Specific hydrolysis of the cohesive ends of bacteriophage lambda DNA by three single strand-specific nucleases.

Procedures have been worked out for Aspergillus nuclease S1 and mung been nuclease to quantitatively cleave off both of the 12-nucleotide long, single-stranded cohesive ends of lambdaDNA. This cleavage is indicated by the almost complete elimination of the repair incorporation of radioactive nucleotides by DNA polymerase into the digested DNA. With S1 nuclease, cleavage was complete at 10 degrees as well as at 30 degrees. Under the conditions for quantitative cleavage of the single-stranded regions there was no digestion of the double-stranded lambdaDNA. The mung bean nuclease cleaved off the cohesive ends completely at 30 degrees but at 5 degrees, the cleavage was not complete even at high enzyme concentration. The nearest neighbor analysis of the repaired DNA indicates that at 5 degrees about four nucleotides remained undigested. The mung bean nuclease also introduced, under the conditions used, some nicks into double-stranded DNA as determined by the repair incorporation. The Escherichia coli exonuclease VII cleaved off part of the cohesive ends of lambdaDNA, leaving two nucleotides on each end as single-stranded tails.     

Incision at nucleotide insertions/deletions and base pair mismatches by the SP nuclease of spinach

Spinach leaves contain a highly active nuclease called SP. The purified enzyme incises single-stranded DNA, RNA, and double-stranded DNA that has been destabilized by A-T-rich regions and DNA lesions [Strickland et al. (1991) Biochemistry 30, 9749-9756]. This broad range of activity has suggested that SP may be similar to a family of nucleases represented by S1, P1, and the mung bean nuclease. However, unlike these single-stranded nucleases that require acidic pH and low ionic strength conditions, SP has a neutral pH optimum and is active over a wide range of salt concentrations. We have extended these findings and showed that an outstanding substrate for SP is a mismatched DNA duplex. For base-substitution mismatches, SP incises at all mismatches except those containing a guanine residue. SP also cuts at insertion/deletions of one or more nucleotides. Where the extrahelical DNA loop contains one nucleotide, the preference of extrahelical nucleotide is A > T approximately C but undetectable at G. The inability of SP to cut at guanine residues and the favoring of A-T-rich regions distinguish SP from the CEL I family of neutral pH mismatch endonucleases recently discovered in celery and other plants [Oleykowski et al. (1998) Nucleic Acids Res. 26, 4597-4602]. SP, like CEL I, does not turn over after incision at a mismatched site in vitro. Similar to CEL I, the presence of a DNA polymerase or a DNA ligase allows SP to turn over and stimulate its activity in vitro by about 20-fold. The possibility that the SP nuclease may be a natural variant of the CEL I family of mismatch endonucleases is discussed.     

Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region.

DNA unwinding of autonomously replicating sequence 1 (ARS1) from the yeast Saccharomyces cerevisiae was investigated. When a negatively supercoiled plasmid DNA containing ARS1 was digested with single-strand-specific mung bean nuclease, a discrete region in the vector DNA was preferentially digested. The regions containing the core consensus A domain and the 3'-flanking B domain of ARS1 were weakly digested. When the DNA was incubated with the multisubunit single-stranded DNA-binding protein (SSB, also called RPA [replication protein A]) from human and yeast cells prior to mung bean nuclease digestion, the cleavage in the A and B domains was greatly increased. Furthermore, a region corresponding to the 5'-flanking C domain of ARS1 was digested. These results indicate that three domains of ARS1, each of which is important for replication in yeast cells, closely correspond to the regions where the DNA duplex is easily unwound by torsional stress. SSB may stimulate the unwinding of the ARS1 region by its preferential binding to the destabilized three domains. Mung bean nuclease digestion of the substitution mutants with mutations of ARS1 (Y. Marahrens and B. Stillman, Science 255:817-823, 1992) revealed that the sequences in the B2 and A elements are responsible for the unwinding of the B domain and the region containing the A domain, respectively.     

Characterization of the genome of the Rhodococcus rhodochrous bacteriophage NJL.

