Cleavage Point Research Articles

The stereochemistry of a four-way DNA junction: a theoretical study

The stereochemical conformation of the four-way helical junction in DNA (the Holliday junction; the postulated central intermediate of genetic recombination) has been analysed, using molecular mechanical computer modelling. A version of the AMBER program package was employed, that had been modified to include the influence of counterions and a global optimisation procedure. Starting from an extended planar structure, the conformation was varied in order to minimise the energy, and we discuss three structures obtained by this procedure. One structure is closely related to a square-planar cross, in which there is no stacking interaction between the four double helical stems. This structure is probably closely similar to that observed experimentally in the absence of cations. The remaining two structures are based on related, yet distinct, conformations, in which there is pairwise coaxial stacking of neighbouring stems. In these structures, the four DNA stems adopt the form of two quasi-continuous helices, in which base stacking is very similar to that found in standard B-DNA geometry. The two stacked helices so formed are not aligned parallel to each other, but subtend an angle of approximately 60 degrees. The strands that exchange between one stacked helix and the other are disposed about the smaller angle of the cross (i.e. 60 degrees rather than 120 degrees), generating an approximately antiparallel alignment of DNA sequences. This structure is precisely the stacked X-structure proposed on the basis of experimental data. The calculations indicate distortions from standard B-DNA conformation that are required to adopt the stacked X-structure; a widening of the minor groove at the junction, and reorientation of the central phosphate groups of the exchanging strands. An important feature of the stacked X-structure is that it presents two structurally distinct sides. These may be recognised differently by enzymes, providing a rationalisation for the points of cleavage by Holliday resolvases.

II-Q restriction endonucleases—new class of type II enzymes

Unique restriction endonucleases Bpu 10l and Bsil have been isolated from Bacillus pumilas and Bacillus sphaericus, respectively. The recognition sequences and cleavage points of these enzymes have been determinated as 5'-CC1TNAGC-3'/3'-GGANT1CG-5' for Bpu 10l and 5'-C1TCGTG-3'/3'-GAGCA1C-5' for Bsil. Restriction endonucleases Bpu 10l and Bsil represent a new class of enzymes which recognize non-palindromic nucleotide sequences and hydrolize DNA within the recognition sequence. Bpu 10l and Bsil recognition sequences may be regarded as quasipalindromic and the enzymes may be designated as type II-Q restriction endonucleases.

Recognition and cleavage signals for mRNA processing lie within local domains of the phage f1 RNA precursors

In Escherichia coli infected with the filamentous phage f1, a number of the abundant phage mRNAs, species C-G, are products of post-transcriptional processing. The approach of cloning the phage sequences likely to include the processing signals in a plasmid under transcriptional control of the lambda PL promoter (Blumer, K. J., and Steege, D. A. (1984) Nucleic Acids Res. 12, 1847-1861) was extended to additional sites to show that processing at all five major sites is mediated by nuclease activity encoded by the bacterial genome. Primer extension methods were used to map more accurately in the f1 DNA sequence the 5' end points of the processed RNAs. The DNA segments that encode the mRNA processing signals were delimited from parallel series of 5'-3' and 3'-5' deletions made into the regions in which the RNA 5' ends map. For each deletion variant, in vivo f1 mRNA processing activity was assessed by primer extension and S1 nuclease mapping methods. The data indicate that the processing signals are comprised of relatively local regions near the point of RNA cleavage. Whereas cleavage occurs at the 5' border of the sequences that comprise the D, E, and F processing sites and thereby places most of the recognition information in the mature or product portion of the precursor, it occurs more centrally within the region comprising the C site. The C and D sites function independently as substrates for cleavage, with the necessary information contained in regions of 70 and 90 nucleotides, respectively. Cleavage at the E site appears to require a region of 130 nucleotides which completely contains the F site. From the effects on processing activity of deleting sequences in this region, the overlapping E and F processing sites appear to consist functionally of two subdomains. Each has a cleavage site at its immediate 5' end which can be substituted by foreign sequences, but both utilize a common recognition domain downstream from the point of strand scission.

