[Pharmacokinetics of 11 active components of Psoraleae Fructus in normal and diabetic rats]

A total of 11 active ingredients including psoralen, isopsoralen, bakuchiol, bavachalcone, bavachinin, corylin, coryfolin, isobavachalcone, neobavaisoflavone, bakuchalcone, and corylifol A from Psoraleae Fructus in the plasma samples of diabetic and normal rats were simultaneously determined by UHPLC-MS/MS. The pharmacokinetic parameters were calculated to elucidate the pharmacokinetic profiles of coumarins, flavonoids, and monoterpene phenols in normal and diabetic rats. The rat model of type 2 diabetes mellitus(T2DM) was induced by a high-sugar and high-fat diet combined with injection of 1% streptozotocin every two days. The plasma samples were collected at different time points after the rats were administrated with Psoraleae Fructus. The proteins in the plasma samples were precipitated by ethyl acetate, and the plasma concentrations of the 11 components of Psoraleae Fructus were determined by UHPLC-MS/MS. The pharmacokinetic parameters were calculated by DAS 3.0. The results showed that the pharmacokinetic beha-viors of 8 components including psoralen, isopsoralen, bakuchiol, and bavachinin from Psoraleae Fructus in both female and male mo-del rats were significantly different from those in normal rats. Among them, the coumarins including psoralen, isopsoralen, and corylin showed lowered levels in the blood of both female and male model rats. The flavonoids(bavachinin, corylifol A, and bakuchalcone) and the monoterpene phenol bakuchiol showed decreased levels in the female model rats but elevated levels in the male model rats. It is suggested that the dosage of Psoraleae Fructus should be reasonably adjusted for the patients of different genders at the time of clinical administration.

Unique Crosslinking Properties of Psoralen-Conjugated Oligonucleotides Developed by Novel Psoralen N-Hydroxysuccinimide Esters

Psoralens and their derivatives, such as trioxsalen, have unique crosslinking features to DNA. However, psoralen monomers do not have sequence-specific crosslinking ability with the target DNA. With the development of psoralen-conjugated oligonucleotides (Ps-Oligos), sequence-specific crosslinking with target DNA has become achievable, thereby expanding the application of psoralen-conjugated molecules in gene transcription inhibition, gene knockout, and targeted recombination by genome editing. In this study, we developed two novel psoralen N-hydroxysuccinimide (NHS) esters that allow the introduction of psoralens into any amino-modified oligonucleotides. Quantitative evaluation of the photo-crosslinking efficiencies of the Ps-Oligos to target single-stranded DNAs revealed that the crosslinking selectivity to 5-mC is the unique feature of trioxsalen. We found that the introduction of an oligonucleotide via a linker at the C-5 position of psoralen can promote favorable crosslinking to target double-stranded DNA. We believe our findings are essential information for the development of Ps-Oligos as novel gene regulation tools.

[Quality evaluation of Psoraleae Fructus based on QAMS method and TLC identification]

The present study established a determination method of Psoraleae Fructus by quantitative analysis of multi-components by the single marker(QAMS) and further improved the thin-layer chromatography(TLC) method. The QAMS method was established by UPLC with psoralen as the internal marker, and the content of psoralenoside, isopsoralenoside, psoralen, and isopsoralen was simultaneously determined. As revealed by the comparison with results of the external standard method, the QAMS method was accurate and feasible. According to the current quality standards of Psoraleae Fructus, the TLC method was further optimized and improved, and bakuchiol was added for identification based on the original TLC method with psoralen and isopsoralen as indicators. This study provides a reference for improving the quality control method of Psoraleae Fructus.

Light- and laser-based treatments for granuloma annulare: A systematic review

BACKGROUND

Granuloma annulare (GA) is challenging to treat, especially when generalized. A systematic review to support the use of light- and laser-based treatments for GA is lacking.

METHODS

We performed a systematic review by searching Cochrane, MEDLINE, and Embase. Title, abstract, full-text screening, and data extraction were done in duplicate. Quality appraisal was performed using the Joanna Briggs Institute critical appraisal tool for case series.

RESULTS

Thirty-one case series met the inclusion criteria, representing a total of 336 patients. Overall, psoralen ultraviolet light A (PUVA) showed the greatest frequency of cases with complete response (59%, n = 77/131), followed by photodynamic therapy (PDT) (52%, n = 13/25), ultraviolet light B (UVB)/narrowband UVB (nbUVB)/excimer laser (40%, n = 19/47), UVA1 (31%, n = 27/86), and lasers (29%, n = 8/28). Overall across treatment modalities, higher response rates were seen in localized GA compared to generalized GA.

CONCLUSIONS

The body of evidence for light- and laser-based treatment of GA is sparse. Our results suggest that PUVA has a high clearance rate for GA but its use may be limited by concerns of carcinogenesis. Although PDT has the second highest clearance rate, adverse effects, small sample sizes, impractical treatment delivery (especially with generalized disease), and long-term concerns of carcinogenesis may limit its use. Although UVB/nbUVB/excimer laser appeared slightly less effective than other light therapies, we recommend UVB/nbUVB/excimer laser therapy as a first-line treatment for patients with generalized GA given wider availability and a favorable long-term safety profile.

Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription

DNA supercoiling is a key regulator of all DNA metabolic processes including replication, transcription, and recombination, yet a reliable genomic assay for supercoiling is lacking. Here, we present a robust and flexible method (Psora-seq) to measure whole-genome supercoiling at high resolution. Using this tool in Escherichia coli, we observe a supercoiling landscape that is well correlated to transcription. Supercoiling twin-domains generated by RNA polymerase complexes span 25 kb in each direction - an order of magnitude farther than previous measurements in any organism. Thus, ribosomal and many other highly expressed genes strongly affect the topology of about 40 neighboring genes each, creating highly integrated gene circuits. Genomic patterns of supercoiling revealed by Psora-seq could be aptly predicted from modeling based on gene expression levels alone, indicating that transcription is the major determinant of chromosome supercoiling. Large-scale supercoiling patterns were highly symmetrical between left and right chromosome arms (replichores), indicating that DNA replication also strongly influences supercoiling. Skew in the axis of symmetry from the natural ori-ter axis supports previous indications that the rightward replication fork is delayed several minutes after initiation. Implications of supercoiling on DNA replication and chromosome domain structure are discussed.

