BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction

Chemical-induced formation of BZ-junction with base extrusion

The crystal structure of BZ-junction reveals that left-handed Z-DNA stabilized by Z-DNA binding domain (Zα) is continuously stacked to right-handed B-DNA with AT bases' extrusion in the junction site. However, this structure might not fully represent the BZ-junction in solution due to the possibility of the junction formation either by crystal packing or Zα interaction. Therefore, we investigated BZ-junction in solution with chemical Z-DNA inducers using CD and 2-aminopurine base-extrusion assay. We confirmed the formation of Z-DNA and BZ-junction with base-extrusion by chemical Z-DNA inducers. However, neither typical Z-DNA nor base-extrusion could be detected with some inducers such as spermine, suggesting that the energy barrier for the formation of the BZ junction might vary depending on the Z-DNA induction conditions.

Structural diversity of supercoiled DNA

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

DNA supercoiling strongly affects its metabolism. By electron cryo-tomography, biochemical assays and molecular dynamics simulations, here the authors show that supercoiled DNA minicircles adopt unique and wide distributions of three-dimensional conformations, many with disrupted base pairs.

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp over the same MD timescales. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA.

Enzymes used in molecular biology: a useful guide

Since molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. Thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. This review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. We provide a description of the most commonly used enzymes of each group, and explain their properties and mechanism of action. By pointing out key requirements for each enzymatic activity and clarifying their limitations, we aim at guiding the reader in selecting appropriate enzymatic source and optimal experimental conditions for molecular cloning experiments.

Kinking the double helix by bending deformation

DNA bending and torsional deformations that often occur during its functioning inside the cell can cause local disruptions of the regular helical structure. The disruptions created by negative torsional stress have been studied in detail, but those caused by bending stress have only been analyzed theoretically. By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm. First, we developed an efficient method to obtain covalently closed DNA minicircles. To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases. The data showed that the regular DNA structure is disrupted by bending deformation in the 64-65-bp minicircles, but not in the 85-86-bp minicircles. Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.

Single-strand-specific nucleases

Single-strand-specific nucleases are multifunctional enzymes and widespread in distribution. Their ability to act selectively on single-stranded nucleic acids and single-stranded regions in double-stranded nucleic acids has led to their extensive application as probes for the structural determination of nucleic acids. Intracellularly, they have been implicated in recombination, repair and replication, whereas extracellular enzymes have a role in nutrition. Although more than 30 single-strand-specific nucleases from various sources have been isolated till now, only a few enzymes (S1 nuclease from Aspergillus oryzae, P1 nuclease from Penicillium citrinum and nucleases from Alteromonas espejiana, Neurospora crassa, Ustilago maydis and mung bean) have been characterized to a significant extent. Recently, some of these enzymes have been cloned, their crystal structures solved and their interactions with different substrates have been established. The detection, purification, characteristics, structure-function correlations, biological role and applications of single-strand-specific nucleases are reviewed.

Sugar non-specific endonucleases

Sugar non-specific endonucleases are multifunctional enzymes and are widespread in distribution. Apart from nutrition, they have also been implicated in cellular functions like replication, recombination and repair. Their ability to recognize different DNA structures has also been exploited for the determination of nucleic acid structure. Although more than 30 non-specific endonucleases have been isolated to date, very little information is available regarding their structure-function correlations except that of staphylococcal and Serratia nucleases. However, during the past few years, the primary structure, nature of the active site based on sequence homology, and the probable mechanism of action have been postulated for some of the enzymes. This review describes the purification, characteristics, biological role and applications of sugar non-specific endonucleases.

Kinetics and mechanism of BAL 31 nuclease action on small substrates and single-stranded DNA

Kinetic and mechanistic aspects of the action of two forms of the BAL 31 nuclease (EC 3.1.11) from Alteromonas espejiana on model substrates, small oligonucleotides, larger oligonucleotides and poly[d(A)] have been examined. The minimal oligonucleotide substrate is a 5'-phosphorylated dinucleotide and a phosphodiester not containing a nucleotide residue is not cleaved. Both forms act predominantly in an exonucleolytic fashion on single-stranded DNA polymers in a highly processive manner; however, the mechanism becomes distributive for small oligomers (3-4 nucleotide residues). The direction of attack is from the 5' end, in contrast to the mode of digestion of duplex DNA which involves attack at the 3' termini. An endonucleolytic mode of attack also exists, but at a level 2-3% or less of that of the terminally directed cleavage. Apparent values for the catalytic efficiency of the action on long DNA polymers are too large to fit a simple kinetic scheme involving a direct enzyme-substrate encounter and lead to an interpretation in which nuclease molecules are non-productively bound away from the 5' ends and undergo facilitated diffusion to yield productive (terminally bound) enzyme-substrate complexes.

