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Maroto-Díaz M, Elie BT, Gómez-Sal P, Pérez-Serrano J, Gómez R, Contel M, Javier de la Mata F. Synthesis and anticancer activity of carbosilane metallodendrimers based on arene ruthenium(ii) complexes. Dalton Trans 2016; 45:7049-66. [PMID: 26990859 PMCID: PMC4863959 DOI: 10.1039/c6dt00465b] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A series of new organometallic carbosilane dendrimers (first and second generation) and the corresponding non-dendritic mononuclear based on ruthenium arene fragments are described. The metallodendrimers were prepared by reactions of the precursor [Ru(η(6)-p-cymene)Cl2]2 with carbosilane dendrimers functionalized with N-donor monodentate ligands such as NH2- and pyridine, or with N,O-, N,N-chelating imine ligands. While the dendrimer precursors are insoluble in DMSO or water, novel metallodendrimers are soluble in DMSO and some of them are even highly soluble in water. The molecular structure of the "Ru-NH2" mononuclear compound (zero generation) was determined by single-crystal X-ray crystallography. The cytotoxicity activity of these dendritic structures was evaluated in several human cancer cell lines and compared with that of the corresponding mononuclear ruthenium complexes. Most compounds display significant cytotoxic activities in the low micromolar range with the first generation ruthenium dendrimers being the most active compounds. The cell death type for selected compounds has been studied as well as their reactivity towards relevant biomolecules such as DNA, Human Serum Albumin (HSA) and Cathepsin-B. All the data point to a mode of action different from that of cisplatin for most complexes. First generation ruthenium dendrimers inhibit Cathepsin-B, which may suggest potential antimetastatic properties of these compounds.
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Affiliation(s)
- Marta Maroto-Díaz
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Campus Universitario, E-28871 Alcalá de Henares, Spain. and Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - Benelita T Elie
- Department of Chemistry, Brooklyn College and The Graduate Center, The City University of New York, Brooklyn, New York 11210, USA. and Biology PhD Program, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Pilar Gómez-Sal
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Campus Universitario, E-28871 Alcalá de Henares, Spain.
| | - Jorge Pérez-Serrano
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Campus Universitario, E-28871 Alcalá de Henares, Spain
| | - Rafael Gómez
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Campus Universitario, E-28871 Alcalá de Henares, Spain. and Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - María Contel
- Department of Chemistry, Brooklyn College and The Graduate Center, The City University of New York, Brooklyn, New York 11210, USA. and Biology PhD Program, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - F Javier de la Mata
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Campus Universitario, E-28871 Alcalá de Henares, Spain. and Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
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He G, Vasilieva E, Bashkin JK, Dupureur CM. Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis. Anal Biochem 2013; 439:99-101. [PMID: 23608054 PMCID: PMC3713177 DOI: 10.1016/j.ab.2013.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/08/2013] [Accepted: 04/10/2013] [Indexed: 12/17/2022]
Abstract
The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the potential for indexing errors can be significant when mapping small ligand-DNA interactions. Described here is a mechanism for avoiding such errors based on a summary of standard labeling, cleavage, and indexing chemistries and a comparison among them for analysis of these interactions by capillary electrophoresis. The length dependence of the difference between Sanger and Maxam-Gilbert indexing is examined for a number of duplexes of mixed sequence.
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Affiliation(s)
- Gaofei He
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - James K. Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Cynthia M. Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
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3
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Abstract
Phage G1 gp67 is a 23 kDa protein that binds to the Staphylococcus aureus (Sau) RNA polymerase (RNAP) σ(A) subunit and blocks cell growth by inhibiting transcription. We show that gp67 has little to no effect on transcription from most promoters but is a potent inhibitor of ribosomal RNA transcription. A 2.0-Å-resolution crystal structure of the complex between gp67 and Sau σ(A) domain 4 (σ(A)(4)) explains how gp67 joins the RNAP promoter complex through σ(A)(4) without significantly affecting σ(A)(4) function. Our results indicate that gp67 forms a complex with RNAP at most, if not all, σ(A)-dependent promoters, but selectively inhibits promoters that depend on an interaction between upstream DNA and the RNAP α-subunit C-terminal domain (αCTD). Thus, we reveal a promoter-specific transcription inhibition mechanism by which gp67 interacts with the RNAP promoter complex through one subunit (σ(A)), and selectively affects the function of another subunit (αCTD) depending on promoter usage.