Design, Synthesis, and Biological Evaluation of Novel Psoralen-Based 1,3,4-Oxadiazoles as Potent Fungicide Candidates Targeting Pyruvate Kinase

Pyruvate kinase (PK) has been considered as a promising fungicide target discovered in our previous studies. Natural compounds are important sources for discovery and development of new pesticides. To continue our ongoing studies on the discovery of novel PK-targeted fungicides, a series of novel psoralen derivatives including a 1,3,4-oxadiazole moiety were designed by a computer-aided pesticide molecular design method, synthesized, and evaluated for their fungicidal activity. The bioassay results indicated that compounds 11d, 11e, 11g, 11i, and 12a showed excellent in vitro fungicidal activity against Botrytis cinerea with EC₅₀ values of 4.8, 3.3, 6.3, 5.4, and 3.9 μg/mL, respectively. They were more active than the corresponding positive control YZK-C22 [3-(4-methyl-1,2,3-thiadiazol-5-yl)-6-(trichloromethyl)-[1,2,4]-triazolo-[3,4-b][1,3,4]-thiadiazole] (with an EC₅₀ value of 13.4 μg/mL). Compounds 11g and 11i displayed promising in vivo fungicidal activity against B. cinerea with 80 and 70% inhibition at a concentration of 200 μg/mL, respectively. They possessed much higher fungicidal activity than the positive control psoralen and comparable activity with the positive control pyrisoxazole. Enzymatic assays indicated that 11i showed good BcPK inhibition with an IC₅₀ value of 39.6 μmol/L, comparable to the positive control YZK-C22 (32.4 μmol/L). Molecular docking provided a possible binding mode of 11i in the BcPK active site. Our studies suggested that the psoralen-based 1,3,4-oxadiazole 11i could be used as a new fungicidal lead targeting PK for further structural optimization.

Studying Single-Stranded DNA Gaps at Replication Intermediates by Electron Microscopy

Single-stranded DNA gaps are frequent structures that accumulate on newly synthesized DNA under conditions of replication stress. The identification of these single-stranded DNA gaps has been instrumental to uncover the mechanisms that allow the DNA replication machinery to skip intrinsic replication obstacles or DNA lesions. DNA fiber assays provide an essential tool for detecting perturbations in DNA replication fork dynamics genome-wide at single molecule resolution along with identifying the presence of single-stranded gaps when used in combination with S1 nuclease. However, electron microscopy is the only technique allowing the actual visualization and localization of single-stranded DNA gaps on replication forks. This chapter provides a detailed method for visualizing single-stranded DNA gaps at the replication fork by electron microscopy including psoralen cross-linking of cultured mammalian cells, extraction of genomic DNA, and finally enrichment of replication intermediates followed by spreading and platinum rotary shadowing of the DNA onto grids. Discussion on identification and analysis of these gaps as well as on the advantages and disadvantages of electron microscopy relative to the DNA fiber technique is also included.

Psoralen-loaded polymeric lipid nanoparticles combined with paclitaxel for the treatment of triple-negative breast cancer

Background: Chemotherapeutic drugs are associated with toxic effects. Metastasis is the leading cause of death in breast cancer patients. Aim: To evaluate the antitumor effect of paclitaxel (PTX) combined with psoralen-loaded polymeric lipid nanoparticles (PSO-PLNs) in triple-negative breast cancer. Methods: After treatment of samples, cell viability, apoptosis, migration, invasion, expression of proteins in the IRAK1/NF-κB/FAK signal pathway, biodistribution and pathological characteristics were detected. Results: Compared with the control group, the PTX + PSO-PLNs group showed increased apoptosis and reduced migration, invasion and expression of phosphorylated IRAK1 and NF-κB, with significant inhibition of tumor growth and lung metastases and no obvious toxicity. Conclusion: Combined administration of PTX and PSO-PLNs exerted a synergistic effect and significantly inhibited the growth and metastasis of triple-negative breast cancer.

Assessing Homologous Recombination and Interstrand Cross-Link Repair in Embryonal Carcinoma Testicular Germ Cell Tumor Cell Lines

Testicular germ cell tumors (TGCTs) are typically exquisitely sensitive to DNA interstrand cross-link (ICLs) agents. ICLs covalently link both strands of the DNA duplex, impeding fundamental cellular processes like DNA replication to cause cell death. A leading drug used for the treatment of TGCTs is cisplatin, which introduces ICLs and leads to formation of double strand breaks (DSBs), a DNA lesion that can be repaired in the S/G2 phases of the cell cycle by homologous recombination (HR, also termed homology-direct repair). Although most TGCTs respond to cisplatin-induced ICLs, a fraction is resistant to treatment. One proposed mechanism of TGCT resistance to cisplatin is an enhanced ability to repair DSBs by HR. Other than HR, repair of the ICL-lesions requires additional DNA repair mechanisms, whose action might also be implemented in therapy-resistant cells. This chapter describes GFP assays to measure (a) HR proficiency following formation of a DSB by the endonuclease I-SceI, and (b) HR repair induced by site-specific ICL formation involving psoralen. These experimental approaches can be used to determine the proficiency of TGCT cell lines in DSB repair by HR in comparison to HR repair of ICLs, providing tools to better characterize their recombination profile. Protocols of these assays have been adapted for use in Embryonal Carcinoma (EC) TGCT cell lines. Assays only require transient introduction of plasmids within cells, affording the advantage of testing multiple cell lines in a relatively short time.

[Effect of psoralen on the stability after orthodontic tooth movement in rats]

PURPOSE

This study was designed to investigate the effect of psoralen on periodontal tissue reconstruction after orthodontic tooth movement(OTM) in rats.

METHODS

Thirty-six male 6-week-old Wistar rats were randomly divided into 2 groups: the experimental group and the control group. The experimental group and the control group were all installed between the central incisor and the left maxillary first molars to pull the first molars away from the force device; after 21 days, the force was removed and the rats in 2 groups were given drug gavage. Rats in the experimental group were given a gavage of psoralen 8 mg/kg per day, while rats in the control group were given the same amount of 0.9% sodium chloride everyday. Maxillary casts were made every week during the experimental and were scanned by 3D Scanner to measure relapse distance, and histologic examination was conducted. After 28 days, the rats were sacrificed and rats' upper jaw was separated. The remaining sections were immunohistochemically stained with BMP2 and BMP4. SPSS 19.0 software package was used for statistical analysis. RESULTS：Both groups had relapse after the force device was removed. Significant decrease of relapse percentage was observed in the experimental group compared with the control group at day 7，day 14，day 21 and day 28（P<0.05）. The speed of relapse of both groups were fastest in the first week and slowed down in the second, third and fourth week gradually. The speed of relapse in the experimental group in the first week was significantly less than in the control group(P<0.05).The expression of BMP2 and BMP4 within periodontal membrane and alveolar bone was significantly higher in the experimental group than in the control group(P<0.05).