Inhibition of the B to Z transition in poly(dGdC).poly(dGdC) by covalent attachment of ethidium: equilibrium studies

The effects of covalent modification of poly(dGdC).poly(dGdC) and poly(dGm5dC).poly(dGm5dC) by ethidium monoazide (a photoreactive analogue of ethidium) on the salt-induced B to Z transition are examined. Earlier studies have shown ethidium monoazide to bind DNA (in the absence of light) in a manner identical to that of the parent ethidium bromide. Photolysis of the ethidium monoazide-DNA complex with visible light results in the covalent attachment of the photoreactive analogue to the DNA. This ability to form a covalent adduct was utilized to probe the effects of an intercalating irreversibly bound adduct on the salt-induced B to Z transition of the poly(dGdC).poly(dGdC) and poly(dGm5dC).poly(dGm5dC) polynucleotides. In the absence of drug, the salt-induced transition from the B to Z structure occurs in a highly cooperative manner. In contrast, this cooperativity is diminished as the concentration of covalently attached drug is increased. The degree of inhibition of the B to Z transition is quantitated as a function of the concentration of covalently attached drug. At a concentration of one drug bound per four base pairs for poly(dGdC).poly(dGdC) and seven base pairs for poly(dGm5dC).poly(dGm5dC), total inhibition of this transition is achieved. Lower concentrations of bound drug were effective in the partial inhibition of this transition. The effects of the covalently bound intercalator on the energetics of the B to Z transition were determined and demonstrated that the adduct is effective in locking the alternating copolymer in a right-handed conformation under high salt conditions.

Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI

We have been investigating the structure, dynamics, and ligand-binding properties of the interface that exists between a right-handed conformation and a left-handed conformation (i.e., a B-Z junction) in synthetic DNA oligomers. Since exo- and endonuclease activity is known to be sensitive to the conformation of the template DNA, we have designed and synthesized a DNA oligonucleotide of 20 base pairs (designated as BZ-III) with an MboI recognition site (GATC) at the location of a potential B-Z junction. The activity of the MboI enzyme toward this molecule and DNA oligomers that contain multiple MboI sites located at B-Z junctions was monitored in the absence and presence of the Z-conformation-inducing reagent cobalt hexaammine. In all cases, the activity of the enzyme was enhanced in the presence of cobalt hexaammine. The activity of MboI toward BZ-III, in the presence and absence of cobalt hexaammine, was also examined when the DNA oligomer is also in the presence of the DNA binding drugs actinomycin D, ametantrone, or ethidium bromide. In all cases, the activity of the enzyme was inhibited in the presence of drug. The results suggest that B-Z junctions are structurally unique and that this uniqueness may alter nuclease activity at sites in or near the junction.

Vectors containing infrequently cleaved restriction sites for use in BAL 31 nuclease-assisted and end-label-mediated analysis of cloned DNA fragments

Cloning vectors derived from plasmids pUC8 and pUC18 and phage M13mp10 were constructed so as to have multiple cloning sites (MCS) flanked by the recognition/cleavage sites for the Sfi I and Not I restriction nucleases. Cleavage of vectors containing cloned DNA fragments with either of the infrequently cleaving Sfi I or Not I endonucleases will usually yield linear DNAs cleaved only at the corresponding site in the MCS, so that the cloned insert can be degraded unidirectionally by the duplex exonuclease activity of the BAL 31 nucleases until an amount equal to the length of the vector has been degraded. The ends of the above constructs resulting from cleavage with Not I or Sfi I can readily be labeled, with labeling at only the terminus of the cloned DNA available for the Sfi I site. The BAL 31 nuclease-mediated procedures enhance a previous technique for mapping of restriction enzyme fragments, allow for localization of sequences in cloned segments for which a probe is available, and improve a method for sequencing cloned inserts through the production of sets of nested unidirectional deletions from either end of the parent cloned fragment. The advantages of end-label-mediated restriction site mapping using the above vectors over existing such procedures are also demonstrated.

The inhibition of restriction endonucleases due to Z-DNA in negatively supercoiled plasmid

Plasmid pGC20 containing the (dGC)9 insert in SmaI recognition site has been used to study the inhibition of cleavage by different restriction endonuclease due to Z-DNA formation in (dCG)10 sequence of the negatively supercoiled plasmid. Data obtained indicate the different sensitivity of restriction endonucleases to DNA conformational perturbations resulted from the Z-DNA formation. Therefore, the inhibition of DNA cleavage by a particular restriction endonuclease cannot serve as a criterion for the estimation of the length of B-Z junctions in circular supercoiled DNAs.

Paranemic structures of DNA and their role in DNA unwinding

A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.

