high specificity for their own promoter sequences. In this work the primary determinant of T7 versus T3 promoter specificity has been localized to a single amino acid residue at position 748 in the T7 RNAP. Substitution of this residue (Asn) with the corresponding residue found in T3 RNAP (Asp) results in a switch in promoter specificity, and specifically alters recognition of the base pairs (bp) at positions -11 and, possibly, -10 in the promoter. A complementary mutation in T3 RNAP (T3-D749N) results in a similar switch in promoter preference for that enzyme. The hierarchy of bp preference by the mutant and wild-type enzymes for bp at -10 and -11, and the results of previous experiments, lead to a model for specificity in which it is proposed that N748 in T7 RNAP (and D749 in T3 RNAP) make specific hydrogen bonds with bases at -11 and -10 on the non-template strand in the major groove. The specificity determining region of T7 RNAP does not appear to exhibit homology to any known sequence-dependent DNA binding motif.

Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding

Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, theE. colicatabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKayet al.1982; Weber & Steitz, 1987), acrorepressor from phage λ (Andersonet al.1981), and the DNA-binding proteolytic fragment ofλcIrepressor protein (Pabo & Lewis, 1982) Although crystallographic studies of theE. coli lacrepressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitzet al.1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure ofλcrorepressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP,λcro,λcIrepressor fragment, 434 repressor fragment (Andersonet al.1987), 434crorepressor (Wolbergeret al.1988),E. coli trprepressor (Schevitzet al.1985),E. coli metrepressor (Raffertyet al.1989)],EcoRI restriction endonuclease (McClarinet al.1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfullet al.1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment ofE. coliDNA polymerase I (Olliset al.1985) and theE. coliHu protein (Tanakaet al., 1984)].

Substrate recognition by the EcoRI endonuclease

The EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 A resolution as an enzyme-DNA complex, EcoRI also serves as a paradigm for other restriction enzymes and as an important model of DNA-protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double-strand breaks induce the Escherichia coli SOS response and thereby increase beta-galactosidase expression from SOS::lacZ gene fusions. By site-directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.

Non-C-G recognition sequences of DNA cytosine-5-methyltransferase from rat liver

The eukaryotic DNA cytosine-5-methyltransferase (E.C.2.1.1.37) is known to methylate cytosine in DNA mainly, but not exclusively in C-G. In the present study the minor, non-C-G recognition sequences of a rat DNA methyltransferase were analyzed by Maxam-Gilbert sequencing of in vitro methylated SV40 DNA. The enzyme methylates C-A and C-T at a 50-fold lower initial rate than C-G. Methylation of C-C at the 5'C was not observed in the piece of DNA sequenced. The methylation of C-A is very low in the trinucleotides ACA and CAC, the other C-A containing trinucleotides in DNA are much better methylacceptors. C-T was found methylated predominantly in the sequences CCTAA, ACTAA, and ACTGT. A comparison of the activity with different substrates is in favour of the enzyme making its recognition in the major groove of the DNA.

Mutant Trp repressors with new DNA-binding specificities

Oligonucleotide-directed mutagenesis of the codons for glutamine-68 (Gln68), lysine-72 (Lys72), isoleucine-79 (Ile79), alanine-80 (Ala80), and threonine-81 (Thr81) of the Escherichia coli trpR (tryptophan aporepressor) gene was used to make mutant repressors with each of 36 different amino acid changes. Mutant repressors were tested for binding to each member of a set of 28 different operators closely related to the consensus trp operator. Of the 36 mutant repressors, 11 bind a subset of the 28 operators; 5 of these have new binding specificities. These new specificities indicate that the hydroxyl group of Thr81 makes a specific contact with one of the four critical base pairs in a trp operator half-site, and the methyl group of Thr81 determines specificity at a second, critical base pair. The Trp repressor does not use the first two amino acids of its "recognition alpha-helix," Ile79 and Ala80, to make sequence-specific DNA contacts, and interacts with its operator in vivo in a way fundamentally different from the way that phage lambda repressor, lambda Cro protein, and coliphage 434 repressor contact their respective binding sites.

DNA binding by proteins

Study of proteins that recognize specific DNA sequences has yielded much information, but the field is still in its infancy. Already two major structural motifs have been discovered, the helix-turn-helix and zinc finger, and numerous examples of DNA-binding proteins containing either of them are known. The restriction enzyme Eco RI uses yet a different motif. Additional motifs are likely to be found as well. There is a growing understanding of some of the physical chemistry involved in protein-DNA binding, but much remains to be learned before it becomes possible to engineer a protein that binds to a specific DNA sequence.