CONCLUSIONS

Psoralen can accelerate the reconstruction of periodontal tissues of orthodontic tooth and reduce relapse.

Acaricidal activity and sublethal effects of an oxymatrine-based biopesticide on two-spotted spider mite (Acari: Tetranychidae)

Lethal and sublethal effects of the biopesticide Kingbo (oxymatrine 0.2 % + psoralen 0.4 %) on the two-spotted spider mite (Tetranychus urticae Koch) were investigated in laboratory bioassays. The biopesticide was applied to bean leaf discs or primary leaves by using a Potter spray tower. Acute toxicity tests showed no significant ovicidal action: toxic effect (LC50 = 55.49 μl/l) was the result of a residual activity against larvae that hatched from the treated eggs. Preovipositional females and female teleiochrysales showed similar susceptibility (LC50 = 52.68 and 59.03 μl/l, respectively), whereas larvae, protonymphs and female deutonymphs were the most susceptible stages (LC50 = 6.88, 13.03, and 8.80 μl/l, respectively). In a choice test, females preferred the untreated halves of leaves over the halves treated with 2,000, 1,000, and 500 μl/l in the first 24 h, and their oviposition in those treatments was significantly greater on the untreated halves after 24 and 48 h, as well as the summed oviposition over 72 h. Viability and reproduction of survivors, as well as population growth, were strongly affected after the treatments of preovipositional females and female teleiochrysales with 100, 50 and 25 μl/l. On the other hand, sublethal effects on the females that survived treatment at the egg stage or reached adulthood from the eggs laid on the treated surface (treatments with 50 and 25 μl/l) were significantly weaker. Acaricidal and sublethal effects of the biopesticide Kingbo were discussed as a starting point for further research aimed to improve management of T. urticae populations. Regulatory issues and safety concerns regarding further commercialization of this biopesticide are addressed as well.

[Combined therapy of psoralen plus ultraviolet A followed by narrow band ultraviolet B photochemotherapy for early stage mycosis fungoides]

OBJECTIVE

Only a few clinical reports in the treatment of early mycosis fungoides (MF)(IA, IB, IIA stage) are available in the literature. The purpose of this study was to compare the efficacy and safety of narrow-band UVB and psoralen plus ultraviolet A (PUVA) photochemoterapy in 24 patients with early-stage MF, and explore a new approach for the treatment of early mycosis fungoides.

METHODS

A total of 24 identified early mycosis fungoides patients received PUVA, NB-UVB and a combined therapy of PUVA followed by NB-UVB (n = 9/6/9) irradiation. A retrospective study was carried out to analyze the sex, age of onset, TNM stage, treatment, and duration of treatment, and times of treatment, duration of maintenance treatment, effective and recurrence in these patients. The data were analyzed using SPSS 17.0 and a two-sided test at the α = 0.05 level of significance was conducted.

RESULTS

Of the 24 patients studied, the average treatment was 104.5 (95% CI, 75.71-133.29) times. The average duration of treatment was 12.88 (95% CI, 9.90-15.85) months. The average maintenance treatment time was 11.08 (95% CI, 2.13-20.04) months. The effective rate (CR+PR) of PUVA treatment was 88.9%, recurrence rate was 11.1% (n = 9). In the NB-UVB treatment group, the effective rate was 100.0%, and the recurrence rate was 33.3% (n = 6). In the PUVA followed by NB-UVB (combination therapy) treatment group, the effective rate was 77.8% and the recurrence rate was 55.6% (n = 9). There were no significant differences among the three groups in terms of number of treatments, treatment duration, maintenance treatment duration, effective rate and recurrence rate (P > 0.05).

CONCLUSIONS

PUVA and NB-UVB are effective and safe in the targeted therapy of early stage mycosis fungoides. The combined therapy of PUVA followed by NB-UVB can reduce the total PUVA dose and risk of developing skin cancer.

Killed but metabolically active vaccines

Beginning in the 20th century and continuing into the new millennia, vaccines against numerous diseases have had an unquestioned principal role of both enhancing the quality of life and increasing life expectancy (Rappuoli R, Mandl CW, Black S, De Gregorio E: Vaccines for the twenty-first century society. Nat Rev Immunol 2011, 11:865-872). Despite this success and the development of sophisticated new vaccine technologies, there remain multiple infectious diseases including tuberculosis, malaria and AIDS that await an effective prophylactic vaccine. In addition, there have been recent clinical successes among individuals with cancer using vaccine treatment strategies-so-called therapeutic vaccines-that stimulate tumor specific immunity and increase survival (Kantoff PW, Higano CS, Shore ND, Berger ER, Small EJ, Penson DF, Redfern CH, Ferrari AC, Dreicer R, Sims RB, et al.: Sipuleucel-T immunotherapy for castration-resistant prostate cancer. New Engl J Med 2010, 363:411-422). Here we summarize a new class of vaccines termed Killed But Metabolically Active (KBMA). KBMA vaccines are whole pathogenic or attenuated organisms killed through photochemical inactivation and cannot cause disease, yet retain sufficient metabolic activity to initiate a potent immune response. KBMA vaccines have two broad applications. First, recombinant KBMA vaccines encoding selected antigens relevant to infectious disease or cancer can be used to elicit a desired immune response. In the second application, KBMA vaccines can be derived from attenuated forms of a targeted pathogen, allowing for the presentation of the entire antigenic repertoire to the immune system, of particular importance when the correlates of protection are unknown.