Mechanism of exonuclease action of BAL 31 nuclease

Two kinetically and molecularly distinct forms ('fast' (F) and 'slow' (S] of nuclease BAL 31 from Alteromonas espejiana effect the length reduction of linear duplex DNAs through a 3'----5'-directed exonuclease activity in conjunction with an endonuclease activity against the 5'-terminated single-stranded tails generated by the exonuclease activity. No evidence for a 5'----3' mode of exonuclease action was seen. Single-stranded DNA is degraded predominantly by the 3'----5' exonuclease action. There is a pronounced decrease, to roughly constant values, of the average lengths of the tails in partially digested duplexes at a constant extent of digestion with increasing nuclease concentration. This decrease correlates with an increasing extent of ligatability, in the absence of repair, under conditions favoring the joining of fully base-paired ends. The exonuclease action, at least against duplex substrates, is quasi-processive and removes approx. 18 and 28 nucleotides per productive enzyme-substrate encounter for the S and F species, respectively. The dependence on Ca2+ and Mg2+ concentrations of the activities has been determined.

Precursor-product relationship of larger to smaller molecular forms of the BAL 31 nuclease from Alteromonas espejiana: preferential removal of duplex exonuclease relative to endonuclease activity by proteolysis

Two molecularly and kinetically distinct major species of the extracellular nuclease BAL 31 from Alteromonas espejiana, previously characterized as the "fast" (F) and "slow" (S) BAL 31 nucleases, have been evidenced to derive from proteolysis starting from a still larger (approximately 120 kDa) precursor nuclease. The expected protease activity in the culture fluid has been confirmed and is strongly dependent on the cell growth phase. The disappearance of the largest nuclease species with the concomitant sequential appearance of first the F and then the S species has been demonstrated for nuclease obtained from culture supernatants as a function of cell growth phase. Nuclease from periplasmic extracts displayed very little of the F and S nucleases. Treatment of purified F nuclease with Pronase or subtilisin readily converted it to species with only a few percent of the native exonuclease activity against duplex DNA but retaining much of the initial activity against single-stranded DNA. Electrophoresis in nuclease-detecting gels demonstrated a parallel conversion of the larger species to one indistinguishable in molecular weight from the S species. The observed loss of exonuclease activity could correspond to the conversion of the F to the S nuclease. However, treatment of S nuclease with subtilisin resulted in a drastic reduction of exonuclease activity of this enzyme on duplex DNA with retention of most of the activity against single-stranded and nicked circular duplex DNA substrates. Evidence of internal proteolysis of the S nuclease could be seen after electrophoresis in denaturing gels but only after the denaturation buffer was adjusted to 6 M in urea. The preferential removal of the exonuclease activity may enhance the usefulness of the BAL 31 nuclease in such applications as heteroduplex mapping.

Non-contiguous regions of Z-DNA in a DNA dodecamer

The conformation of the self-complimentary DNA dodecamer d(br5CGbr5CGAATTbr5CGbr5CG) has been investigated in a variety of salt and solvent conditions by one and two-dimensional 1H NMR. In low salt aqueous solutions, the molecule forms a regular B-DNA structure similar to the unmodified dodecamer. However, in aqueous solution containing high salt concentration and methanol, the dodecamer adopts a structure in which the br5CGbr5CG ends of the molecule are in a Z-DNA like conformation and the AATT region is neither standard B-DNA nor Z-DNA. The implications of these results for the structure of junctions between B and Z-DNA and the sequence specificity of Z-DNA are discussed.

Plasticity of DNA conformation around the Drosophila melanogaster alcohol dehydrogenase gene under torsional stress

Genomic DNA of eukaryotes is thought to be organized into multiple topological domains whose conformation can be independently regulated by torsional stress. We have demonstrated the formation of altered DNA structures around the Drosophila melanogaster alcohol dehydrogenase (Adh) gene by sensitivity to endonucleases and by binding single-strand binding (SSB) protein. Several altered DNA structures were detected only on torsionally stressed DNA at specific sites. Some corresponded to the two initiation cap sites and the poly(A) addition sites and others were found in the 5'-flanking regions of both the adult and larval cap sites and in the 3'-flanking region of the Adh gene. In particular, the 5'-flanking regions both exhibited a plasticity of DNA conformation according to the strength of torsional stress and the concentration of Mg2+. SSB protein bound preferentially to the non-coding regions of the Adh gene only on torsionally stressed DNA and not on relaxed or linear DNA. The observed binding preference appeared to correspond to the thermodynamic stability of the base-pairs involved. These results suggest that DNA conformation is specifically organized around the Adh gene for gene function. The plasticity of DNA may play a role in the regulation of transcriptional activation.

Supercoil-stabilized left-handed DNA in the plasmid (dA-dT)16 insert formed in the presence of Ni2+

The (dA-dT)16 insert of the plasmid pAT32 was probed with diethyl pyrocarbonate (DEPC) and nuclease Bal3l in the presence of Ni2+ known to be able to induce transition to left-handed conformation in the synthetic poly(dA-dT).poly(dA-T). It has been shown that this insert in a supercoiled plasmid displays a DEPC modification pattern characteristic of left-handed DNA under conditions not sufficient to induce a left-handed structure in the linear plasmid and poly(dA-dT).poly(dA-T).

Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing

Structural distortions on the boundary between right-handed and left-handed segments in the superhelical plasmid pPK2 (a derivative of pUC19 containing (dC-dG)n segments cloned into polylinker) were studied by means of chemical probes. Strong osmium tetroxide, pyridine (Os,py) modification of DNA at native superhelical density (sigma) was found in four thymines surrounding the (dC-dG)13 segment. These results correlated with restriction cleavage inhibition (due to modification): BamHI cleavage was strongly inhibited, unlike the neighbouring XbaI and SalI (weak or no inhibition). In the (dC-dG)8 segment considerably weaker modification of the B-Z junctions was observed, accompanied by weak inhibition of BamHI cleavage, while the neighbouring SmaI and KpnI were not affected. Os,py modification of DNA at native sigma was not detected by nuclease S1 cleavage at and (dC-dG)n segment. However, this enzyme recognized and cleaved at the B-Z junction, osmium modified at more negative sigma. The results obtained with the glyoxal and diethyl pyrocarbonate modification support the idea of very narrow B-Z junctions at native sigma.

IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: coexistence of B and Z conformations

Tridecamers containing a central no-base residue (X) have been synthesized and hybridized to their complementary strands, so as to constitute duplexes consisting of two hexamers separated by central mismatched X-A or X-T pairs. The effect of the introduction of this deoxyribose derivative on duplex stability was investigated by measuring UV absorbance as a function of salt concentration and temperature. As expected, the duplexes containing the abnormal base pairs (X-T and X-A) are less stable when compared to the totally complementary duplexes (A-T and T-A). The X-T mismatched duplex shows the most unstable thermodynamical behaviour. The conformational changes of these duplexes were studied by IR spectroscopy in condensed phase as a function of water content. At high relative humidity, the IR spectra show that these tridecamers form B-type double stranded duplex structures. If the water content is decreased, only the duplexes m5CGm5CGCTXAGCTTC GCGCGAATCGAAG and, to a lesser degree, m5CGm5CGCTXAGCTTC GCGGCATTCGAAG undergo a partial B---Z transition involving the methylated hexamer, the conformation of the second segment remaining of the B type. These results show that only one apurinic residue leads to a flexible junction between B and Z forms in a short duplex containing 5-methyl-2'-deoxycytidines.

Preliminary spectroscopic characterization of a synthetic DNA oligomer containing a B-Z junction at high salt

It is well known that the local conformation of a segment of DNA is dependent upon both the sequence of the segment and the conditions under which the DNA is prepared. In extreme cases, the DNA may contain regions of both right and left-handed conformations, mandating the existence of a conformational junction between the two. These B-Z junctions have been observed in plasmids but, to date, no model systems have been characterized to determine the molecular nature of these junctions. Preliminary CD, UV, and NMR studies on such a model are presented here. A 16 base pair oligonucleotide, containing a potential B-Z junction, has been synthesized and characterized by the above techniques. The results suggest that this molecule contains both right and left-handed conformations under condition of high salt, and thus a B-Z junction.

Length-dependent cruciform extrusion in d(GTAC)n sequences

pBR322-derived plasmids have been constructed carrying d(GTAC)n.d(GTAC)n inserts of different lengths, in order to investigate the effect of insert size on cruciform extrusion and/or the B-Z transition. Plasmids with n ranging from 4 to 12 are hypersensitive to cleavage by the single-strand specific nucleases, S1 nuclease and Bal31 nuclease. Hypersensitive sites associated with the smaller alternating purine-pyrimidine tracts, however, coexist with the major pBR322 sites. Site-selective cleavage of these plasmids with the resolvase, T7 endonuclease I, demonstrates that all the inserts form cruciform structures when stably integrated into negatively supercoiled plasmids. An increase in the negative superhelical density of the DNA's induces cruciform formation within the insert region, resulting in a reduction in torsional stress consistent with the size of the insert. Moreover, as n decreases, the superhelical density required to stabilise the cruciform state increases. Therefore, the cruciform geometry is the favoured conformation of these d(GTAC)n.d(GTAC)n sequences under torsional stress. The stability of these cruciforms increases as n increases, with cruciformation occurring at lower superhelical densities and to the exclusion of the other pBR322 cruciforms.

Tailored removal of flanking homopolymer sequences from cDNA clones

Terminal homopolymer sequences introduced during the synthesis and cloning of cDNA molecules often interfere with subsequent expression of the cloned cDNA. We describe a general method for the removal of homopolymer flanking sequences from cDNA inserts and subsequent tailoring of the resulting termini. The cDNA insert containing homopolymer tails is first subcloned into the multiple cloning site of an appropriate transcription vector. cDNA copies are then generated from in vitro-synthesized transcripts using oligonucleotide primers complementary to the nucleotide sequences adjacent to the homopolymer tails. The resulting double-stranded cDNA contains the homopolymer flanking sequences as 3'-terminal extensions that are conveniently removed by the 3'----5' exonuclease activity of T4 DNA polymerase. If the oligonucleotide primers also contain 5'-terminal noncomplementary sequences that specify potential restriction endonuclease sites, those sites are subsequently generated by the 5'----3' polymerase activity of the T4 DNA polymerase. Thus, in the same reaction, flanking homopolymer sequences are removed and the resulting termini are tailored to specify desired sequences.