Temperate bacteriophage NJL of Rhodococcus rhodochrous has a 49-kb linear double-stranded DNA with cohesive ends (cos). NJL DNA has unique target sites for HindIII and SspI, two target sites each for NheI and ScaI, and no cleavage site for AxyI, DraI, EcoRI, SacI, and SphI. The single-stranded regions of cos ends were ligated to each other with T4 DNA ligase, removed with mung bean nuclease, or blunted with the Klenow large fragment of DNA polymerase I; then the sequences of the cos ends were determined. Comparison of these sequences revealed that the single-stranded regions are complementary and 18 bases long and protrude at the 3' ends; they have the following sequences: 5'-TTGGCACCGTGGGAGGAG-3' and 3'-AACCGTGGCAC CCTCCTC-5'. A physical map of NJL was constructed by a cos mapping method based on information about the structure of the cohesive ends and multiple digestions with restriction endonucleases.     

l-DOPA (l-3,4-dihydroxyphenylalanine) affects rooting potential and associated biochemical changes in hypocotyl of mung bean, and inhibits mitotic activity in onion root tips

A study was undertaken to explore the effect of l-DOPA (l-3,4-dihydroxyphenylalanine) on the rooting potential of hypocotyl cuttings of mung bean (Phaseolus aureus Roxb. var. SML-32) and related biochemical changes at the post-expression phase. At lower concentrations of (0.0001–0.1 mM) l-DOPA, there was no change in rooting potential, though the average number of roots per cutting and root length were significantly decreased (except at 0.0001 mM). However, at 1.0 mM concentration, a 50% inhibition in rooting potential was noticed and the root number and length were severely reduced. In contrast, at 2.5 mM l-DOPA, none of the hypocotyl cutting rooted. The decrease in rooting potential was associated with a significant effect on the biochemical changes measured in terms of protein and carbohydrate metabolism and activity of peroxidases. In the l-DOPA treated hypocotyl cuttings, there was a significant reduction in the protein and carbohydrate content, whereas activities of associated enzymes proteases and amylases decreased, particularly at higher treatment concentration (>1.0 mM). It indicated negative effect of l-DOPA on these two important metabolic processes. Likewise, activity of peroxidases also decreased in the l-DOPA treated hypocotyl mung bean cuttings thereby indicating its role in suppressing rhizogenesis as the enzyme is involved in lignification process during cell division. l-DOPA suppressed mitotic activity in the root tip cells of onion indicating thereby its interference with the cell division, which is required for the formation of new meristematic tissue during rhizogenesis. Based on the obtained results, it is concluded that l-DOPA interferes with the various biochemical processes in the mung bean hypocotyl cuttings thereby affecting their rooting potential.     

Caffeic acid affects early growth, and morphogenetic response of hypocotyl cuttings of mung bean (Phaseolus aureus)

Caffeic acid (CA) is one of the most common cinnamic acids ubiquitously present in plants and implicated in a variety of interactions including allelopathy among plants and microbes. This study investigated the possible interference of CA with root growth and the process of rhizogenesis in hypocotyl cuttings of mung bean (Phaseolus aureus=Vigna radiata). Results indicated that CA (0-1000 microM) significantly suppressed root growth of mung bean, and impaired adventitious root formation and root length in the mung bean hypocotyl cuttings. Further investigations into the role of CA in hampering root formation indicated its interference with the biochemical processes involved in rooting process at the three stages - root initiation (third day; RI), root expression (fifth day; RE), and post-expression (seventh day; PE) - of rhizogenesis. CA caused significant changes in the activities of proteases, peroxidases (PODs), and polyphenol oxidases (PPOs) during root development and decreased the content of total endogenous phenolics (TP) in the hypocotyl cuttings. The enhanced activity of PODs and PPOs, though, relates to lignification and/or phenolic metabolism during rhizogenesis; yet their protective role to CA-induced stress, especially during the PE phase, is not ruled out. At 1000 microM CA, where rooting was significantly affected, TP content was very high during the RI phase, thus indicating its non-utilization. The study concludes that CA interferes with the rooting potential of mung bean hypocotyl cuttings by altering the activities of PODs and PPOs and the endogenous TP content that play a key role in rhizogenesis.     