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4
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Volle CB, Delaney S. CAG/CTG repeats alter the affinity for the histone core and the positioning of DNA in the nucleosome. Biochemistry 2012; 51:9814-25. [PMID: 23157165 DOI: 10.1021/bi301416v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trinucleotide repeats (TNRs) occur throughout the genome, and their expansion has been linked to several neurodegenerative disorders, including Huntington's disease. TNRs have been studied using both oligonucleotides and plasmids; however, less is know about how repetitive DNA responds to genomic packaging. Here, we investigate the behavior of CAG/CTG repeats incorporated into nucleosome core particles, the most basic unit of chromatin packaging. To assess the general interaction between CAG/CTG repeats and the histone core, we determined the efficiency with which various TNR-containing DNA substrates form nucleosomes, revealing that even short CAG/CTG tracts are robust incorporators. However, the presence of the Huntington gene flanking sequence (htt) decreases the rate of incorporation. Enzymatic and chemical probing revealed repositioning of the DNA in the nucleosome as the number of CAG/CTG repeats increased, regardless of the flanking sequence. Notably, the periodicity of the repeat tract remained unchanged as a function of length and is consistently 10.7 bp per helical turn. In contrast, the periodicity of the nonrepetitive flanking sequence varies and is smaller than the repeat tract at ~10.0-10.5 bp per turn. Furthermore, while the CAG/CTG repeats remain as a canonical duplex in the nucleosome, nucleosome formation causes kinking in a secondary repeat tract in the htt gene, comprised of CCG/CGG repeats. This work highlights the innate ability of CAG/CTG repeats to incorporate and to position in nucleosomes and how that behavior is modulated by the htt flanking sequence. In addition, it illuminates the differences in packaging of healthy and diseased length repeat tracts within the genome.
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Affiliation(s)
- Catherine B Volle
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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Ellis T, Evans DA, Martin CRH, Hartley JA. A 96-well DNase I footprinting screen for drug-DNA interactions. Nucleic Acids Res 2007; 35:e89. [PMID: 17586817 PMCID: PMC1919508 DOI: 10.1093/nar/gkm467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The established protocol for DNase I footprinting has been modified to allow multiple parallel reactions to be rapidly performed in 96-well microtitre plates. By scrutinizing every aspect of the traditional method and making appropriate modifications it has been possible to considerably reduce the time, risk of sample loss and complexity of footprinting, whilst dramatically increasing the yield of data (30-fold). A semi-automated analysis system has also been developed to present footprinting data as an estimate of the binding affinity of each tested compound to any base pair in the assessed DNA sequence, giving an intuitive ‘one compound–one line’ scheme. Here, we demonstrate the screening capabilities of the 96-well assay and the subsequent data analysis using a series of six pyrrolobenzodiazepine-polypyrrole compounds and human Topoisomerase II alpha promoter DNA. The dramatic increase in throughput, quantified data and decreased handling time allow, for the first time, DNase I footprinting to be used as a screening tool to assess DNA-binding agents.
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Affiliation(s)
- Tom Ellis
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - David A. Evans
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - Christopher R. H. Martin
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - John A. Hartley
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
- *To whom correspondence should be addressed. +44 (0)20 7679 9326+44 (0)20 7436 2956
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Crampton N, Bonass WA, Kirkham J, Rivetti C, Thomson NH. Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res 2006; 34:5416-25. [PMID: 17012275 PMCID: PMC1636470 DOI: 10.1093/nar/gkl668] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2006] [Revised: 07/14/2006] [Accepted: 08/30/2006] [Indexed: 12/01/2022] Open
Abstract
Atomic force microscopy (AFM) has been used to image, at single molecule resolution, transcription events by Escherichia coli RNA polymerase (RNAP) on a linear DNA template with two convergently aligned lambda(pr) promoters. For the first time experimentally, the outcome of collision events during convergent transcription by two identical RNAP has been studied. Measurement of the positions of the RNAP on the DNA, allows distinction of open promoter complexes (OPCs) and elongating complexes (EC) and collided complexes (CC). This discontinuous time-course enables subsequent analysis of collision events where both RNAP remain bound on the DNA. After collision, the elongating RNAP has caused the other (usually stalled) RNAP to back-track along the template. The final positions of the two RNAP indicate that these are collisions between an EC and a stalled EC (SEC) or OPC (previously referred to as sitting-ducks). Interestingly, the distances between the two RNAP show that they are not always at closest approach after 'collision' has caused their arrest.
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Affiliation(s)
- Neal Crampton
- Department of Oral Biology, University of LeedsLeeds LS2 9LU, UK
- Institute of Molecular Biophysics, School of Physics and Astronomy, University of LeedsLeeds LS2 9JT, UK
| | | | - Jennifer Kirkham
- Department of Oral Biology, University of LeedsLeeds LS2 9LU, UK
| | - Claudio Rivetti
- Department of Biochemistry and Molecular Biology, University of Parma43100 Parma, Italy
| | - Neil H. Thomson
- Department of Oral Biology, University of LeedsLeeds LS2 9LU, UK
- Institute of Molecular Biophysics, School of Physics and Astronomy, University of LeedsLeeds LS2 9JT, UK
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Lemke K, Wojciechowski M, Laine W, Bailly C, Colson P, Baginski M, Larsen AK, Skladanowski A. Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities. Nucleic Acids Res 2005; 33:6034-47. [PMID: 16254080 PMCID: PMC1270948 DOI: 10.1093/nar/gki904] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 09/29/2005] [Accepted: 09/29/2005] [Indexed: 11/12/2022] Open
Abstract
We recently reported that the antitumor triazoloacridone, compound C-1305, is a topoisomerase II poison with unusual properties. In this study we characterize the DNA interactions of C-1305 in vitro, in comparison with other topoisomerase II inhibitors. Our results show that C-1305 binds to DNA by intercalation and possesses higher affinity for GC- than AT-DNA as revealed by surface plasmon resonance studies. Chemical probing with DEPC indicated that C-1305 induces structural perturbations in DNA regions with three adjacent guanine residues. Importantly, this effect was highly specific for C-1305 since none of the other 22 DNA interacting drugs tested was able to induce similar structural changes in DNA. Compound C-1305 induced stronger structural changes in guanine triplets at higher pH which suggested that protonation/deprotonation of the drug is important for this drug-specific effect. Molecular modeling analysis predicts that the zwitterionic form of C-1305 intercalates within the guanine triplet, resulting in widening of both DNA grooves and aligning of the triazole ring with the N7 atoms of guanines. Our results show that C-1305 binds to DNA and induces very specific and unusual structural changes in guanine triplets which likely plays an important role in the cytotoxic and antitumor activity of this unique compound.