Reaction conditions affect the specificity of bromoacetaldehyde as a probe for DNA cruciforms and B-Z junctions

The reaction of bromoacetaldehyde (BAA) was investigated further with recombinant plasmids containing tracts of (CG)16, in pRW756, or (CA)32, in pRW777, which adopt left-handed Z-structures under the influence of negative supercoiling. The cruciform structures adopted by the inverted repeat sequences near the replication origins of the pBR322 vectors served as internal controls for the number of unpaired bases. The extent of reaction with the B-Z junctions and the cruciforms was dependent on the reaction and analysis conditions, the method of preparation of BAA, ionic conditions, and the amount of negative supercoiling. In contrast to the previous results of Kang and Wells, B-Z junctions in addition to cruciforms do react with BAA. However, more forcing conditions are required to detect this reaction since B-Z junctions appear to be less reactive than the single stranded loops of cruciforms. The site of reaction with DNA was readily mapped with high precision at the nucleotide level. Also, a simple method is described for determining the concentration of BAA as well as its intrinsic reactivity in a given ionic medium.

Searching for potential Z-DNA in genomic Escherichia coli DNA

The Clarke-Carbon library with Escherichia coli DNA cloned into plasmid ColE1 was partially screened for Z-DNA with the monoclonal antibody Z-D11 using the retardation of the covalently closed circular DNA-protein complex by nitrocellulose filters. About 85% of the plasmids tested at "natural" supercoil density bound to the filter. Together with binding studies of the iodinated antibody, one Z-DNA segment per about 18,000 base-pairs of E. coli DNA is observed. One clone containing the region around the lactose operon, pLC20-30, was studied in detail. Subcloning a partial Sau3A digest and selection with antibodies gave three different Z-forming sites. They were mapped to within about +/- 20 base-pairs by preparing unidirectional deletion clones, selection of protein binding plasmids on nitrocellulose filters and subsequent sizing on agarose gels. The size of the Z-DNA-forming segments was estimated from two-dimensional gels of topoisomer mixtures. Together with results from sequencing of the plasmid DNA using exonuclease III to create single-stranded templates, stretches of alternating purine-pyrimidine tracts of 12 to 15 base-pairs were found to be responsible for Z-DNA formation. One of the sites was found in the middle of the lacZ gene, where it might be an obstacle for RNA polymerase. The methods used here should also be helpful for studying other DNA-protein sites, especially if they exist only in supercoiled DNA.

1H nuclear magnetic resonance study of the dynamic properties of the B and Z-forms of poly[d(A-br5C).d(G-T)]

Poly[d(A-br5C).d(G-T)], a synthetic polynucleotide with a 50% A-T base composition, undergoes a reversible, highly co-operative transition between the right-handed B and left-handed Z conformations. The latter is stabilized at both elevated temperature and ionic strength. The B and Z-forms of poly[d(A-br5C).d(G-T)] coexist in 4.6 M-NaCl at 45 degrees C. Due to slow exchange, two sets of Tim and Gim resonances are observed and can be assigned to the B and Z conformations (the chemical shifts are, respectively, Tim = 13.4, 14.1 p.p.m. (parts/million); and Gim = 11.9, 12.4 p.p.m.). Measurements of the 1H spin-lattice (R1) and spin-spin (R2) relaxation rates of the exchangeable thymine (Tim) and guanine (Gim) imino protons have been used to probe the internal dynamics of the B and Z-forms of poly[d(A-br5C).d(G-T)] and the mechanism of the B-Z transition. The proton exchange behavior in the B and Z conformations is quite different. At elevated temperature, R1 for both Tim and Gim in the B conformation is dominated by exchange with the solvent, with Tim exchanging more rapidly than Gim. This demonstrates that exchange involves the opening of single base-pairs and that neighboring A-T and G-br5C base-pairs exchange independently of each other. B-form poly[d(A-br5C).d(G-T)] is unusual in that there is an acceleration of the Tim exchange rate with increasing NaCl concentration. Conversion to the Z-form by addition of 4.5 M-NaCl dramatically reduces both the Tim and Gim exchange rates (estimated to be less than 2 s-1 at 70 degrees C). Thus, the G-br5C base-pair and, in particular, the A-T base-pair are stabilized in the Z conformation. By measuring relaxation rates at 45 to 50 degrees C where the B and Z-forms are in equilibrium, we find that the B-Z interconversion rates are less than two per second. In the B conformation at 25 degrees C, the dipolar contributions to the imino proton relaxation rates are about one-third of those expected on the basis of a rigid rod model for 65 base-pair fragments, a difference we assign to large amplitude (30 degrees high frequency (less than 100 ns) out-of-plane motions of the bases. Conversion to the Z conformation has little effect on the dipolar contributions to relaxation, i.e. on the internal motions.(ABSTRACT TRUNCATED AT 400 WORDS)