Calculation of individual cleavage rates from partial digests in restriction endonuclease kinetics

A correction for results obtained by an analysis of DNA molecules partially cleaved with restriction endonuclease was suggested. The correction was proved on model data. Applications to (i) electron-microscopic analysis of singly cleaved molecules, (ii) partial digestion of a circular molecule followed by complete digestion with a second enzyme, (iii) systems with great cleavage differences, and (iv) partial cleavage of end-labelled molecules were discussed.

Isolation and some properties of the site-specific endonuclease and methylase Bme2161 from Bacillus megaterium 216

The site-specific endonuclease Bme2161 was isolated as a homogeneous preparation by chromatography on phosphocellulose, hydroxyapatite and heparin-agarose. The molecular mass of the enzyme, determined by gel filtration and by electrophoresis under denaturing conditions, was found to be 60 kDa and 30 kDa respectively. These data indicate that the native enzyme consists of two identical subunits. The enzyme recognized the decreases pentanucleotide sequence 5'-GGACC-3' X 3'-CCTGG-5' and cleaves the sequence as indicated by arrows. The increases optimal concentration for endonuclease reaction is 6-7 mM Mg2+. The endonuclease relaxes its specificity in the presence of glycerol or dimethyl sulfoxide at low Mg2+ concentration (1-3 mM). Methylase Bme2161, which protects DNA against endonuclease Bme2161 action by DNA methylation, was isolated from the same bacterial strain.

Properties and uses of restriction endonucleases

It is clear that we have still not exhausted all the restriction endonuclease specificities to be found in nature. Recently discovered BsmI is the first endonuclease recognizing a nonpalindromic sequence that cleaves within the site. Certainly other endonucleases belonging to this class will soon be discovered. More endonucleases are now being sought that recognize longer recognition sequences, because large fragments can now be readily separated by pulse-field electrophoresis. New sources of endonucleases are also being found; for example, a group of viruses that grow on Chlorella algae produce type II-like site-specific endonucleases. As the number and variety of known restriction endonucleases increase, the number and variety of applications keep pace. There is still no end in sight.

Relaxed specificity of the EcoRV restriction endonuclease

The EcoRV restriction endonuclease normally shows a high specificity for its recognition site on DNA, GATATC. In standard reactions, it cleaves DNA at this site several orders of magnitude more readily than at any alternative sequence. But in the presence of dimethyl sulphoxide and at high pH, the EcoRV enzyme cleaves DNA at several sites that differ from its recognition site by one nucleotide. Of the 18 (3 X 6) possible sequences that differ from GATATC by one base, all were cleaved readily except for the following 4 sites: TATATC, CATATC, GATATA and GATATG. However, two of the sites that could be cleaved by EcoRV in the presence of dimethyl sulphoxide, GAGATC and GATCTC, were only cleaved on DNA that lacked dam methylation: both contain the sequence GATC, the recognition site for the dam methylase of Escherichia coli.

Specificity of restriction endonucleases and methylases--a review

The properties and sources of all known restriction endonucleases and methylases are listed. The enzymes are cross-indexed (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the double-stranded DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (integrated into Table II), the structure of the generated fragment ends (Table III), and the sensitivity to different kinds of DNA methylation (Table V). In Table IV the conversion of two- and four-base 5'-protruding ends into new recognition sequences is compiled which is obtained by the fill-in reaction with Klenow fragment of the Escherichia coli DNA polymerase I or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments. Table VI classifies the restriction methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises restriction endonucleases which are known to be inhibited or activated by the modified nucleotides. The detailed sequences of those overlapping restriction sites are also included which become resistant to cleavage after the sequential action of corresponding restriction methylases and endonucleases [N11, M21]. By this approach large DNA fragments can be generated which is helpful in the construction of genomic libraries. The data given in both Tables IV and VI allow the design of novel sequence specificities. These procedures complement the creation of universal cleavage specificities applying class IIS enzymes and bivalent DNA adapter molecules [P17, S82].