Purification and analysis of colonization factor antigen I, coli surface antigen 1, and coli surface antigen 3 fimbriae from enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli fimbriae are immunogenic and play a key role in intestinal colonization. Native colonization factor antigen I, coli surface antigen 1, and coli surface antigen 3 fimbriae were purified by a common method involving shearing, differential centrifugation, gel filtration, and density gradient ultracentrifugation. The compositions and N-terminal sequences were determined. Coli surface antigen 3 possesses two N-terminal isoforms, one of which matches the published DNA sequence, except for the previously proposed signal sequence cleavage point.

Heterogeneity of anti-U demonstrable by the use of papain-treated red cells.

When red cells (RBCs) are treated with papain, one form of the U antigen, which we have named UPS (U papain-sensitive), is almost completely removed or denatured. A second form, UPR (U papain-resistant), remains unaltered on the treated RBCs. Tests on 42 examples of anti-U showed that two contained only anti-UPS, 19 contained only -UPR, and 21 contained separable -UPS and -UPR. In those sera containing both antibodies, anti-UPR was always the stronger of the two. These findings suggest 1) that UPS is located on the Ss sialoglycoprotein (glycophorin B) at a position distal to a papain-sensitive site or that the cleavage point is within the portion of the SGP that comprises UPS, and 2) that UPR is located between the papain-sensitive site and the RBC membrane. The UPS determinant was not denatured by neuraminidase, L-cysteine, trypsin, ficin, or alpha-chymotrypsin, and it was only partially denatured by pronase. The finding that RBCs treated with para-chloromercuribenzoic acid or para-chloromercuriphenyl sulfonic acid did not react with anti-UPR but did continue to react with anti-UPS suggests that the in situ configuration of UPR, but not UPS, is dependent on the presence of one or more disulfide bonds. RBCs of the S-s-U+(weak) phenotype were shown to carry markedly reduced amounts of both UPS and UPR.

Trypsin activation of atrial muscarinic K+ channels

The atrial muscarinic K+ channel normally is opened by the activated G protein, Gk. Based on the assumption that an inactivating particle keeps the channel closed, several protein-modifying agents including trypsin, papain, glyoxal, and phenylglycoxal that remove Na+-channel inactivation were tested. K+ channels were studied in inside-out excised membrane patches from primary cultures of neonatal rat atrial myocytes. Of the agents tested, only trypsin activated muscarinic K+ channels, and it did so irreversibly. Trypsin was effective in the absence of muscarinic agonist or intracellular Mg2+ and guanosine 5'-triphosphate. Heat-denatured trypsin was ineffective, and trypsin inhibitor blocked the effect. Because trypsin is known to inactivate G proteins, the effect was probably on the K+ channel or a structure closely associated with it. Trypsin activation produced single-channel currents in which inward rectification, single-channel conductance, mean open time, and burst duration were indistinguishable from muscarinic activation. Trypsin cleaves proteins at lysine or arginine residues, and the arginine-specific reagents, glyoxal and phenylgloxal, did not activate K+ channels. We conclude that trypsin disrupts an inhibitory gating mechanism that normally holds the channel closed in the absence of activated Gk. The inhibitory gate is physically distinct from the gate that mediates bursting and must contain at least one trypsin cleavage point located at a lysine residue accessible from the cytoplasmic surface of the cell membrane.

Identification of point of specific enzymic cleavage of P1,P4-bis(5′-adenosy) tetraphosphate by negative ion FAB mass spectrometry

Identification of point of specific enzymic cleavage of P1,P4-bis(5′-adenosy) tetraphosphate by negative ion FAB mass spectrometry

Atrial dipeptidyl carboxyhydrolase is a zinc-metallo proteinase which possesses tripeptidyl carboxyhydrolase activity