A dominant influence of flanking sequences on a local structural transition in DNA

We have discovered a striking dependence of a structural transition in DNA on sequences that are distanced from those directly participating in the transformation. The dominant factor determining the selection of kinetic properties of cruciform extrusion is the sequence of the DNA that flanks the inverted repeat. The sequence of the inverted repeat itself appears to have little or no influence. The critical sequences that confer the unusual kinetics exhibited by the ColE1 cruciform are very A+T-rich. A single such sequence is sufficient, which may be as short as 100 bp, and it can control inverted repeats placed at either end. The effects operate in cis, are independent of polarity, and may be effective over relatively long distances. The influence of context has wide implications, possibly including the control of gene expression.

Homologous pairing of DNA molecules by Ustilago rec1 protein is promoted by sequences of Z-DNA

Plasmids containing Z-DNA stretches can be paired and linked by combined action of Ustilago rec1 protein and topoisomerase. The product formed is a hemicatenated dimer in which two DNA rings are topologically intertwined at a region of homology. Superhelicity governs the reaction. Formation of linked product is coupled with formation of Z-DNA in the plasmid, a process dependent on the superhelix density. Pairing appears to initiate within the Z-DNA sequence, not at the unwound B-Z junction. The reaction can be blocked by a Z-DNA-specific binding protein, namely Z-DNA antibody. Plasmids with alternating Z-DNA dG-dC sequences at different sites on otherwise homologous molecules can be linked at the dG-dC sequences. However, a plasmid with a (dG-dC)n.(dG-dC)n Z-DNA stretch cannot be linked with a plasmid containing a (dG-dT)n.(dC-dA)n Z-DNA stretch.

NMR, CD and IR spectroscopies of a tridecanucleotide containing a no-base residue: coexistence of B and Z conformations

The synthesis of the tridecadeoxynucleotide d(CGm5CGCGxACATGT), where x is the 1-cyano-2-deoxy-beta-D-erythropentofuranose, is described. The NMR, IR, CD studies at various salt concentrations and temperatures of this oligomer show that the B and Z conformations are simultaneously present in the same short DNA fragment. A single apurinic residue is sufficient for the coexistence of the B and Z helices on this oligomer.

Recognition of the structural distortions at the junctions between B and Z segments in negatively supercoiled DNA by osmium tetroxide

It has been shown for the first time that conformational junction between contiguous right-handed B and left-handed Z segments can be recognized by a chemical probe. Plasmid pRW751 containing (dC-dG)13 and (dC-dG)16 blocks was treated with osmium tetroxide, pyridine (a reagent known to be single-strand selective) at physiological ionic conditions (0.1 and 0.2 M NaCl) and neutral pH. Mapping of the osmium binding sites by restriction enzyme digestion followed by nuclease S1 cleavage has revealed selective binding of osmium at, or near to, the end of the (dC-dG)n segments proximal to the 95 bp lac sequence. The junction of the shorter (dC-dG)13 segment was modified to a substantially greater extent than that of the longer segment. Partial inhibition of DNA cleavage by BamHI was observed at the restriction sites neighbouring to the both (dC-dG)n segments as a result of DNA modification by osmium tetroxide. The site-selective modification occurred only in supercoiled and not in relaxed molecules. Differences in the sensitivity of the B/Z junctions in pRW751 to the osmium tetroxide were explained by different structural features of these junctions.

Hypervariable telomeric sequences from the human sex chromosomes are pseudoautosomal

Pairing of human X and Y chromosomes during meiosis initiates within the so-called pairing region at the telomeres or the chromosome short arms. Using DNA from the Y chromosome we found sequence homology in the pairing region of the human X and Y chromosomes. This DNA is telomeric, contains repetitive sequences and is highly polymorphic in the population. The polymorphism has allowed family studies which show the sequences are not inherited as though linked to the sex chromosomes. This 'pseudoautosomal' pattern of inheritance points to an obligate recombination in the pairing region of the sex chromosomes during male meiosis.

Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene

We have studied the structure adopted by an (A-T)34 sequence from a Xenopus globin gene when present in a negatively supercoiled plasmid. A variety of enzyme and chemical probing experiments and electrophoretic migration shift methods reveal that the sequence adopts cruciform geometry at moderate levels of supercoiling. The structure has the lowest free energy of formation yet observed for a cruciform, and no detectable kinetic barrier preventing rapid interconversion between extruded and unextruded conformations. Analysis of band-shift experiments reveals a twist change on cruciform formation of -5.8, slightly smaller than the -6.5 we would predict on the basis of a transition from B DNA. An attractive explanation consistent with this discrepancy is that the (A-T)34 stretch is locally underwound to about 11.7 base-pairs/helical turn at low levels of supercoiling. This calculation is made on the assumption that the cruciform junction is structurally similar to those examined previously, which is supported by the nuclease digestion results. This perturbed helical structure could be of considerable biological significance.

