Adenosine-guanosine preferential photocleavage of DNA by azido-benzoyl- and diazocyclopenta-dienylcarbonyloxy derivatives of 9-aminoacridine.

The photoreactions of 9-[6-(4-azidobenzamido)hexylamino]acridine (AHA) and 9-[6-(2-diazocyclopentadienylcarbonyloxy)hexylamino]acridine (DHA) with double stranded DNA result in formation of single strand nicks and alkali labile sites (adducts) with an efficiency of 6 x 10(-3) nicks per AHA and 3 x 10(-2) nicks per DHA molecule. The alkali dependent DNA cleavage by AHA shows a pronounced A+G preference whereas that by DHA is practically sequence independent. In the presence of diacridines, however, DHA exhibits a preference for cleavage at guanosines. These DNA photocleaving reagents could be useful for DNA photofootprinting and photosequencing.     

Novel DNA photocleaving agents with high DNA sequence specificity related to the antibiotic bleomycin A2.

We have designed and synthesized a series of novel DNA photocleaving agents which break DNA with high sequence specificity. These compounds contain the non-diffusible photoactive p-nitrobenzoyl group covalently linked via a dimethylene (or tetramethylene) spacer to thiazole analogues of the DNA binding portion of the antibiotic bleomycin A2. By using a variety of 5' or 3' 32P-end labeled restriction fragments from plasmid pBR322 as substrate, we have shown that photoactive bithiazole compounds bind DNA at the consensus sequence 5'-AAAT-3' and induce DNA cleavage 3' of the site. Analysis of cleavage sites on the complementary DNA strand and inhibition of DNA breakage by distamycin A indicates these bithiazole derivatives bind and attack the minor groove of DNA. A photoactive unithiazole compound was less specific inducing DNA breakage at the degenerate site 5'-(A/T)(AA/TT)TPu(A/T)-3'. DNA sequence recognition of these derivatives appears to be determined by the thiazole moiety rather than the p-nitrobenzoyl group: use of a tetramethylene group in place of a dimethylene spacer shifted the position of DNA breakage by one base pair. Moreover, much less specific DNA photocleavage was observed for a compound in which p-nitrobenzoyl was linked to the intercalator acridine via a sequence-neutral hexamethylene spacer. The 5'-AAAT-3' specificity of photoactive bithiazole derivatives contrasts with that of bleomycin A2 which cleaves DNA most frequently at 5'-GPy-3' sequences. These results suggest that the cleavage specificity exhibited by bleomycin is not simply determined by its bithiazole/sulphonium terminus, and the contributions from other features, e.g. its metal-chelating domain, must be considered. The novel thiazole-based DNA cleavage agents described here should prove useful as reagents for probing DNA structure and for elucidating the molecular basis of DNA recognition by bleomycin and other ligands.     

Novel thiazonaphthalimides as efficient antitumor and DNA photocleaving agents: effects of intercalation, side chains, and substituent groups

A series of novel antitumor and DNA photocleaving agents was designed and synthesized by fusing a (substituted) thiazole ring to the naphthalimide skeletons. C1, the most active compound against A549, was about 30-fold more cytotoxic than the compound amonafide. A1, the most active compound against P388, was about 6-fold more cytotoxic than amonafide. C2, the most efficient DNA intercalator, showed the strongest DNA photocleaving activity via superoxide anion produced under UV light at 360 nm.     

New reagents for the introduction of the thiomethyl group at sulfhydryl residues of proteins with concomitant spectrophotometric titration of the sulfhydryls: Methyl 3-nitro-2-pyridyl disulfide and methyl 2-pyridyl disulfide

Two new reagents for the titration of sulfhydryl groups in peptides and proteins and for their temporary blocking with the thiomethyl group have been developed. The sulfhydryl groups in cysteine, glutathione, and papain react quantiatively under mild conditions with these reagents, methyl 3-nitro-2-pyridyl disulfide and methyl 2-pyridyl disulfide, with concomitant methanethiolation and without the need to employ a large excess of reagent. Because of the chromophoric properties of the 3-nitro-2-thiopyridone and 2-thiopyridone products, spectrophotometric titration of the sulfhydryl groups can be carried out, accompanying their methanethiolation. The modification of the sulfhydryl groups in peptides and proteins with thiomethyl is rapidly and completely reversible upon addition of thiols such as l-cysteine.     