The yeast rDNA locus: a model system to study DNA repair in chromatin

Most of the studies on the effect of chromatin structure and chromatin remodeling on DNA repair are based on in vitro reconstituted assays. In such experiments individual nucleosomes are either released by nuclease digestion of native chromatin fibers or are assembled from purified histones. Though reconstituted assays are valid approaches to follow NER in chromatin they are of somehow limited physiological relevance since single core particles do not exist in vivo [K. van Holde, J. Zlatanova, The nucleosome core particle: does it have structural and physiological relevance? Bioessays 21 (1999) 776-778]. This is particularly true for studies involving core histones tails, as in their natural chromatin context histones tails participate in interactions that are not necessarily present in vitro [J.C. Hansen, C. Tse, A.P. Wolffe, Structure and function of the core histone N-termini: more than meets the eye, Biochemistry 37 (1998) 17637-17641; J.J. Hayes, J.C. Hansen, Nucleosomes and chromatin fiber, Curr. Opin. Genet. Dev. 11 (2001) 124-129]. Indeed it was found that human DNA ligase I has the capability to ligate a nick on the surface of a 215bp nucleosome but not a nick in a nucleosome lacking linker DNA, possibly because of forced interactions between histone tails and core DNA present in the latter complex [D.R. Chafin, J.M. Vitolo, L.A. Henricksen, B.A. Bambara, J.J. Hayes, Human DNA ligase I efficiently seals nicks in nucleosomes, EMBO J. 19 (2000) 5492-5501]. In addition, chromatin remodeling could also occur in the higher ordered folding of chromatin and involve multiple arrays of nucleosomes [P.J. Horn, C.L. Peterson, Chromatin higher order folding: wrapping up transcription, Science 297 (2002) 1824-1827]. By studying the chromatin structure of ribosomal genes in yeast, our knowledge of the fate of nucleosomes during transcription and DNA replication has improved considerably [R. Lucchini, J.M. Sogo, The dynamic structure of ribosomal RNA gene chromatin, in: M.R. Paule (Ed.), Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I, Springer-Verlag/R.G. Landes Company, 1998, pp. 254-276]. How nuclear processes such as DNA repair take place in chromatin is still largely unknown, and in this review I discuss how the yeast rDNA locus may be exploited to investigate DNA repair and chromatin modification in vivo.

Killed but metabolically active microbes: a new vaccine paradigm for eliciting effector T-cell responses and protective immunity

We developed a new class of vaccines, based on killed but metabolically active (KBMA) bacteria, that simultaneously takes advantage of the potency of live vaccines and the safety of killed vaccines. We removed genes required for nucleotide excision repair (uvrAB), rendering microbial-based vaccines exquisitely sensitive to photochemical inactivation with psoralen and long-wavelength ultraviolet light. Colony formation of the nucleotide excision repair mutants was blocked by infrequent, randomly distributed psoralen crosslinks, but the bacterial population was able to express its genes, synthesize and secrete proteins. Using the intracellular pathogen Listeria monocytogenes as a model platform, recombinant psoralen-inactivated Lm DeltauvrAB vaccines induced potent CD4(+) and CD8(+) T-cell responses and protected mice against virus challenge in an infectious disease model and provided therapeutic benefit in a mouse cancer model. Microbial KBMA vaccines used either as a recombinant vaccine platform or as a modified form of the pathogen itself may have broad use for the treatment of infectious disease and cancer.

Construction of recombinant vaccinia viruses using PUV-inactivated virus as a helper

Recombinant vaccinia viruses (VVs) are widely used as expression vectors in molecular biology and immunology and are now under evaluation for gene therapy. The current techniques for inserting foreign DNA into the large VV genome are based on either homologous recombination between transfer plasmids and VVgenomes or direct DNA ligation and packaging using replication-deficient poxviruses. Here, we describe efficient new versions of both methods that produce 90%-100% of the recombinant viruses. In the new homologous recombination method, VV DNA "arms" obtained by NotI digestion and intact transfer plasmids were used for co-transfection. In the direct DNA ligation method, foreign DNA was inserted into a unique NotI restriction site of the VVgenome. In both methods, the generation of recombinant viruses was carried out in cells infected with a non-replicating, psoralen-UV (PUV)-inactivated helper VV. The convenience of these new techniques is demonstrated by the construction of recombinant VVs that produce E. coli beta-galactosidase. An important feature of these strategies is that any VV strain can be used as a helper virus after PUV inactivation.

Multiple rounds of transcription by RNA polymerase II at covalently cross-linked templates

An important control point for gene regulation is the frequency of initiations leading to different numbers of RNA polymerases simultaneously transcribing the same gene. To date, the only direct assay for multiple-round transcription by RNA polymerase II in vitro required G-free cassette-containing templates and GTP-free conditions and was thus restricted in application. Here we used instead templates containing a triplex-directed interstrand psoralen-DNA cross-link to block RNA polymerase II elongation at a specific location. Covalently cross-linked templates allowed simultaneous detection of both specific initiation and reinitiation with any combination of promoter and transcribed sequence. In reconstituted systems, identical stacking of RNA polymerases was observed when the first polymerase was halted by GTP deprivation at the end of a G-free cassette or by a covalent cross-link downstream of different transcribed sequences. In contrast to transcription of G-free cassettes, reinitiation was unaffected by the transcription factor SII on sequences containing all four nucleotides. In crude nuclear extracts, transcription of covalently cross-linked templates yielded a reinitiation pattern with a wider spacing than in more purified fractions, indicating that the elongation complexes from nuclear extract contained a different form of RNA polymerase II or a different complement of associated factors.

Transient gene expression from yeast artificial chromosome DNA in mammalian cells is enhanced by adenovirus

The introduction of high molecular weight DNA into mammalian cells is useful for gene expression studies. However, current transfection strategies are inefficient, necessitating propagation of stable DNA transformants prior to analysis of gene expression. Here we demonstrate that transient lipid-mediated DNA transfection can be used to assess gene expression from yeast artificial chromosomes (YACs) containing the 230 kb cystic fibrosis transmembrane conductance regulator gene ( CFTR ) and Escherichia coli lacZ . We also show that psoralen-UV inactivated adenovirus significantly enhances transfection efficiency. The ability to deliver high molecular weight DNA using lipid-mediated transfection should expedite the analysis of large human genes contained within artificial chromosome vectors.

Antisense oligonucleotide binding to U5 snRNP induces a conformational change that exposes the conserved loop of U5 snRNA

Conformational rearrangements of the spliceosomal small nuclear RNAs (U snRNAs) are essential for proper assembly of the active site prior to the first catalytic step of splicing. We have previously shown that conformational changes caused by binding of an antisense 2'-O-methyl RNA oligonucleotide (BU5Ae) to U5 snRNA nt 68-88 disrupted the U4/U5/U6 complex and induced formation of the U1/U4/U5 and U2/U6 complexes. Here we show that the conformational change induced by BU5Ae exposes the invariant loop of U5 that binds the 5'exon and also reorganizes internal loop 1 (IL1) and the top of stem 2. Interestingly, we have also previously found that the U1/U4/U5 complex induced by BU5Ae brings the invariant loop of U5 into close proximity with the 5'-end of U1. Taken together, these data suggest that U1 and U5 may both contribute to the ability of the U1/U4/U5 complex to bind the 5' splice site.