Representation of DNA sequences by use of helical wheels to identify pattern formation with protein binding potential

Similar to the protein segments with helical potential the three-dimensional structures of DNA sequences can be represented by a two-dimensional projection along the axis of the double helix. We will call this projection according to Schiffer and Edmundson "helical wheel". In the first place the wheels are employed here as graphical restatements of known sequences which represent binding sites of restriction-modification enzymes. Specific recognition of these sites has to be based on sequence related multi contact interactions of weak bonds. Because of the spatial and directional characteristics of H-bonds we will utilize the pattern formation of H-bond donor--and acceptor groups protruding into the major groove of the helix to identify the particular sequences. The characteristics of these patterns can be readily visualized and compared by examination of these wheels.

Cloning of DNA segments of phage 2C, which allows autonomous plasmid replication in Bacillus subtilis

The chromosome of Bacillus subtilis phage 2C is a 100-MDa double-stranded DNA molecule, containing hydroxymethyluracil in place of thymine and carrying redundant ends each encompassing 10% of the genome. 2C DNA was cleaved with EcoRI and HindIII, and cloned in the shuttle plasmids pSC 540 and pCP 115, both containing segments originating from B. subtilis and Escherichia coli plasmids. These chimaerical plasmids, carrying the chloramphenicol resistance gene, were unable to replicate in B. subtilis; this ability was restored, however, after the insertion of viral DNA segments. Physical maps of the recombinant plasmids were made; a large deletion of the E. coli-derived segment of pSC 540 was observed (which paralleled a loss of replication in this host), whereas addition of 2C DNA segments in pCP 115 was not accompanied by deletion (replication in E. coli was conserved in this case). Cloned viral segments mapped mostly, but not exclusively, within the redundant ends of 2C DNA. It is suggested that the thirteen recombinant clones carried the replication origin region of phage 2C DNA, and that these sequences originated within or close to the redundant extremities of the viral chromosome.

Recognition sequences of restriction endonucleases and methylases--a review

The properties and sources of all known endonucleases and methylases acting site-specifically on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies within their recognition sequences (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328 and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (Table III), the structure of the restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA methylation (Table V). Table VI classifies the methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises those restriction endonucleases, which are known to be inhibited by the modified nucleotides. Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the length of the generated fragments ordered according to size, and the effects of the Escherichia coli dam- and dcmI-coded methylases M X Eco dam and M X Eco dcmI on the particular recognition sites.

Kinked DNA in crystalline complex with EcoRI endonuclease

The 3 A electron density map of a co-crystalline recognition complex between EcoRI endonuclease and the oligonucleotide TCGCGAATTCGCG reveals that a tight, complementary interface between the enzyme and the major groove of the DNA is the major determinant of sequence specificity. The DNA contains a torsional kink and other departures from the B conformation which unwind the DNA and thereby widen the major groove in the recognition site.

Transcriptionally active and inactive genes are similarly modified by chemical carcinogens or X-ray in normal human fibroblasts

Chemical carcinogens and ionizing radiation induce DNA modifications and strand breaks in cells. This damage is reported to be affected by chromatin proteins or chromatin of a higher structure order. To compare the sensitivity of transcriptionally active and inactive genes on chromatin toward DNA-damaging agents, we treated normal human fibroblasts (WI-38) cells in N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), X-ray, 4-hydroxyaminoquinoline 1-oxide or N-acetoxy-2-acetylaminofluorene, and high molecular weight DNA was isolated. After digestion with EcoRI to completion, the DNA was electrophoresed on an alkaline agarose gel, blotted on a nitrocellulose filter and hybridized with a transcriptionally active gene probe (human type I(alpha 2) procollagen gene) or an inactive gene probe (human beta-globin gene). The results show that both genes are similarly modified by these agents. Repair of DNA damage caused by MNNG also occurred similarly in collagen and beta-globin genes after removal of MNNG.

The influence of sequences adjacent to the recognition site on the cleavage of oligodeoxynucleotides by the EcoRI endonuclease

We have investigated the influence of the nucleotide sequence adjacent to the recognition site on the rate of cleavage of DNA by the restriction endonuclease EcoRI. For this purpose two decadeoxynucleotides, d(G-G-G-A-A-T-T-C-T-T) (Ia) and d(A-A-G-A-A-T-T-C-C-C) (Ib) were synthesized. The duplex Ia X Ib is cleaved by EcoRI preferentially in the dA-rich strand (approximately 10 times over the dG-rich strand). The individual nucleotides Ia and Ib are also cleaved by EcoRI, Ib at a higher rate than Ia and both at a lower rate than Ia X Ib. The temperature dependence of the reaction rate shows that only double-stranded oligodeoxynucleotides are substrates for the EcoRI endonuclease. We have, furthermore, synthesized oligomers of d(G-G-A-A-T-T-C-C), which contain two, three and four EcoRI sites, respectively. These oligodeoxynucleotides are preferentially cleaved at the sites next to the 5' end, where the recognition site is only flanked by one dG X dC base pair, in contrast to the other sites which are flanked by three such pairs. These data indicate that sequences adjacent to the recognition site influence the rate of cleavage: dA X dT base pairs enhance and dG X dC base pairs slow down the hydrolytic activity of the EcoRI endonuclease.

Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties

The deoxyribooctanucleotide d(G-G-A-A-T-T-C-C), containing the recognition sequence for EcoRI, d(G-A-A-T-T-C), and analogs containing modified sugar moieties were tested for their activity in cleavage with EcoRI. These analogs, with replacement in the third position from the 5' end, were synthesized using 9-beta-D-arabinosyladenine (aA), 2'-deoxy-2'-fluoroadenosine (Afl) and adenosine (rA). Duplex formation by the three analogs was confirmed by measurements of ultraviolet/temperature profiles. It was found that EcoRI cleaved these duplexes less efficiently than d(G-G-A-A-T-T-C-C). The adenosine-containing analog d(G-G)-rA-d(A-T-T-C-C) was cleaved much more slowly than d(G-G)-aA-d(A-T-T-C-C) and d(G-G-Afl-A-T-T-C-C). The corresponding ribooctamer G-G-A-A-U-U-C-C showed a higher melting temperature than the deoxyoctamers but its duplex was not cleaved by this enzyme. An analog with 2'-deoxy-2'-fluoroguanosine at the second position was cleaved by the endonuclease faster than the natural deoxyoctamer.

Restriction enzyme cleavage of ultraviolet-damaged simian virus 40 and pBR322 DNA

Cleavage of specific DNA sequences by the restriction enzymes EcoRI, HindIII and TaqI was prevented when the DNA was irradiated with ultraviolet light. Most of the effects were attributed to cyclobutane pyrimidine dimers in the recognition sequences; the effectiveness of irradiation was directly proportional to the number of potential dimer sites in the DNA. Combining EcoRI with dimer-specific endonuclease digestion revealed that pyrimidine dimers blocked cleavage within one base-pair on the strand opposite to the dimer but did not block cleavage three to four base-pairs away on the same strand. These are the probable limits for the range of influence of pyrimidine dimers along the DNA, at least for this enzyme. The effect of irradiation on cleavage by TaqI seemed far greater than expected for the cyclobutane dimer yield, possibly because of effects from photoproducts flanking the tetranucleotide recognition sequence and the effect of non-cyclobutane (6-4)pyrimidine photoproducts involving adjacent T and C bases.

Evidence for a restriction/modification-like system in Anacystis nidulans infected by cyanophage AS-1

Anacystis nidulans infected by AS-1 cyanophage contains an endonuclease (AS-1 endonuclease) which splits host DNA but not AS-1 phage DNA [Szekeres, M. (1981) Virology, 111, 1-10]. AS-1 phage DNA proved to be resistant not only to AS-1 endonuclease but also to a number of restriction endonucleases the recognition sites of which contain a central dG-dC dinucleotide. Since an unmodified 5'dG-dC dinucleotide was shown to be present at the sites at which DNA is cleaved by AS-1 endonuclease, the results suggest that the sites attacked preferentially by the AS-1 endonuclease are specifically protected on the AS-1 DNA molecule. The modification of AS-1 DNA was shown to occur specifically in infected Anacystis because AS-1 DNA fragments which are normally resistant to AS-1 endonuclease became susceptible to this enzyme if inserted into pBR322 plasmid and cloned in Escherichia coli. AS-1 DNA was shown to contain about 5% of a modified nucleotide which was not 5-methyldeoxycytidylic acid. Results presented and our earlier data suggest that in Anacystis infected by AS-1 phage, a restriction/modification-like system operates which is able to eliminate 'unwanted' (host) DNA selectively.

The molecular basis of DNA-protein recognition inferred from the structure of cro repressor

Recognition by cro repressor protein of its specific DNA binding sites appears to occur via multidentate hydrogen bonds between amino acid side chains of the protein and base-pair atoms in the major groove of right-handed B-form DNA. Most of the sequence-specific interactions between cro and DNA, as well as a number of sequence-independent ones, are mediated by a two-alpha-helical unit which appears to be common to many proteins that regulate gene expression.