Novel heterocyclic family of phenyl naphthothiazole carboxamides derived from naphthalimides: synthesis, antitumor evaluation, and DNA photocleavage

A new heterocyclic family of (2-(dimethylamino)ethyl)-2-substituted phenylnaphtho[2,1-d]thiazole-5-carboxamides modified from naphthalimides was designed, synthesized, and quantitatively evaluated as antitumor agents and photonucleases. All these compounds were found to be more cytotoxic against P388 than against A549. B(3) (m-NO(2)) was found to be the strongest inhibitor for P388 with IC(50) of 1.49 microM, while B(2) was the most cytotoxic compound against A549 with IC(50) of 12 microM. B(4) (p-CH(3)), the most efficient DNA photocleaver, showed detectable DNA cleavage at 0.5 microM and total cleavage from form I to 100% form II at 50 microM. The photocleaving mechanism was changed with the modification to be via superoxide anion and radical.     

Synthesis, antitumor evaluation and DNA photocleaving activity of novel methylthiazonaphthalimides with aminoalkyl side chains

A series of methylthiazonaphthalimides was synthesized and quantitatively evaluated as efficient DNA intercalators, antitumor agents and DNA photocleavers. A(1) showed both efficient antitumor activities against cell lines of A549 and P388 with IC50 of 82.8 and 31 nM, respectively. A(3) was the strongest antitumor agent against A549 with the IC50 of 20.8 nM. A(2), the most efficient DNA intercalator, was found to be the strongest DNA photocleaver via superoxide anion. An explanation was given for the disaccord between antitumor and DNA photocleaving activities.     

The significant effect of the carbohydrate structures on the DNA photocleavage of the quinoxaline-carbohydrate hybrids

The novel DNA interactive quinoxaline-carbohydrate hybrids possessing disaccharides as the carbohydrate moieties were designed and synthesized, and their DNA photocleaving abilities were evaluated in order to examine the effect of the disaccharide structures. The configurations of the glycosidic bonds in the disaccharide strongly affected the DNA photocleaving ability, and two beta-glycosidic bond linkages were very effective for the DNA photocleavage. Furthermore, the quinoxaline-disaccharide hybrids exhibited selective cytotoxicity against cancer cells with photoirradiation.     

Novel 2-aminothiazonaphthalimides as visible light activatable photonucleases: effects of intercalation, heterocyclic-fused area and side chains

A new family of 2-aminothiazonaphthalimides with different side chains as novel intercalative and visible light activatable photonucleases, was designed, synthesized and quantitatively evaluated. The order of their photocleaving abilities was parallel to that of their intercalative properties. The compound with linear heterocyclic-fused chromophore could intercalate into and photocleave DNA more efficiently than the one with angular heterocyclic-fused chromophore. B(2), the most efficient compound, caused obvious DNA damage at 1 microM. Mechanism experiment showed that superoxide anion was involved.     

Psoralen photofootprinting of protein-binding sites on DNA

Using a BAL31 exonuclease assay to determine the sites of 4,5',8-trimethylpsoralen photocrosslinking in DNA we have shown that 5'-TA sites which are accessible to psoralen DNA interstrand photocrosslinking in naked DNA become inaccessible when protein, in casu, lambda-repressor E. coli or RNA polymerase are bound at their recognition DNA sequences (OR1 operator or deo1 promoter, respectively). These results show that psoralens can be used as photofootprinting reagents to study specific protein-DNA interactions.     