A novel U1/U5 interaction indicates proximity between U1 and U5 snRNAs during an early step of mRNA splicing

The five spliceosomal snRNAs (U1, U2, U4, U5, and U6) undergo an ordered sequence of conformational changes as mRNA splicing progresses. We have shown that an antisense RNA oligonucleotide complementary to U5 snRNA induces a novel U1/U4/U5 complex that may be a transitional stage in the displacement of U1 from the 5' splice site by U5. Here we identify a novel site-specific crosslink between the 5' end of U1 and the invariant loop of U5 snRNA. This crosslink can be induced in nuclear extract by an antisense oligonucleotide directed against U5 snRNA, but can also be detected during an early step of the splicing reaction in the absence of oligonucleotide. Our data indicate proximity between U1 and U5 snRNPs before the first catalytic step of splicing, and may suggest that U1 helps to direct U5 to the 5' splice site.

Replication-deficient adenoviral vector for gene transfer potentiates airway neurogenic inflammation

Human trials for the treatment of cystic fibrosis lung disease with adenoviral vectors have been complicated by acute inflammatory reactions of unknown etiology. Because replicating respiratory viruses can potentiate tachykinin-mediated neurogenic inflammatory responses in airways, we studied whether the endotracheal administration of a replication-deficient adenoviral vector potentiated this response. The vector Ad5CMVLacZ was administered endotracheally to rats and the leakage of Evans blue dye was used to measure the capsaicin-induced neurogenic albumin extravasation. These studies show that neurogenic albumin extravasation is significantly potentiated in the airways of rats after administration of Ad5CMVLacZ. This inflammatory response can be blocked by selective antagonists of the substance P receptor or by glucocorticoids. Therefore, (1) the acute airway inflammation observed in patients after exposure to adenoviral vectors may exhibit a neurogenic component, which can be blocked pharmacologically, and (2) preclinical adenoviral vector safety studies of other organs innervated by the tachykinin system, e.g., coronary arteries and gastrointestinal tract, should include assessment of neurogenic inflammation.

Detection of covalent triplex within human cells

Triple helix-forming oligonucleotides covalently linked to psoralen can be specifically cross-linked to both strands of DNA at the triplex-duplex junction following UV irradiation. We have previously shown that a 15mer psoralen-oligonucleotide conjugate forming a triple helix on the promoter of the alpha subunit gene of the interleukin-2 receptor inhibits transcription of reporter plasmids transfected into living cells after irradiation. In the present work, we directly demonstrate covalent triple helix formation at the target site inside cells. A primer extension assay using Taq polymerase was developed to quantitate the DNA which had reacted with the psoralen of the triple helix-forming oligonucleotide. Photoaddition of the psoralen at the DNA target site was demonstrated, not only when the preformed triplex was electroporated inside cells, but also when the oligonucleotide was added to the culture medium after plasmid electroporation and before irradiation of the cells.

A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site

The mechanism by which intron-containing RNAs are recognized by the splicing machinery is only partly understood. A nuclear cap-binding complex (CBC), which specifically recognizes the monomethyl guanosine cap structure carried by RNA polymerase II transcripts, has previously been shown to play a role in pre-mRNA splicing. Using a combination of splicing complex and psoralen cross-linking analysis we demonstrate that CBC is required for efficient recognition of the 5' splice site by U1 snRNP during formation of E (early) complex on a pre-mRNA containing a single intron. However, in a pre-mRNA containing two introns, CBC is not required for splicing of the cap distal intron. In this case, the presence of an intact polypyrimidine tract in the cap-proximal intron renders splicing of the cap-distal intron independent of CBC. These results support models in which the splice sites in a pre-mRNA are originally recognized by interactions spanning exons. The defects in splicing and U1 snRNP binding caused by CBC depletion can be specifically reversed by recombinant CBC. In summary, efficient recognition of the cap-proximal 5' splice site by U1 snRNP is facilitated by CBC in what may be one of the earliest steps in pre-mRNA recognition. Data in Colot et al. (this issue) indicate that this function of CBC is conserved in humans and yeast.

A non-radioactive method for identifying enzyme-amplified products of the reticuloendotheliosis proviral env and LTR genes using psoralen-biotin labelled probes

A novel polymerase chain reaction (PCR) system based on the env gene of reticuloendotheliosis virus (REV) strain REV-A for the detection of proviral DNA is described. The designed PCR product of 807 bp was identified using an internal probe of 278 bp produced by nested PCR from REV-infected DNA CEF. The env-gene PCR was then compared with the previously described PCR for proviral REV-long terminal repeat and the PCR product served also as the probe. The probes were labelled with the psoralen-biotin system by photoactivation and the southern blot hybridization signal was detected colorimetricaly. The advantages of using a non-radioactive means of probe labelling were demonstrated clearly in that study, as well as the effective labeling of probes with psoralen-biotin and the simple colorimetric method of detection. The env-gene PCR detected all eleven REV strains used in the study. These included three REV prototype strains and eight Israeli REV isolates. Both PCR systems had similar levels of sensitivity.

Sequence-specific labeling of superhelical DNA by triple helix formation and psoralen crosslinking

Site-specific labeling of covalently closed circular DNA was achieved by using triple helix-forming oligonucleotides 10, 11 and 27 nt in length. The sequences consisted exclusively of pyrimidines (C and T) with a reactive psoralen at the 5'-end and a biotin at the 3'-end. The probes were directed to different target sites on the plasmids pUC18 (2686 bp), pUC18/4A (2799 bp) and pUC1 8/4A-H 1 (2530 bp). After triple helix formation at acid pH the oligonucleotides were photocrosslinked to the target DNAs via the psoralen moiety, endowing the covalent adduct with unconditional stability, e.g. under conditions unfavorable for preservation of the triplex, such as neutral pH. Complex formation was monitored after polyacrylamide gel electrophoresis by streptavidin-alkaline phosphatase (SAP)-induced chemiluminescence. The yield of triple helix increased with the molar ratio of oligonucleotide to target and the length of the probe sequence (27mer > 11mer). The covalent adduct DNA were visualized by scanning force microscopy (SFM) using avidin or streptavidin as protein tags for the biotin group on the oligonucleotide probes. We discuss the versatility of triple helix DNA complexes for studying the conformation of superhelical DNA.

Identification of double Holliday junctions as intermediates in meiotic recombination

During meiosis, branched DNA molecules containing information from both parental chromosomes occur in vivo at loci where meiosis-specific double-stranded breaks occur. We demonstrate here that these joint molecules are recombination intermediates: they contain single strands that have undergone exchange of information. Moreover, these joint molecules are resolved into both parental and recombinant duplexes when treated in vitro with Holliday junction-resolving endonucleases RuvC or T4 endo VII. Taken together with previous observations, these results strongly suggest that joint molecules are double Holliday junctions.