HhaI methylase and restriction endonuclease as probes for B to Z DNA conformational changes in d(GCGC) sequences

The capacity of the modification methylase (MHhaI) and restriction endonuclease (HhaI) form Haemophilus haemolyticus to methylate and cleave, respectively, recognition sites which are in right-handed B or left-handed Z structures was determined in vitro. Plasmids containing tracts of (dC-dG) as well as numerous individual d(GCGC) sites distributed around the vector were studied. Negative supercoiling was used to convert the (dC-dG) tracts (approximately 30 bp in length) from a right-handed to a left-handed conformation. (Methyl-3H)-SAM was used to localize and quantitate modified d(GCGC) recognition sites, whereas cleavage by HhaI was used to detect unmethylated sites. In the left-handed Z-form, the (dC-dG) blocks were not methylated by MHhaI and not cleaved by HhaI. A two-dimensional gel analysis of a family of 33 topoisomers treated with MHhaI revealed that the lack of methylation in the (dC-dG) blocks was directly correlated to the supercoil-induced B to Z transition in these segments. These results are significant with respect to enzyme-DNA interactions in general and provide the basis for using HhaI and MHhaI as probes for different DNA structures and conformational transitions under physiological conditions.

Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment

We have determined the nucleotide sequences around two alternative sites cleaved in supercoiled PM2 DNA by single-strand-specific mung bean nuclease in different ionic environments. In 10 mM Tris-HC1 (pH 7.0, 37 degrees C), the major site is a dA+dT-rich sequence which maps with a known early denaturation region at 0.75 map units. About 30 cleavages occurred in a 135 bp region. Cleavages were largely excluded at (dA)n . (dT)n (n = 3-7) sequences. Cleavage patterns of this type have not been previously observed in dA+dT-rich sequences. With the addition of 0.1 M NaC1 the major alternative site occurred in a hyphenated inverted repeat sequence 500 bp away (0.70 map units) and did not map to an early denaturation region. One major and 4 minor cleavages occurred in the region between the repeats, suggesting that a hairpin containing at most a 12 bp stem and 10 base loop is recognized. The basis for nuclease recognition of the dA+dT-rich sequence is not clear. The differences in the sequences and cleavage patterns at the alternative sites indicate that their secondary structures differ.

Transcriptionally active chromatin

Eukaryotic chromatin has a dynamic, complex hierarchical structure. Active gene transcription takes place on only a small proportion of it at a time. While many workers have tried to characterize active chromatin, we are still far from understanding all the biochemical, morphological and compositional features that distinguish it from inactive nuclear material. Active genes are apparently packaged in an altered nucleosome structure and are associated with domains of chromatin that are less condensed or more open than inactive domains. Active genes are more sensitive to nuclease digestions and probably contain specific nonhistone proteins which may establish and/or maintain the active state. Variant or modified histones as well as altered configurations or modifications of the DNA itself may likewise be involved. Practically nothing is known about the mechanisms that control these nuclear characteristics. However, controlled accessibility to regions of chromatin and specific sequences of DNA may be one of the primary regulatory mechanisms by which higher cells establish potentially active chromatin domains. Another control mechanism may be compartmentalization of active chromatin to certain regions within the nucleus, perhaps to the nuclear matrix. Topological constraints and DNA supercoiling may influence the active regions of chromatin and be involved in eukaryotic genomic functions. Further, the chromatin structure of various DNA regulatory sequences, such as promoters, terminators and enhancers, appears to partially regulate transcriptional activity.

A single apurinic site can elicit BAL 31 nuclease-catalyzed cleavage in duplex DNA

The extracellular nuclease from Alteromonas espejiana BAL 31 is a highly sensitive endonucleolytic probe for lesions that distort the helical structure of duplex DNA. The nuclease can be isolated as two distinct molecular species, the 'fast' (F) and 'slow' (S) species, which have different kinetic properties. When nonsupercoiled, covalently closed circular phage PM2 DNA containing apurinic sites introduced by heating at acid pH was incubated with individual fractions from a chromatographic column which separated the two nuclease species, cleavage of the DNA was observed which was greatly in excess of control levels using nonmodified DNA. The initial rates of such cleavage clearly paralleled the peaks of both absorbance and nuclease activity against single-stranded and linear duplex substrates. When samples of apurinic DNA were incubated with pooled fractions from the same column representing pure F and S nucleases, respectively, the rate and extent of the cleavage observed was dependent upon the average number of apurinic sites per molecule. Cleavage was readily detectable in samples containing an average of 1.1 apurinic sites per molecule with both species of the enzyme. These results indicate that either species of the BAL 31 nuclease can recognize and cleave in response to a single apurinic site in duplex DNA. The F nuclease appears to be approx. 2.5-times as efficient in cleaving DNA containing apurinic lesions as the S enzyme in extended incubations.