N-aroyloxylthioxo-naphthalimides as DNA photocleavers of aroyloxyl oxygen radicals: synthesis, evaluation, and substituents' effect

Novel N-Aroyloxylthioxo-naphthalimides as highly efficient 'time-resolved' DNA photocleavers of aroyloxyl radicals type were designed and synthesized. The substituents at the aroyloxyl moiety have an important and unusual influence on the DNA photocleavage, and DNA photodamages of the compounds were unusually not depended on the electronic effects of substituents on the corresponding oxygen-centered radicals. With AM1 semi-empirical quantum calculation, it was found that their photocleaving activities were correlated with the densities of electron clouds on the N-O bonds in the triplet state. N-(m-Dichloro-benzoyloxy)-thioxo-naphthalimide could photodamage DNA effectively at less than the concentration of 2 microM.     

Biocatalytic synthesis of 2′-deoxynucleotide 5′-triphosphates from bacterial genomic DNA: Proof of principle

2′-deoxynucleoside 5′-triphosphates (dNTPs) are the building blocks of DNA and are key reagents which are incorporated by polymerase enzymes during nucleic acid amplification techniques, such as polymerase chain reaction (PCR). These techniques are of high importance, not only in molecular biology research, but also in molecular diagnostics. dNTPs are generally produced by a bottom-up technique which relies on synthesis or isolation of purified small molecules like deoxynucleosides. However, the disproportionately high cost of dNTPs in low- and middle-income countries (LMICs) and the requirement for cold chain storage during international shipping makes an adequate supply of these molecules challenging. To reduce supply chain dependency and promote domestic manufacturing in LMICs, a unique top-down biocatalytic synthesis method is described to produce dNTPs. Readily available bacterial genomic DNA provides a crude source material to generate dNTPs and is extracted directly from Escherichia coli (step 1). Nuclease enzymes are then used to digest the genomic DNA creating monophosphorylated deoxynucleotides (dNMPs) (step 2). Design and recombinant production and characterization of E. coli nucleotide kinases is presented to further phosphorylate the monophosphorylated products to generate dNTPs (step 3). Direct use of the in-house produced dNTPs in nucleic acid amplification is shown (step 4) and their successful use as reagents in the application of PCR, thereby providing proof of principle for the future development of recombinant nucleases and design of a recombinant solid-state bioreactor for on-demand dNTP production.     

Photocleavage of DNA by the p-nitrobenzoyl group covalently linked to proflavine.

We have synthesized two novel DNA photocleaving agents,3,6-diamino-10-[6-(4-nitrobenzoyloxy)hexyl]acridinium chloride and 3,6-diamino-10-[6-(4-nitrobenzamido)-hexyl]acridinium chloride, and studied their DNA binding mode and cleavage properties. These compounds contain the photoactive p-nitrobenzoyl group attached to proflavine via an amide or ester linker group and a polymethylene chain. Spectroscopic and viscometric studies have shown that the compounds bind DNA by an intercalative mode. The presence of covalently-bonded intercalator is essential for the UV (310 nm) induced DNA scission. Above a critical ratio, an increase in the relative concentration of compound to DNA did not induce further cleavage. The cleavage efficiency was dependent on the type of linker group. These results are discussed in regard to possible mechanisms for photoinduced DNA breakage.     

Synthetic control of interchromophoric interaction in cationic bis-porphyrins toward efficient DNA photocleavage and singlet oxygen production in aqueous solution

We have synthesized cationic bis-porphyrins and their zinc(II) complexes with two TMPyP-like chromophores bridged by p- or m-xylylenediamine to develop effective DNA photocleaving agents. The xylylene linkers and zinc ion were introduced to control interchromophoric interaction that should be involved in photosensitization of the cationic bis-porphyrins. The molar absorptivities of all the bis-porphyrins in aqueous solution remained unchanged over a wide range of concentrations, indicating the absence of self-aggregation property. In particular, the molar absorptivity of the zinc(II) complex of the p-xylylenediamine-linked bis-porphyrin in aqueous solution was 2.0 times as large as that of unichromophoric ZnTMPyP, suggesting the absence of both intermolecular and intramolecular interchromophoric interaction. The metal-free p-xylylenediamine-linked bis-porphyrin showed the more efficient conversion ability of supercoiled to nicked circular pUC18 plasmid DNA by photosensitization than the metal-free m-xylylenediamine-linked one. Furthermore, the zinc complexes of the bis-porphyrins exhibited the more potent DNA photocleavage than did the metal-free bis-porphyrins. Singlet oxygen productivity of the four cationic bis-porphyrins was determined by measuring the decomposition rate of 1,3-diphenylisobenzofuran. The amount of singlet oxygen generated by photosensitization of the zinc(II) complex of the p-xylylenediamine-linked bis-porphyrin in aqueous solution was 2.1 times as large as ZnTMPyP, indicating the full singlet oxygen productivity. A significant relationship between the DNA photocleaving abilities and the singlet oxygen productivities of the cationic porphyrins in aqueous solution was found. Hence, the degree of the intramolecular interchromophoric interaction, the DNA photocleaving ability, and the singlet oxygen productivity of the cationic bis-porphyrins in aqueous solution were successfully controlled by means of the introduction of the appropriate linker and metal ion.     