Scanning for mutations in the human prion protein open reading frame by temporal temperature gradient gel electrophoresis

Gerstmann-Sträussler-Scheinker syndrome (GSS), fatal familial insomnia (FFI) and familial Creutzfeldt-Jakob disease (CJD) are caused by point mutations or octarepeat insertions in the prion protein (PrP) gene. In the present work a method was established that is appropriate for a thorough screening for mutations in the PrP gene and is generally applicable to screenings of any given gene. Temperature gradient gel electrophoresis (TGGE) was modified at two critical steps by UV cross-linking of the DNA strands and by replacing the spatial gradient with a temporal one. The shift of a DNA band in temporal temperature gradient gel electrophoresis (tTGGE) due to a mutation can be calculated as a function of the position of the mutation in the sequence. Appropriate DNA fragments were selected for polymerase chain reaction (PCR) amplification and analysis by tTGGE on the basis that the predicted band shifts amount to more than 10% of the migration distance for all possible mutations. The accuracy of the prediction was tested experimentally with ten known mutations in the human PrP gene, and quantitative agreement between theory and experiment was achieved. Thus, this screening method is also a suitable means to verify the absence of mutations in a given gene segment.

The influenza virus NS1 protein binds to a specific region in human U6 snRNA and inhibits U6-U2 and U6-U4 snRNA interactions during splicing

The influenza virus NS1 protein is a unique posttranscriptional regulator that has two activities: inhibition of the nuclear export of poly A-containing mRNAs and inhibition of pre-mRNA splicing. Here we demonstrate that this protein binds to a specific region in one of the human spliceosomal snRNAs, U6 snRNA. Using U6 deletion mutations, we show that the binding of the NS1 protein requires both chains of a stem-bulge structure encompassing nucleotides 27-46 and nucleotides 83-101 of human U6 snRNA. A chemical modification/interference assay indicated that the primary binding site is centered around a purine-containing bulge in this stem-bulge structure. These results provide strong evidence that this postulated secondary structure in U6 snRNA actually exists. The NS1 protein also binds to a model U6-U4 snRNA complex, suggesting that the U6 stem-bulge comprising the NS1 protein binding site is also present in natural U6-U4 snRNA complexes. The U6 stem-bulge includes the U6 sequence that forms helix II with U2 snRNA during splicing, an interaction that is essential for mammalian splicing. We demonstrate that the NS1 protein blocks formation of the U6-U2 helix II both in a model system and during in vitro splicing. In addition, we show that the NS1 protein inhibits formation of U6-U4 snRNA complexes during in vitro splicing, presumably because the binding site of the NS1 protein includes the 3'-terminal region of U6 snRNA that has been shown to be important for the formation of U6-U4 complexes. We postulate that the inhibition of U6-U2 and U6-U4 snRNA complex formation is largely responsible for the inhibition of pre-mRNA splicing by the NS1 protein.

Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation

As an alternative to standard gene transfer techniques for genetic manipulation, we have investigated the use of triple helix-forming oligonucleotides to target mutations to selected genes within mammalian cells. By treating monkey COS cells with oligonucleotides linked to psoralen, we have generated targeted mutations in a simian virus 40 (SV40) vector contained within the cells via intracellular triple helix formation. Oligonucleotide entry into the cells and sequence-specific triplex formation within the SV40 DNA deliver the psoralen to the targeted site. Photoactivation of the psoralen by long-wavelength UV light yields adducts and thereby mutations at that site. We engineered into the SV40 vector novel supF mutation reporter genes containing modified polypurine sites amenable to triplex formation. By comparing the abilities of a series of oligonucleotides to target these new sites, we show that targeted mutagenesis in vivo depends on the strength and specificity of the third-strand binding. Oligonucleotides with weak target site binding affinity or with only partial target site homology were ineffective at inducing mutations in the SV40 vectors within the COS cells. We also show that the targeted mutagenesis is dependent on the oligonucleotide concentration and is influenced by the timing of the oligonucleotide treatment and of the UV irradiation of the cells. Frequencies of intracellular targeted mutagenesis in the range of 1 to 2% were observed, depending upon the conditions of the experiment. DNA sequence analysis revealed that most of the mutations were T.A-to-A.T transversions precisely at the targeted psoralen intercalation site. Several deletions encompassing that site were also seen. The ability to target mutations to selected sites within mammalian cells by using modified triplex-forming oligonucleotides may provide a new research tool and may eventually lead to therapeutic applications.

Target-specific arrest of mRNA translation by antisense 2'-O-alkyloligoribonucleotides

We describe a novel experimental approach to investigate mRNA translation. Antisense 2'-O-allyl oligoribonucleotides (oligos) efficiently arrest translation of targeted mRNAs in rabbit reticulocyte lysate and wheat germ extract while displaying minimal non-specific effects on translation. Oligo/mRNA-hybrids positioned anywhere within the 5' UTR or the first approximately 20 nucleotides of the open reading frame block cap-dependent translation initiation with high specificity. The thermodynamic stability of hybrids between 2'-O-alkyl oligos and RNA permits translational inhibition with oligos as short as 10 nucleotides. This inhibition is independent of RNase H cleavage or modifications which render the mRNA untranslatable. We show that 2'-O-alkyl oligos can also be employed to interfere with cap-independent internal initiation of translation and to arrest translation elongation. The latter is accomplished by UV-crosslinking of psoralen-tagged 2'-O-methyloligoribonucleotides to the mRNA within the open reading frame. The utility of 2'-O-alkyloligoribonucleotides to arrest translation from defined positions within an mRNA provides new approaches to investigate mRNA translation.

Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide

Triple-helical DNA can be formed by oligonucleotides that bind as third strands of DNA in a sequence-specific manner in the major groove in homopurine/homopyrimidine stretches in duplex DNA. Such triple helix-forming oligonucleotides have been used to inhibit gene expression by blocking transcription factor access to promoter sites in transient expression assays. In an alternative approach to genetic manipulation using triplex DNA, we show that triplex-forming oligonucleotides can be used to produce site-specific, targeted mutations in a viral genome in order to achieve a permanent, heritable effect on gene function and expression. We use a triplex-forming oligonucleotide linked to a psoralen derivative at its 5' end to achieve targeted mutagenesis in a simian virus 40 (SV40) vector genome. Site-specific triplex formation delivers the psoralen to the targeted site in the SV40 DNA. Photoactivation of the psoralen yields adducts and thereby mutations at that site. Mutations were produced in the target gene in over 6% of the viral genomes. DNA sequence analysis of the mutations in the target gene showed that all were in the targeted region, and 55% were found to be the same T:A-to-A:T transversion precisely at the targeted base pair. In control experiments, no mutagenesis above the background frequency in the assay was produced by a non-triplex-forming, psoralen-linked oligonucleotide unless a vast excess of this oligonucleotide was used, demonstrating the specificity of the targeted mutagenesis. This frequency of targeted mutagenesis of SV40 in monkey cells represents a 30-fold increase relative to similar experiments using lambda phage in bacteria, suggesting that fixation of the triplex-directed lesion into a mutation occurs more efficiently in mammalian cells. If the ability to reproducibly and predictably target mutations to sites in viral DNA in vitro by using modified oligonucleotides can be extended to DNA in vivo, this approach may prove useful as a technique for gene therapy, as a strategy for antiviral therapeutics, and as a tool for genetic engineering.

Disruption of the nucleosomes at the replication fork

The fate of parental nucleosomes during chromatin replication was studied in vitro using in vitro assembled chromatin containing the whole SV40 genome as well as salt-treated and native SV40 minichromosomes. In vitro assembled minichromosomes were able to replicate efficiently in vitro, when the DNA was preincubated with T-antigen, a cytosolic S100 extract and three deoxynucleoside triphosphates prior to chromatin assembly, indicating that the origin has to be free of nucleosomes for replication initiation. The chromatin structure of the newly synthesized daughter strands in replicating molecules was analysed by psoralen cross-linking of the DNA and by micrococcal nuclease digestion. A 5- and 10-fold excess of protein-free competitor DNA present during minichromosome replication traps the segregating histones. In opposition to published data this suggests that the parental histones remain only loosely or not attached to the DNA in the region of the replication fork. Replication in the putative absence of free histones shows that a subnucleosomal particle is randomly assembled on the daughter strands. The data are compatible with the formation of a H3/H4 tetramer complex under these conditions, supporting the notion that under physiological conditions nucleosome core assembly on the newly synthesized daughter strands occurs by the binding of H2A/H2B dimers to a H3/H4 tetramer complex.

Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.

Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae

The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, characteristic for transcriptionally active rRNA genes devoid of nucleosomes, whereas the other class showed a crosslinking pattern indistinguishable from that of bulk chromatin and was interpreted to represent the inactive rRNA gene copies. By crosslinking the same strain growing in complex or minimal medium, we have shown that yeast cells can modulate the proportion of active (non-nucleosomal) and inactive (nucleosomal) rRNA gene copies in response to variations in environmental conditions which suggests that yeast can regulate rRNA synthesis by varying the number of active gene copies, in contrast to the vertebrate cells studied so far. Whereas intergenic spacers flanking inactive rRNA gene copies are packaged in a regular nucleosomal array, spacers flanking active genes show an unusual crosslinking pattern suggesting a complex interaction of regulatory factors and histones with DNA.

Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length

We have used new methods for chromatin isolation, together with conventional methods for measuring the nucleosome repeat length, to determine the repeat length of Schizosaccharomyces pombe chromatin. We obtain a result of 156(+/- 2) bp. Equivalent results are obtained using a psoralen crosslinking method for measuring the repeat length in viable spheroplasts. That result, together with other control experiments, rules out many possible artifacts. The measured value of 156(+/- 2) bp is smaller than the length of DNA found in the chromatosome. Thus, the chromatosome cannot be the fundamental unit of chromatin structure in all eukaryotes. The crossed linker model of chromatin higher order structure is incompatible with a nucleosome repeat length of 156 bp, and thus cannot apply to all eukaryotes. The solenoid model of higher order structure is compatible with this repeat length only if the solenoid is right-handed. We note two other properties of this chromatin. (1) Early in digestion, the DNA length of mononucleosomes from S. pombe and Aspergillus nidulans exceeds the nucleosome repeat length. (2) Many methods for isolating chromatin from S. pombe yield an apparent nucleosome repeat length of less than or equal to 140 bp; this result is found to be an artifactual consequence of nucleosome sliding.

Defective DNA endonuclease activities in Fanconi's anemia cells, complementation groups A and B

Cells from patients with the inherited disorder, Fanconi's anemia (FA), were analyzed for endonucleases which recognize DNA interstrand cross-links and monoadducts produced by psoralen plus UVA irradiation. Two chromatin-associated DNA endonuclease activities, defective in their ability to incise DNA-containing adducts produced by psoralen plus UVA light, have been identified and isolated in nuclei of FA cells. In FA complementation group A (FA-A) cells, one endonuclease activity, pI 4.6, which recognizes psoralen intercalation and interstrand cross-links, has 25% of the activity of the normal human endonuclease, pI 4.6, on 8-methoxypsoralen (8-MOP) plus UVA-damaged DNA. In FA complementation group B (FA-B) cells, a second endonuclease activity, pI 7.6, which recognizes psoralen monoadducts, has 50% and 55% of the activity, respectively, of the corresponding normal endonuclease on 8-MOP or angelicin plus UVA-damaged DNA. Kinetic analysis reveals that both the FA-A endonuclease activity, pI 4.6, and the FA-B endonuclease activity, pI 7.6, have decreased affinity for psoralen plus UVA-damaged DNA. Both the normal and FA endonucleases showed approximately a 2.5-fold increase in activity on psoralen plus UVA-damaged reconstituted nucleosomal DNA compared to damaged non-nucleosomal DNA, indicating that interaction of these FA endonucleases with nucleosomal DNA is not impaired. These deficiencies in two nuclear DNA endonuclease activities from FA-A and FA-B cells correlate with decreased levels of unscheduled DNA synthesis (UDS), in response to 8-MOP or angelicin plus UVA irradiation, in these cells in culture.