Supercoil-dependent features of DNA structure at Drosophila locus 67B1

We have analyzed the pattern of supercoil-dependent, single strand-specific nuclease cleavage sites across 11.6 kb (11.6 X 10(3) base-pairs) of cloned Drosophila melanogaster DNA from locus 67B1. This region contains coding sequences for the heat shock proteins hsp23, hsp26 and hsp28 as well as for a 1.6 kb developmentally regulated transcript (R). Two major sites are detected on digestion with S1 nuclease or mung bean nuclease. The most prominent site maps 100 base-pairs upstream of hsp26 in a very pyrimidine-rich region adjacent to a known region of chromatin DNAase I hypersensitivity. The other site is located approximately 800 base-pairs upstream of hsp28 in an area devoid of such chromatin-specific features. BAL31 nuclease produces a different array, with three to six strong cleavages located in the spacer DNA approx. 0.1 to 1.0 kb upstream of the DNAase I hypersensitive sites of hsp28, hsp23 and R. Thus, for each gene in the cluster a localized sequence sensitive to the winding state of the DNA is observed 5' to the gene. However, there is no precise coincidence of any of the major sites sensitive to BAL31 nuclease in the supercoiled plasmid with the sequences sensitive to DNAase I in chromatin. While all of the enzymes utilized in this study have prominent single strand-specific endonucleolytic activity, it is clear that they recognize different variants in the DNA structure induced by supercoiling. At least two classes of DNA perturbation have been detected.

Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA

Plasmids containing (C-G)n inserts have been used to study the inhibition of cleavage by restriction endonucleases due to Z-DNA formation in negatively supercoiled plasmids. The enzyme BssHII, which recognizes G-C-G-C-G-C, is strongly inhibited when the insert forms Z-DNA. The BamHI recognition sequence (G-G-A-T-C-C) was placed in four different positions near the B-Z junction and the inhibition of BamHI cleavage was determined as a function of negative superhelical density. Formation of Z-DNA in the (C-G)n insert inhibited cleavage by BamHI when its recognition sequence was located immediately adjacent to the insert or four base pairs away from it. However, no inhibition was found when the BamHI recognition site was eight base pairs away. These experiments help to define the limits of the structural perturbation associated with the B-Z junction.

Interactions of anti-poly[d(G-br5C)] IgG with synthetic, viral and cellular Z DNAs

Enzymatically synthesized poly[d(G-br5C)] was used to prepare specific polyclonal and monoclonal anti-Z DNA IgGs. The binding specificities of these antibodies were characterized using left-handed polynucleotides with the sequences d(G-x5C)n and d(A-x5C)n.d(G-T)n (mean = aza, methyl, bromo, or iodo). Polyclonal anti-poly[d(G-br5C)] IgG binds the convex surface of the Z helix as evidenced by the strong requirement for a methyl or halogen group at the C5 position of cytosine. Little or no anti-poly[d(G-br5C)] IgG binding occurs to left-handed DNAs carrying a phosphorothioate substitution in the dGpdC bond or an N-5 aza substitution in the cytosine ring. Anti-poly[d(G-br5C)] IgG can stabilize transient Z DNA structures in both polymer families, thereby displacing the equilibrium in solution between the right-and left-handed DNA conformations. Anti-poly[d(G-br5C)] IgG binding sites are found in all tested covalently closed circular natural DNAs (Form I) at their extracted negative superhelical densities, but not in any of the corresponding relaxed Form II or linear Form III DNAs. Binding of anti-poly[d(G-br5-C)] IgG leads to a reduction in the electrophoretic mobility of Form I DNA (e.g. SV40, phi X174, or pBR322) and to the formation of dimers comprised of the bivalent antibody and two supercoiled Form I DNA molecules. The dimers are converted to monomers by DTT treatment. The formation of IgG-DNA complexes is dependent on external conditions (ionic strength, temperature), the properties of the DNA (torsional stress, sequence), and the immunoglobulin (specificity, valency, and concentration). Higher order oligomeric species, indicative of two or more left-handed segments per DNA molecule are formed in reactions of anti-poly[d(G-br5C)] IgG with M13 RF I DNA but not with SV40, pBR322, or phi X174 DNAs. However, oligomers of the latter are generated with other anti-Z DNA IgGs having a broader spectrum of anti-Z DNA reactivity. Conditions which destabilize natural Z sequences in deproteinized supercoiled genomes are: monovalent salt concentrations at or above the 'physiological' range, high temperature, and topological relaxation with DNA gyrase (in the absence of ATP) or with type I topoisomerases. DNA gyrase (plus ATP) catalyses an increase in DNA negative superhelical density which leads to greater anti-Z DNA IgG binding, indicating the formation of additional left-handed regions. Polytene chromosomes of insect larvae bind anti-poly[d(G-br5C)] IgG specifically and stably at Z DNA sites. The distribution of this IgG binding differs in certain regions from that displayed by anti-Z DNA IgG probes with other sequence specificities.(ABSTRACT TRUNCATED AT 400 WORDS)