Use of baculovirus expression vectors: development of diagnostic reagents, vaccines and morphological counterparts of bluetongue virus

Abstract The productivity and flexibility of insect baculovirus expression vectors and the ability of the baculovirus genome to incorporate (and express) large amounts of foreign DNA allows this system to be used for both single and multiple gene expression. Using the system, bluetongue virus (BTV) genes have been expressed to develop diagnostic reagents and vaccines as well as to understand the basic structures of virions. BTV which causes disease in ruminants in many parts of the world, consists of 10 double-stranded RNA segments enclosed by double capsids that are composed by 7 structural proteins. Since each protein is encoded by a single RNA species, DNA clones of all 10 RNA species were synthesized and individually expressed in baculovirus vectors at high levels. This has yielded proteins that have been shown to be excellent diagnostic and vaccine reagents. In addition, multiple expression vectors have been used to synthesize morphological structures (viral and subviral) representing BTV.     

Plasmid pGW16, a derivative of pKM101, increases post-UV DNA synthesis, but sensitises some strains of Escherichia coli to UV

Plasmid pKM101, which carries muc genes that are analogous in function to chromosomal umu genes, protected Escherichia coli strains AB1157 uvrB+ umuC+, JC3890 uvrB umuC+, TK702 uvrB+ umuC and TK501 uvrB umuC against ultraviolet irradiation (UV). Plasmid pGW16, a derivative of pKM101 selected for its increased spontaneous mutator effect, also gave some protection to the UmuC-deficient strains, TK702 and TK501. However, it sensitised the wild-type strain AB1157 to low, but protected against high doses of UV, whilst sensitising strain JC3890 to all UV doses tested. Even though its UV-protecting effects varied, pGW16 was shown to increase both spontaneous and UV-induced mutation in all strains. Another derivative of pKM101, plasmid pGW12, was shown to have lost all spontaneous and UV-induced mutator effects and did not affect post-UV survival. Plasmids pKM101 and pGW16 increased post-UV DNA synthesis in strains AB1157 and TK702, whereas pGW12 had no effect. Similarly, the wild-type UV-protecting plasmids R46, R446b and R124 increased post-UV DNA synthesis in strain TK501, but the non-UV-protecting plasmids R1, RP4 and R6K had no effect. These results accord with the model for error-prone DNA repair that requires umu or muc gene products for chain elongation after base insertion opposite non-coding lesions. They also suggest that the UV-sensitizing effects of pGW16 on umu+ strains can be explained in terms of overactive DNA repair resulting in lethal, rather than repaired UV-induced lesions.     