Atrial dipeptidyl carboxyhydrolase readily converts one atrial natriuretic peptide, atriopeptin II (Ser103-Arg125 peptide), to another, atriopeptin I (Ser103-Ser123 peptide), by selective removal of the C-terminal dipeptide, Phe-Arg. The atrial peptides possess natriuretic, diuretic, smooth muscle relaxant, and cardiodynamic properties and their existence has shown the mammalian heart to be an endocrine organ. After inactivating the bovine atrial enzyme with EDTA, activity is restored by the addition of Co+2, Zn+2 and Mn+2 but not by Cu+2, Mg+2, Ca+2, or Cd+2. The enzyme is thus likely to be a zinc-metallo proteinase. In addition to its dipeptidyl activity, the enzyme also displays tripeptidyl carboxyhydrolase activity with atriopeptin III (Ser103-Try126 peptide) as substrate. The hydrolytic products resulting from tripeptidyl cleavage are atriopeptin I and Phe-Arg-Tyr. However, with [mercaptopropionyl105,(D)Ala107]-atriopeptin III-NH2 peptide (a potent agonist of atriopeptin III) as substrate, the enzyme acts exclusively as a tripeptidyl carboxyhydrolase. To examine the basis for this shift in cleavage point, pentapeptides based on the C-terminal sequence of atriopeptin III were prepared; a C-terminal Tyr or Tyr-NH2 residue is not sufficient to cause the change in cleavage point. The amidated pentapeptide is not a substrate but is a competitive inhibitor of hydrolysis of the corresponding free-acid peptide.

19] Mechanistic studies utilizing oxygen-18 analyzed by carbon-13 and nitrogen-15 nuclear magnetic resonance spectroscopy

Publisher Summary This chapter discusses the mechanistic studies utilizing 18 0, as analyzed by 13 C and 15 N nuclear magnetic resonance (NMR) spectroscopy. Specifically, the mechanistic studies covered include rates of hydrolysis reaction, the point of bond cleavage, and oxygen exchange reactions. Although the design of experiments involving reactions at carbon-oxygen bonds is largely dictated by the reaction being studied, considerable flexibility in the experimental design does exist. Reactions in which the carbon-oxygen bond is broken and reformed permit complementary experimental designs wherein the oxygen-18 isotope may be incorporated into the substrate or it may be present in the aqueous solvent. When 180 is incorporated into the substrate, the 18 0 label is replaced by 16 0 from the normal aqueous solvent as the reaction proceeds, and the label is essentially lost “irreversibly” to the bulk solvent, termed in the chapter as an out-exchange. An advantage to this experimental design is the conservation of the 18 O label. Utilizing NMR to study these reactions has the advantage that the reactions are assayed in a nearly continuous mode, sample handling is minimized, conversion to volatile derivatives is not necessary, and positional information is obtained directly.

Propylbenzilylcholine Mustard Labels an Acidic Residue in Transmembrane Helix 3 of the Muscarinic Receptor

Muscarinic acetylcholine receptors were purified from rat forebrain and labeled with [3H]N-(2-chloroethyl)N-(2',3'-[3H2]propyl)-2-aminoethylbenzilate. Cleavage of the labeled muscarinic acetylcholine receptors with a lysine-specific protease yielded labeled, glycosylated peptides about 130 and 200 residues in length, which came from different receptor sequences. The probable cleavage sites are in the second intracellular loop and in the second extracellular or third intracellular loop. The N-terminal 130 residues are disulfide-bonded to another part of the receptor structure, supporting the presence of a link between the second and third extracellular loops. The [3H]propylbenzilylcholine mustard-receptor link is cleaved by nucleophiles, acids, and bases under denaturing conditions, suggesting modification of an acidic residue. Cyanogen bromide cleavage points to transmembrane helix 3 as the site of label attachment.

The human gastrin precursor. Characterization of phosphorylated forms and fragments.

There is a potential phosphorylation site in the C-terminal region of the precursor for the acid-stimulating hormone gastrin, which is immediately adjacent to an important cleavage point. In the present study we have sought to identify, separate, quantify and characterize phosphorylated and unphosphorylated forms of human progastrin and its fragments. Identification was made by two radioimmunoassays: (a) a novel assay employing an antibody raised to intact human progastrin; and (b) an assay using antibody reacting with the C-terminal tryptic fragment of human progastrin, as well as progastrin itself. Two forms of human progastrin isolated from a gastrinoma were separated by ion-exchange h.p.l.c., and had similar elution positions on reverse-phase h.p.l.c. and on gel filtration. The more acidic peptide contained close to equimolar amounts of phosphate. On trypsinization, peptides were released that co-eluted on ion-exchange h.p.l.c. with, and had the immunochemical properties of, naturally occurring C-terminal fragments of progastrin. One of the latter was isolated and shown by Edman degradation after derivatization with ethanethiol to have the sequence Ser (P)-Ala-Glu-Asp-Glu-Asn. Similar peptides occur in antral mucosa resected from ulcer patients. The unphosphorylated forms of progastrin predominated, whereas the phosphorylated forms of the C-terminal fragments were predominant. This distribution could be explained by preferential cleavage of phosphorylated progastrin. We conclude that in human progastrin, Ser-96 can occur in the phosphorylated form; this residue immediately follows a pair of basic residues (Arg-Arg) that are cleaved during synthesis of the biologically active product.