Torsionally tuned cruciform and Z-DNA probes for measuring unrestrained supercoiling at specific sites in DNA of living cells

We describe the development and application of "torsionally tuned" Z-DNA and cruciform probes for analyzing the level of unrestrained supercoiling at specific sites in the DNA of living cells. This approach is applicable for the analysis of dynamic differences in supercoiled DNA in different parts of plasmid, bacterial, or eukaryotic chromosomes. Using a psoralen-based assay, we have shown that the Z-DNA forming sequence (CG)6TA(CG)6, cloned into plasmid pUC8, exists as Z-DNA in 30 to 40% of plasmid molecules in wild-type Escherichia coli. This level suggested an in vivo superhelical density of sigma = -0.034 at the site of insertion in the plasmid. A higher level of Z-DNA found in cells deficient in topoisomerase I (topA10) suggested an in vivo superhelical density of sigma = -0.048. We have constructed a set of torsionally tuned inverted repeated DNA molecules which require different superhelical densities for cruciform formation. Using these inverted repeats and a crosslink assay for cruciforms, we present quantitative evidence for the existence of cruciforms in living E. coli cells. Cruciform formation was dependent on DNA supercoiling in vivo and on the location of the inverted repeat within a plasmid. In topA10 cells cruciforms were detected in less than 0.5% of plasmids when cloned into two different transcriptional units: the lacZ and CAT genes. However, when cloned outside a transcriptional unit, cruciforms were found at levels up to 50% in topA10 cells. More cruciforms were found upstream than downstream from divergent promoters in pBR322. From analysis of the fraction of different inverted repeats existing as cruciforms in vivo and the levels of supercoiling required for cruciform formation in vitro, we estimate in vivo superhelical densities of sigma = -0.034 and -0.041 for the EcoRI site of pUC8-based plasmids in wild-type and topA10 cells, respectively.

Non random positioning of reconstituted nucleosomes on polyomavirus DNA

Nucleosome positioning on linear polyomavirus DNA was evaluated by Fourier transform analysis of data obtained by electron microscopy visualization of reconstituted nucleosomes after photoreaction with trimethylpsoralen. Results show a non random nucleosome positioning and this implies that the histone octamer discriminates among various nucleotide sequences also in the very simple model system adopted in this study. This recognition process appears rather complex because of the limited correlation between nucleosome distribution and DNA curvature, suggesting that other interactions could play a role.

Three-stranded paranemic joints: architecture, topological constraints and movement

The RecA and SSB proteins will catalyze the joining of two DNA molecules containing homologous sequences but lacking homologous ends in a reaction termed paranemic joining. The absence of homologous ends can be achieved by (1) pairing two circular DNAs or (2) using linear DNA(s) with ends lacking homology to the pairing partner. Here we have used electron microscopy (EM) to examine such pairings. Circular M13 single-stranded (ss) DNA enveloped by RecA protein into a presynaptic filament was paired with linear M13mp7 double-stranded (ds) DNA containing non-M13 sequences at its ends. Joint complexes were frequently seen in which the dsDNA was joined with the presynaptic filament over several kilobase (10(3) bases) lengths of the dsDNA. In this region, the presynaptic filament appeared disorganized as contrasted to the customary helical structure of the filament containing only a single strand of DNA. The same ultrastructure, but with greater detail, was observed when the samples were prepared for EM without fixation using a new method of fast-freezing and freeze-drying. EM immunogold staining demonstrated the presence of SSB protein in the disorganized region containing all three strands, but not in the regular helically arranged region. Psoralen photo-crosslinking of the DNA in the joint complexes revealed that the three DNA strands were in close proximity only over a single short (200 to 300 base-pairs) region. The joining of nicked circular M13 dsDNA and presynaptic filaments containing circular M13 ssDNA resulted in the intertwining of the dsDNA about the circular presynaptic filament. The joints produced in this case were short, as was the single region of psoralen photo-crosslinking of the three DNA strands. A model of how these long three-stranded joints form is presented involving the movement of a short "true" paranemic joint along the presynaptic filament.

Human nucleotide excision repair in vitro: repair of pyrimidine dimers, psoralen and cisplatin adducts by HeLa cell-free extract

We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiated DNA and the nicking is only slightly reduced when pyrimidine dimers are eliminated from the substrate by DNA photolyase. In contrast to the nicking assay, the extract gives a strong signal with UV irradiated substrate in the repair synthesis assay. The repair synthesis activity is ATP dependent and is reduced by about 50% by prior treatment of the substrate with DNA photolyase indicating that this fraction of repair synthesis is due to removal of pyrimidine dimers by nucleotide excision. Psoralen and cisplatin adducts which are known to be removed by nucleotide excision repair also elicited repair synthesis activity 5-10 fold above the background synthesis. When M13RF DNA containing a uniquely placed psoralen adduct was used in the reaction, complete repair was achieved in a fraction of molecules as evidenced by the restoration of psoralen inactivated KpnI restriction site. This activity is absent in xeroderma pigmentosum group A cells. We conclude that our cell-free extract contains the human nucleotide excision repair enzyme activity.

Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion

When chromatin is photoreacted with psoralen, crosslinks occur preferentially in the linker DNA between nucleosomes. The pattern of these crosslinks can be analysed by exonuclease digestion of random DNA fragments, since the exonucleases tested stop at sites of psoralen-crosslinks. Further digestion of these fragments with S1-nuclease leads to DNA fragments of nucleosomal and polynucleosomal size, which presumably carry psoralen-crosslinks at both ends. This method of analysis of chromatin structure complements the classical micrococcal nuclease digestion analysis, since it can be performed in vitro as well as in vivo, and since it is independent of pH and ionic conditions.

Use of nonisotopic M13 probes for genetic analysis: application to HLA class II loci

Previously, DNA polymorphisms in the HLA gene cluster have been analyzed using radioactive probes in Southern blot experiments; the restriction fragment length polymorphisms (RFLPs) revealed by this analysis are capable of subdividing HLA serological types. Here, we report the use of DNA probes labeled with biotinylated psoralen to provide nonisotopic detection of HLA class II RFLP patterns. These biotinylated probes contain cDNA sequences encoding the alpha and beta chains of DP, DQ, and DR HLA class II genes as inserts in M13 vectors. The recombinant M13 molecules are partially double-stranded with single-stranded HLA cDNA regions and contain biotinylated psoralen covalently linked to duplex DNA by UV irradiation. Following hybridization, the presence of biotinylated probe bound to target DNA is detected using a streptavidin-horseradish peroxidase conjugate, which converts the colorless substrate 3,3',5,5'-tetramethylbenzidine to a blue precipitate in less than 1 hr. The probe and detection system described here can detect single-copy genes in less than 0.5 microgram of total human DNA on Southern blots and generates the same specific RFLP patterns as do probes labeled with 32P by nick-translation. These biotinylated HLA class II probes have been applied to tissue typing for bone marrow transplantation and the study of insulin-dependent diabetes susceptibility, revealing in each case relevant polymorphisms not detected by serologic typing.