12－烷基化壳聚糖纳米粒-反义内皮素转换酶核酸表达质粒的制备及其性质的研究

摘要：目的：气道给予12－烷基化壳聚糖纳米粒（12－ACSs）包裹的反义内皮素转换酶（ECE）核酸表达质粒,观察对OVA致敏的小鼠变应性气道炎症的影响。方法：通过透射电镜观察12－ACSs/ 反义 ECE质粒复合体纳米粒的形成、形态及大小;应用凝胶阻滞、结合平衡、DNA沉淀和DNA酶消化实验等检测12－ACSs对反义ECE核酸表达质粒的结合保护作用;通过MTT实验检测12－ACSs对细胞的毒性;通过离体培养细胞及活体动物转染实验观察12－ACSs能否携带反义ECE核酸表达质粒成功转染。结果：电镜观察示纳米粒粒径在100－150 nm之间。12－ACSs与反义ECE核酸表达质粒在质量比为1：1时,全部反义ECE质粒被结合。应用DNase I消化后可见,12－ACSs可保护核酸免受破坏。MTT检测结果显示12－ACSs 对16HBE细胞在低浓度下几乎没有毒性。12－ACSs包裹的反义ECE核酸表达质粒的纳米粒能成功转染离体培养的气道上皮细胞及活体动物。结论：12－ACSs能够成功包裹反义ECE质粒并且成功转染16HBE及小鼠,其有可能作为一种基因治疗的载体选择之一。 关键词：哮喘 壳聚糖 纳米粒 内皮素转换酶 基因治疗     

Expression, purification and characterization of cloning-grade zinc finger nuclease

The limited number of naturally occurring rare-cutting restriction enzymes and the slow and tedious engineering of existing restriction enzymes for novel specificities have prompted the design of new strategies for the development of restriction enzymes with specificities for long DNA sequences. One possibility is using zinc finger nucleases (ZFNs)—synthetic restriction enzymes that are custom-designed to target and cleave long DNA sequences and which have been recently shown useful for DNA cloning. Here we report on the purification and biochemical analysis of ZFN-10, a custom-made ZFN. We show that Ni-affinity and gel-filtration purification methods are sufficient to produce a cloning-grade enzyme. We show that ZFN-10 can function as an accurate and reliable ZFN using the same reagents and protocols used for naturally occurring and commercially available recombinant restriction enzymes. We also show that ZFN-10 tolerates a set of target-site substitutions which can be predicted from the specificities of recognition helices incorporated into the structure of its DNA-binding domain. The relative simplicity of ZFN-10 design, expression, purification and analysis suggests that novel ZFNs can potentially be designed and applied for various recombinant DNA applications.     

Origin of sequence specific cleavage of DNA by bleomycins.

A new DNA photocleaving agent which contains bleomycin A2's DNA binding portion and its mono- and terthiazole analogues have been designed and synthesized, and their DNA binding mode and cleavage base specificity have been studied. The photoactive p-nitrobenzoyl group attached at the end of molecules cleaves DNA on UV irradiation. All the oligo-thiazole compounds exhibited high sequence specificity in DNA scission. The bithiazole derivative did not cleave DNA at or near 5'-GpT-3' or 5'-GpC-3' as expected from widely believed DNA binding mechanism of the antibiotics.     

Quantitative analysis of derivatized proteins prepared with pyridyl disulfide-containing cross-linkers by high-performance liquid chromatography

Determination of the introduced moieties into derivatized proteins is an essential step in the preparation and quality control of chemically defined immunoconjugates. For the derivatized proteins using pyridyl disulfide-containing cross-linkers such as N-succinimidyl 3-(2-pyridyldithio)propionate (SPDP) and 4-succinimidyloxycarbonyl-alpha-methyl-alpha-(2-pyridyldithio)tolu ene (SMPT), the derivatization degree (ratio of pyridyl disulfide moieties to protein) has been traditionally determined by measuring the absorbance of both the derivatized protein and 2-thiopyridone (2-TP) released from the dithiothreitol (DTT) treatment (spectrophotometric method). This method, however, causes several problems including false high and low determinations of the protein and 2-TP, respectively, low selectivity, poor reproducibility, and relatively large amounts of sample consumption. A quantitative determination method of the derivatization ratios using bovine serum albumin derivatized with SPDP and SMPT as the model system has been developed. The concentration of protein and 2-TP released from the DTT treatment of derivatized proteins was determined directly without consideration of different reagents used and their concentrations. The present HPLC method was proved to be better in terms of accuracy, selectivity, and reproducibility with micro sample consumption. Moreover, this HPLC method can be directly applied to all derivatized proteins prepared with pyridyl disulfide-containing cross-linkers.