The oxygen-18 isotope shift in carbon-13 nuclear magnetic resonance spectroscopy. 12. Position of bond cleavage in the acid-catalyzed hydrolysis of sucrose

The /sup 18/O isotope-induced shift in /sup 13/C NMR spectroscopy was used to elucidate the point of bond cleavage in the acid-catalyzed hydrolysis of sucrose. Sucrose was hydrolyzed in the presence of H/sub 2//sup 18/O, and the incorporation of /sup 18/O into the several anomeric products was simultaneously assayed as a function of time. While the equilibrium ratio of /sup 18/O was detected in the fructose anomers throughout the course of the hydrolysis, the percentage incorporation of /sup 18/O into the glucose anomers slowly increased to the equilibrium ratio. Independent experimental evidence was obtained with /sup 1/H NMR; the ratio of ..beta..-glucose to ..cap alpha..-glucose was observed to increase from an initially detected value of less than 2:3 to the equilibrium value of greater than 3:2 during the hydrolysis reaction. The data from the NMR experiments were quantitated and compared to theoretical models based on hydrolysis mechanisms involving fructosyl-oxygen bond cleavage and glucosyl-oxygen bond cleavage. The results clearly indicate fructosyl-oxygen bond cleavage under the reaction conditions employed. 39 references, 4 figures.

Mapping of caldesmon: relationship between the high and low molecular weight forms

Caldesmon is a widely distributed contractile protein that occurs in both a high molecular weight [120-150-kilodalton (kDa)] and a low molecular weight (71-80-kDa) form, depending on the tissue. The structural relationship between these two forms was examined by mapping techniques. Partial cyanogen bromide cleavage in conjunction with sodium dodecyl sulfate gel electrophoresis was used to construct a map of the cleavage points and determine the relative position of the fragments in a high molecular weight caldesmon from chicken gizzard (caldesmon125). By use of this map, markers for different regions of the protein were obtained: Antibodies directed toward certain areas were prepared by affinity purification, and specific 125I-labeled tryptic peptides were found to originate from terminal cyanogen bromide fragments. Mapping of a lower molecular weight form of caldesmon (caldesmon72 from chicken liver) revealed the presence of sequences located in both ends of caldesmon125. A terminal 38-kDa fragment of both proteins was apparently identical on the basis of arrangement of cleavage sites, antibody reactivity, and iodopeptide mapping. Fragments from the other end of both proteins exhibited an identical pattern of peptides. These results show that it is sequences located in the central area of caldesmon125 which are missing in caldesmon72, indicating that the smaller molecule is not simply a proteolytic product of the larger. The two forms of caldesmon may be derived from separate genes or by alternative splicing from a single gene.

A comparison of 30-kDa and 10-kDa hormone-containing fragments of bovine thyroglobulin.

Studies have been carried out on reduced and alkylated 19 S bovine thyroglobulin to characterize naturally occurring, iodine-rich fragments. In this report, the purification and properties of a 30-kDa, hormone-enriched polypeptide (TgE) are described and compared to that of a previously reported 10-kDa fragment (TgF). The amino acid sequence of TgF was found to overlap with that of TgE. In spite of its larger size, TgE contains only a single hormone bearing site. Both the 10- and 30-kDa fragments are derived from the NH2-terminal end of the bovine thyroglobulin. These fragments contain the principal hormone-forming site at residue 5 of the thyroglobulin sequence and appear to be formed by cleavage of the parent polypeptide chain. The mechanism which generates these cleavages is not clear since the sequences surrounding the cleavage points which give rise to these peptides are quite different. These two fragments may be precursor and product in such a process. The amino acid sequence contained within TgE includes two putative sites for N-linked glycosylation. Since no glucosamine was observed and only small amounts of neutral sugar were detected, it appears that this part of the molecule is not extensively glycosylated.

An intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in DNA.