脱落酸对绿豆下胚轴不定根发生的影响

以10^-4 mol/L脱落酸(ABA)处理绿豆种子24 h,在幼苗下胚轴长6 cm时,切除根部作为插条,研究ABA对插条不定根发生及插条基部细胞周期时相的影响。结果表明,ABA可促进下胚轴插条不定根发生,增加生根数和生根范围;ABA提高插条基部细胞色氨酸转氨酶、吲哚丙酮酸脱羧酶和吲哚乙醛脱氢酶的比活性,增加吲哚乙酸含量,同时进入细胞周期S期的基部细胞数目增加,促进DNA合成,有利于不定根的发生。     

Promotion of adventitious root formation by 4-chlororesorcinol: A polyphenol oxidase inhibitor

The extent of rooting in cuttings of Phaseolus vulgaris L., and Vigna radiata Wilcz. was affected by 4-chlororesorcinol, a polyphenol oxidase inhibitor. More root primordia and more roots were formed after 4-chlororesorcinol treatment both with and without 10^-5M Indole butyric acid. Promotion of rooting was observed also in cuttings of Elaeagnus pungens, Gypsophilia elegans and Kalanchoe blossfeldiana. The enhancement in bean and mung bean was accompanied by a concomitant wider spatial distribution of the primordia and the resulting adventitious roots. The formation of primordia in the treated cuttings was delayed by 12–24 hours, compared to untreated cuttings. The treatment was effective only when given during the first hours after the preparation of the cutting of bean and mung bean, suggesting involvement in the initiation stage. Hypocotyl extracts of mung bean cuttings, pretreated with 4-chlororesorcinol, exhibited reduced polyphenol oxidase activity. The inhibition was not reversed by washing of the treated extract in 50% acetone or by an overnight dialysis, suggesting tight or maybe even irreversible binding of the inhibitor to the enzyme.Abbreviations 4-CR 4-chlororesorcinol - IBA Indole butyric acid - PPO polyphenol oxidase     

Mung bean nuclease I. Terminally directed hydrolysis of native DNA.

Under conditions which favor the duplex structure of DNA, mung bean nuclease catalyzes a limited number of double-strand cleavages (probably less than 50) in the interior of native T7 DNA. However, under conditions which are not as favorable to a tight helical structure, the large duplex polymers previously produced are completely degraded from their termini with a continuous accumulation of mono-, di-, and trinucleotides. The terminally directed activity is an intrinsic property of the enzyme molecule because (1) it is inactivated and reactivated in parallel with the single-strand activity and (2) the two activities coelectrophorese on analytical gels. Kinetic measurements indicate that the apparent Km for the terminally directed hydrolysis of native DNA is relatively high. The pH optimum for both the hydrolysis of denatured DNA and the terminally directed hydrolysis of native DNA becomes more acidic with increasing salt concentration. The relative preference for single-stranded structures increases as the pH becomes more basic.     

Osmium tetroxide: a new probe for site-specific distortions in supercoiled DNAs.

Supercoiled plasmids Col E1 and cDm 506 (a Col E1 derivative carrying the D. melanogaster histone gene repeat) were treated with OsO4 in presence of pyridine and the reaction products were analyzed using different approaches. Gel electrophoresis showed that OsO4 binding to supercoiled DNA induced its relaxation without nicking. The amount of osmium bound to DNA (as determined electrochemically) increased with the extent of DNA relaxation. As a result of osmium modification of supercoiled cDm 506, a single denaturation "bubble" was observed in the electron microscope. Mapping of the osmium binding site by S1 nuclease cleavage followed by restriction enzyme digestion has revealed one major site in the intergenic spacer between the H1 and H3 histone genes of D. melanogaster. This site differs from the site cleaved by S1 nuclease in supercoiled DNA in the absence of osmium.     

Changes in site specificity of single-strand-specific endonucleases on supercoiled PM2 DNA with temperature and ionic environment.

Mung bean nuclease sites in supercoiled PM2 DNA at neutral pH were located by linearizing the singly-nicked circular DNA product with venom phosphodiesterase followed by restriction endonuclease mapping. The locations of the sites varied with small changes in temperature and in concentration of NaC1 or magnesium ion. Different environmental changes which affect duplex stability in the same direction showed similar effects on the number of sites and in some cases resulted in identical cleavage patterns. Venom phosphodiesterase and P1 nuclease showed cleavage patterns similar to mung bean nuclease under the same environmental conditions and showed similar variations in cleavage patterns when environmental conditions were changed. Relaxed, closed-circular DNA was slowly cleaved at numerous sites whose locations did not vary with environment. Changes in site specificity are likely the result of environmental effects on the conformation of supercoiled DNA as opposed to effects on the single-strand-specific endonucleases themselves.     