Restriction enzyme cleavage of ultraviolet-damaged DNA

SV40 and pBR322 DNAs damaged by ultraviolet light were cleaved abnormally by several restriction enzymes because of damage to pyrimidines in the recognition sequences. The use of a tandemly duplicated plasmid provided a particularly sensitive target molecule for detecting pyrimidine dimers and other possible photoproducts. The relative efficiency with which cleavage was blocked (HindIII greater than TaqI greater than EcoRI greater than BamI greater than SalI much greater than Hha I, Hae III) corresponds approximately to the relative frequency of pyrimidine dimer formation in the recognition sequences, but at a slightly higher frequency in potential sites for the non-cyclobutane T-C product. The pyrimidine dimers appear to have a range of influence that extends 1 to 3 basepairs along the DNA molecule. These effects provide clues to the way DNA damage from mutagens and carcinogens can interfere with specific enzyme-DNA interactions.

Two identical subunits of the EcoRI restriction endonuclease Co-operate in the binding and cleavage of the palindromic substrate

The cleavage of radioactively labelled double-stranded d(G-G-A-A-T-T-C-C) was studied in single turnover experiments with substrate and enzyme both being in the micromolar range. The reaction rate was found to increase with enzyme concentration until a ratio of one tetrameric enzyme to two double-stranded substrates was reached, further increase of the enzyme concentration then leads to a sharp decline of the reaction rate. These findings are interpreted in the following manner. (a) Two subunits of the EcoRI endonuclease co-operate in binding and possibly also in cleaving the palindromic substrate. (b) The enzymatic action of the EcoRI endonuclease is inhibited by excess enzyme, possibly due to unspecific binding of the enzyme-substrate complex. The self-inhibition of EcoRI endonuclease has also been observed with macromolecular substrates.

Cloning and sequencing of restriction fragments generated by Eco RI*

Thirty-four Eco RI* sites have been identified on the nucleotide sequence of CaMV, following cloning of Eco RI* fragments in M13mp2. From this sequencing data, we have deduced that Eco RI* recognizes sites that differ in a single position from the canonical Eco RI sequence, GAATTC. Any substitution can occur at any one of the six positions in the recognition site, with the exception of A leads to T or T leads to A changes within the central tetramer. The Eco RI* restriction patterns of phi x174 and pBR322 are consistent with these recognition criteria. Similarly, Bam HI* cleavage of phi x174 and SV40 (George et al., 1980) produces restriction patterns that are consistent with single-position degeneracy in the canonical Bam HI recognition site. Cohesive termini produced by Eco RI* cleavage were ligated into the Eco RI site of M13mp2, even when there was a base pair mismatch within the four nucleotide overlap. Mismatches were corrected asymmetrically during subsequent replication of M13 in E. coli.

Studies on sequence recognition by type II restriction and modification enzymes

Type II DNA restriction and modification systems are ideally suited for analysis of mechanisms by which proteins specifically recognize unique DNA sequences. Each system is comprised of a unique DNA recognition site and two enzymes, which in those cases examined in detail, are comprised of distinct polypeptide chains. Thus, not only are the DNA substrates extremely well defined, but each system affords the opportunity to compare distinct proteins which interact with a common DNA sequence. This review will focus only on those Type II systems which have been examined in sufficient molecular detail to permit some insight into modes of specific DNA-protein interaction.

Eco RI* specificity and hydrogen bonding

Under standard conditions, Eco RI endonuclease uniquely recognizes the inverted repeat GAATTC. However, this specificity breaks down under non-standard conditions into what has been termed Eco RI* specificity, wherein many other sequences are recognized. We show here that the hydrolysis rates at all known Eco RI* sites can be summarized by the hierarchies: G much greater than A greater than T much greater than C at the first position, A much greater than [G,C] much greater than T at the second and third position, and the corresponding complements at the last three positions. This is consistent with a recognition model which assumes that there are two specific hydrogen bonds per base pair under standard conditions. One or more of these are randomly replaced by water under Eco RI* conditions and the position of a sequence within the appropriate hierarchy is primarily determined by the number of retained hydrogen bonds. These retained hydrogen bonds are common recognition features that can be identified by examining the DNA. The recognition points thereby identified for Eco RI all fall within the major groove of the DNA.