It has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a Holliday-structure which is then converted into complete recombinant products by the second strand exchange. If this hypothesis is correct, one should be able to trap the putative Holliday intermediate by preventing the second strand exchange. In this paper, we show that substitution of phosphorothioate for phosphate in one strand of a recombination site is an effective way to block recombination while permitting the accumulation of a novel structure. This effect is seen only when phosphorothioate is positioned at a point of potential cleavage by Int recombinase, demonstrating that the inhibition of strand exchange is highly specific. Analysis of the novel structure that accumulates in these reactions proves that it contains a Holliday joint. Holliday-structures can also be detected in unblocked recombinations but are present at very low levels. The characteristics of Holliday-structure formation that we describe substantiate the proposed recombination pathway.

The site-specific cleavage of synthetic Holliday junction analogs and related branched DNA structures by bacteriophage T7 endonuclease I.

Various branched DNA structures were created from synthetic, partly complementary oligonucleotides combined under annealing conditions. Appropriate mixtures of oligonucleotides generated three specific branched duplex DNA molecules: (i) a Holliday junction analog having a fixed (immobile) crossover bounded by four duplex DNA branches, (ii) a similar Holliday junction analog which is capable of limited branch migration and, (iii) a Y-junction, with three duplex branches and fixed branch point. Each of these novel structures was specifically cleaved by bacteriophage T7 gene 3 product, endonuclease I. The cleavage reaction "resolved" the two Holliday structure analogs into pairs of duplex DNA products half the size of the original molecules. The point of cleavage in the fixed-junction molecules was predominantly one nucleotide removed to the 5' side of the expected crossover position. Multiple cleavage positions were mapped on the Holliday junction with the mobile, or variable, branch point, to sites consistent with the unrestricted movement of the phosphodiester crossover within the region of limited dyad symmetry which characterizes this molecule. Based on the cleavage pattern observed with this latter substrate, the enzyme displayed a modest degree of sequence specificity, preferring a pyrimidine on the 3' side of the cleavage site. Branched molecules that were partial duplexes (lower order complexes which possessed single-stranded as well as duplex DNA branches) were also substrates for the enzyme. In these molecules, the cleaved phosphodiester bonds were in duplex regions only and predominantly one nucleotide to the 5' side of the branch point. The phosphodiester positions 5' of the branch point in single-stranded arms were not cleaved. Under identical reaction conditions, individually treated oligonucleotides were completely refractory. Thus, cleavage by T7 endonuclease I displays great structural specificity with an efficiency that can vary slightly according to the DNA sequence.

The microheterogeneity of the crystallizable yeast cytoplasmic aspartyl-tRNA synthetase.

Yeast aspartyl-tRNA synthetase is a dimeric enzyme (alpha 2, Mr 125,000) which can be crystallized either alone or complexed with tRNAAsp. When analyzed by electrophoretic methods, the pure enzyme presents structural heterogeneities even when recovered from crystals. Up to three enzyme populations could be identified by polyacrylamide gel electrophoresis and more than ten by isoelectric focusing. They have similar molecular masses and mainly differ in their charge. All are fully active. This microheterogeneity is also revealed by ion-exchange chromatography and chromatofocusing. Several levels of heterogeneity have been defined. A first type, which is reversible, is linked to redox effects and/or to conformational states of the protein. A second one, revealed by immunological methods, is generated by partial and differential proteolysis occurring during enzyme purification from yeast cells harvested in growth phase. As demonstrated by end-group analysis, the fragmentation concerns exclusively the N-terminal end of the enzyme. The main cleavage points are Gln-19, Val-20 and Gly-26. Six minor cuts are observed between positions 14 and 33. The present data are discussed in the perspective of the crystallographic studies on aspartyl-tRNA synthetase.