Adriamycin-mediated introduction of a limited number of single-strand breaks into supercoiled DNA

It was reported previously that Adriamycin converts form I covalently closed circular, supercoiled bacteriophage PM2 DNA to the relaxed circular form II DNA; no form III linear DNA was produced as a result of the extracellular action of Adriamycin in the presence of NADH-dehydrogenase. When form II DNA, produced by the action of Adriamycin, was treated with the BAL 31 nuclease, a single sharp DNA band after agarose gel electrophoresis indicated the presence of only full-length linear form III DNA. As one of its activities, the BAL 31 nuclease introduces a single-strand break in the complementary strand opposite a preexisting single-strand break. When form II DNA, produced by the action of gamma irradiation, was reacted with the BAL enzyme, the resulting linear DNA molecules exhibited a broad range of molecular weights, indicating the presence of many single-strand breaks in the substrate form II DNA. When the Adriamycin-produced form II DNA was treated with restriction endonucleases that cleave PM2 DNA at a single site, either with or without pretreatment with the BAL enzyme, the formation of only full-length linear DNA was observed. Thus, the drug is capable of introducing one or only a very limited number of single-strand breaks into supercoiled DNA; furthermore, these breaks are introduced at random sites along the DNA molecules.     

Biochemical properties and hormonal regulation of barley nuclease

The amino acid composition and NH2-terminal amino acid sequence of barley nuclease (EC 3.1.30.2) were determined. The amino acid composition is similar to that of mung bean nuclease, and therefore the biochemical properties of barley nuclease were characterized and compared with those of mung bean and other plant nucleases. The 3'-nucleotidase activity of barley nuclease is greater for purine than for pyrimidine ribonucleotides. The enzyme has little activity towards ribonucleoside 2' and 5'-monophosphates, and deoxyribonucleoside 3' and 5'-monophosphates, and is also inactive towards the 3'-phosphoester linkage of nucleoside cyclic 2',3' and 3',5'-monophosphates. The enzyme hydrolyzes dinucleoside monophosphates, showing strong preference for purine nucleosides as the 5' residues. Barley nuclease shows significant base preference for homoribonucleic acids, catalyzing the hydrolysis of polycytidylic acid greater than polyuridylic acid greater than polyadenylic acid much greater than polyguanylic acid. The enzyme also has preference for single-stranded nucleic acids. Hydrolysis of nucleic acids is primarily endonucleolytic, whereas the products of digestion possess 5'-phosphomonoester groups. Nuclease activity is inhibited by ethylenediaminetetraacetic acid and zinc is required for reactivation. Secretion of nuclease from barley aleurone layers is dependent on the hormone gibberellic acid [Brown, P.H. and Ho, T.-h. D. (1986) Plant Physiol. 82, 801-806]. Consistent with these results, gibberellic acid induces up to an eight-fold increase in the de novo synthesis of nuclease in aleurone layers. The secreted enzyme is a glycoprotein having an apparent molecular mass of 35 kDa. It consists of a single polypeptide having an asparagine-linked, high-mannose oligosaccharide. The protein portion of the molecule has a molecular mass of 33 kDa.     

The conformation of single-stranded nucleic acids tDNA versus tRNA

Conformational analyses using the single-strand-specific nuclease from mung bean and restriction endonucleases have been performed on a series of DNA fragments related to the sequence of the yeast initiator tRNA(Met). Mung bean nuclease cleaves DNA fragments exclusively in some, but not all, single-stranded regions as predicted by RNA secondary structural rules. Comparison of cleavage patterns of yeast initiator tRNA(Met), tDNA(Met) (a DNA oligomer having the sequence of tRNA(Met] and the anti-tDNA(Met) (the complement of tDNA(Met] suggests that the conformation of the three molecules is very similar. Furthermore, both tDNA and anti-tDNA are cleaved by HhaI and CfoI restriction endonucleases at two GCG/C sites which would be in double-stranded regions (the acceptor and dihydrouridine stem), if the two molecules adopt the tRNA cloverleaf structure. On the other hand, minor cleavage products show that the core region, i.e. the extra loop area, is slightly more exposed in tDNA and in anti-tDNA than in tRNA. Therefore, we submit that the global conformation of nucleic acids is primarily dictated by the interaction of purine and pyrimidine bases with atoms and functional groups common to both RNA and DNA. In this view the 2'-hydroxyl group, in tRNA at least, is an auxiliary structural feature whose role is limited to fostering local interactions, which increase the stability of a given conformation.     