Properties of a multifunctional 3′,5′-cyclic nucleotide phosphodiesterase from Lactuca cotyledons: Comparison with mammalian enzymes capable of hydrolysing pyrimidine cyclic nucleotides

Hydrolysis of 3′,5′-cyclic nucleotides by this Lactuca multifunctional cyclic nucleotide phosphodiesterase yields the corresponding 5′-nucleotides. With 2′,3′-cyclic nucleotides, the point of cleavage is affected by the nature of the base. Equimolar amounts of 2′- and 3′-AMP are produced from 2′,3′-cyclic AMP but four times more 3′-CMP than 2′-CMP is produced from 2′,3′-cyclic CMP. With 2′,3′-cyclic GMP, 2′-GMP is the sole product. The presence of one cyclic nucleotide affects the rate of hydrolysis of another. With 3′,5′-cyclic nucleotide substrates, mixed-type inhibition was exhibited by other 2′,3′- and 3′,5′-cyclic nucleotides. During hydrolysis of3′,5′-cyclic AMP, K i values of 16 and 6 μM were obtained with 3′,5′-cyclic GMP and 2′,3′-cyclic AMP, respectively. Coupled with the K m of 0.73 mM for 3′,5′-cyclic GMP and that of 1.12 mM for 2′,3′-cyclic AMP, the low K i values suggest that more than one binding site is available for each nucleotide. Hill coefficients of 1.26, 0.88 and 0.91, for 3′,5′-cyclic AMP, 3′,5′-cyclic GMP and 3′,5′-cyclic CMP, respectively, together with the linear nature of the Hill plots obtained, indicate that when a single substrate is present, there is no cooperative effect between the sites. The properties of the Lactuca enzyme are compared with those of other plant and mammalian cyclic nucleotide phosphodiesterases and the significance of the occurrence of this enzyme in Lactuca is considered.

Regulatory aspects of the colchicine interactions with tubulin.

Limited proteolysis of tubulin with subtilisin results in the cleavage of both tubulin subunits yielding S-tubulin heterodimer and 4 kDa peptide fragments containing the carboxyl-terminal domains of alpha- and beta-polypeptide chains. S-tubulin binds colchicine and the characterization of the binding of colchicine to S-tubulin molecules showed a decreased rate of decay of colchicine binding activity as compared to that of undigested tubulin. However, S-tubulin exhibited a lower colchicine binding constant than tubulin. Peptide fragments resulting from the controlled tryptic proteolysis of both pure tubulin and S-tubulin were purified by filtration chromatography and presented a strong colchicine binding activity with association constants of 4.5 X 10(6) and 2.7 X 10(6) M-1, respectively. Furthermore, these studies support our initial findings on the localization of the tubulin site for colchicine (Serrano L, Avila J, Maccioni RB: J Biol Chem 259:6607-6611, 1984) and define the colchicine binding domain in a domain of alpha-subunit from the point of limited tryptic cleavage to the site of subtilisin controlled proteolysis of that tubulin subunit. On the basis of these alterations in the interaction of colchicine upon removal of the C-terminal moiety of tubulin and since no change in the number of binding sites was found after subtilisin digestion, we suggest that the carboxyl-terminal region of tubulin subunits modulates the binding of colchicine.

Gene 3 endonuclease of bacteriophage T7 resolves conformationally branched structures in double-stranded DNA

Gene 3 endonuclease of bacteriophage T7 has been expressed from the cloned gene, purified, and characterized as to its activity on different UNA substrates. Besides its known strong preference for cutting single-stranded DNA rather than double-stranded DNA, the enzyme has a strong preference for cutting conformationally branched structures in double-stranded DNA, either X or Y-shaped branches. Three types of branched DNA substrates were used: relaxed circular DNAs containing large cruciform structures (a model for Holliday structures, presumed intermediates in genetic recombination); X-shaped molecules having a limited potential for branch migration, made from the cloned phage and bacterial arms of the lambda attachment site; and Y-shaped molecules, made by hybridizing molecules homologous except for a 2 × 21 base-pair palindrome in one of them. Gene 3 endonuclease cuts two opposing strands at or near the branchpoint to resolve these substrates into linear molecules, and does not cut the potentially single-stranded tips of the stem-and-loop structure generated from the palindrome. The position of the cleavage points on the equivalent arm of two X-shaped molecules, constructed from wild-type and mutant lambda attachment sites, show that the enzyme can cut at several different sites within or slightly 5′ of the limited region of branch migration. The various activities of gene 3 endonuclease are consistent with the known role of this enzyme in genetic recombination, in maturation and packaging of T7 DNA, and in degradation of host DNA, and suggest that the enzyme recognizes a specific structural feature in DNA. Its cleavage specificity, ready availability, and ability to act at physiological pH and ionic conditions may make gene 3 endonuclease useful as a probe for specific DNA structures or for binding of proteins that alter DNA structure.