Enhancement of adventitious root formation in mung bean cuttings by 3,5-dihalo-4-hydroxybenzoic acids and 2,4-dinitrophenol

3,5-Dihalo-4-hydroxybenzoic acids enhanced adventitious root formation in mung bean (Vigna radiata L.) cuttings. 3,5-Diiodo-4-hydroxybenzoic acid was more active than 3,5-dichloro-4-hydroxybenzoic acid, increasing the number of roots formed by about 4-fold. 2,4-Dinitrophenol also enhanced significantly adventitious root formation in mung bean cuttings. The phenolic compounds were active with or without indole-3-acetic acid. The possible mechanism by which these phenolic compounds enhance rooting is discussed.Abbreviations CCCP carbonyl cyanide 3-chlorophenylhydrazone - DIHB 3,5-diiodo-4-hydroxybenzoic acid - DNP 2,4-dinitrophenol     

Specific cleavage of kinetoplast minicircle DNA from Leishmania tarentolae by mung bean nuclease and identification of several additional minicircle sequence classes

Multiple sequence classes of kinetoplast minicircle DNA from Leishmania tarentolae were cleaved by mung bean nuclease in the presence of formamide, yielding unit length linear molecules which retained the anomalous electrophoretic mobility in acrylamide characteristic of minicircle DNA. No specific cleavage site sequence common to all minicircle sequence classes was apparent, although the main region of nuclease cleavage was localized approximately 350 bp from the unique SmaI restriction site of the conserved region found in all minicircle sequence classes. Covalent closure of the minicircle substrate was not a requirement for cleavage, as linearized network-derived or cloned minicircles were also cleaved by mung bean nuclease at similar locations. The partial sequences of several new minicircle sequence classes released from the network by mung bean nuclease are also reported.     

A novel single-stranded DNA-specific endonuclease from pea chloroplasts

A nuclease with novel activities has been isolated and purifiedto apparent homogeneity from pea chloroplasts. The enzyme preferssingle-stranded (ss) circular DNA; its activity being 1500-foldhigher with the ss circular DNA than with the linear double-strandedDNA substrates. The single-stranded DNase activity is stableat moderately high temperature (50 C) and inhibited in thepresence of 75 mM NaCl. It binds negatively supercoiled DNAin the stoichiometric fashion, but behaves catalytically onthe single-stranded circular DNA. Although the DNase activitydoes not recognize any specific nucleotide sequence, the co-operativemode of activity seems to be a novel one. The protein is a monomerof 35 kDa and binds with DNA predominantly through electrostaticinteractions. The drug distamycin blocks the endonuclease activitysuggesting that the protein binds at the minor groove of DNA.A RNase activity has also been found associated with the ss-DNAendonuclease. Key words: Pea, chloroplast, endonuclease     

Interaction of auxins with growth-retarding, -inhibiting and ethylene-producing chemicals in rooting of cuttings

The growth retarding chemical Cycocel significantly synergizedIAA- and IBA-induced rooting of mung bean and IBA-induced rootingof tomato cuttings. In marigold, Cycocel and B-Nine promotedrooting when applied alone but did not synergize auxin-inducedroot formation. Chlorflurenol, a growth-inhibiting morphactin,antagonized auxin-induced rooting of all three species; inhibitionwas especially marked in the presence of IBA. The ethylene-producingchemical Amchem promoted rooting of mung bean and marigold cuttingswhen applied alone. In tomato cuttings, Amchem significantlysynergized IAA-induced root formation. (Received July 5, 1972; )     

The DNase activity of RNase T and its application to DNA cloning.

RNase T is one of eight distinct 3'-->5' exoribonucleases present in Escherichia coli. The enzyme plays an important role in stable RNA metabolism, including tRNA end turnover and 3' maturation of most stable RNAs because it is the only RNase that can efficiently remove residues near a double-stranded (ds) stem. In the course of study of its specificity and mechanism, we found that RNase T also has single-strand-specific DNase activity. Purified RNase T degrades both single-stranded (ss)RNA and ssDNA in a non-processive manner. However, in contrast to its action on RNA, RNase T binds ssDNA much more tightly and shows less sequence specificity. As with RNA, DNA secondary structure strongly affects its degradation by RNase T. Thus, RNase T action on a dsDNA with a single-stranded 3'-extension efficiently generates blunt-ended DNA. This property of RNase T suggested that it might be a useful enzyme for blunt-ended DNA cloning. We show here that RNase T provides much higher cloning efficiency than the currently used mung bean nuclease.