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Affiliation(s)
- Krzysztof Lemke
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
- Group of Biology and Pharmacogenetics of Human Tumors, INSERM U673, Université Pierre et Marie Curie (UPMC-Paris 6), Hôpital Saint-AntoineParis, 75571 Paris 12, France
| | - Marcin Wojciechowski
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
| | - William Laine
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL59045 Lille Cedex, France
| | - Christian Bailly
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL59045 Lille Cedex, France
| | - Pierre Colson
- Biospectroscopy and Physical Chemistry Unit, Department of Chemistry and Natural and Synthetic Drugs Research Center, University of LiègeSart-Tilman, 4000, Liège, Belgium
| | - Maciej Baginski
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
| | - Annette K. Larsen
- Group of Biology and Pharmacogenetics of Human Tumors, INSERM U673, Université Pierre et Marie Curie (UPMC-Paris 6), Hôpital Saint-AntoineParis, 75571 Paris 12, France
| | - Andrzej Skladanowski
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
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Carrasco C, Facompré M, Chisholm JD, Van Vranken DL, Wilson WD, Bailly C. DNA sequence recognition by the indolocarbazole antitumor antibiotic AT2433-B1 and its diastereoisomer. Nucleic Acids Res 2002; 30:1774-81. [PMID: 11937631 PMCID: PMC113207 DOI: 10.1093/nar/30.8.1774] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The antibiotic AT2433-B1 belongs to a therapeutically important class of antitumor agents. This natural product contains an indolocarbazole aglycone connected to a unique disaccharide consisting of a methoxyglucose and an amino sugar subunit, 2,4-dideoxy-4-methylamino-L-xylose. The configuration of the amino sugar distinguishes AT2433-B1 from its diastereoisomer iso-AT2433-B1. Here we have investigated the interaction of these two disaccharide indolocarbazole derivatives with different DNA sequences by means of DNase I footprinting and surface plasmon resonance (SPR). Accurate binding measurements performed at 4 and 25 degrees C using the BIAcore SPR method revealed that AT2433-B1 binds considerably more tightly to a hairpin oligomer containing a [CG](4) block than to an oligomer with a central [AT](4) tract. The kinetic analysis shows that the antibiotic dissociates much more slowly from the GC sequence compared to the AT one. Preferential binding of AT2433-B1 to GC-rich sequences in DNA was independently confirmed by DNase I footprinting experiments performed with a 117 bp DNA restriction fragment. The specific binding sequence 5'-AACGCCAG identified from the footprints was then converted into a biotin-labeled DNA hairpin duplex and compound interactions with this specific sequence were characterized by high resolution BIAcore SPR experiments. Such a combined approach provided a detailed understanding of the molecular basis of DNA recognition. The discovery that the glycosyl antibiotic AT2433-B1 preferentially recognizes defined sequences offers novel opportunities for the future design of sequence-specific DNA-reading small molecules.
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Affiliation(s)
- Carolina Carrasco
- Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret and INSERM U-524, IRCL, Place de Verdun, 59045 Lille, France
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Guelev V, Lee J, Ward J, Sorey S, Hoffman DW, Iverson BL. Peptide bis-intercalator binds DNA via threading mode with sequence specific contacts in the major groove. ACTA ACUST UNITED AC 2001; 8:415-25. [PMID: 11358689 DOI: 10.1016/s1074-5521(01)00013-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND We previously described a general class of DNA polyintercalators in which 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) intercalating units are connected via peptide linkers, resulting in the first known tetrakis- and octakis-intercalators. We showed further that changes in the composition of the peptide tether result in novel DNA binding site specificities. We now examine in detail the DNA binding mode and sequence specific recognition of Compound 1, an NDI bis-intercalator containing the peptide linker gly-gly-gly-lys. RESULTS 1H-NMR structural studies of Compound 1 bound to d(CGGTACCG)(2) confirmed a threading mode of intercalation, with four base pairs between the diimide units. The NMR data, combined with DNAse I footprinting of several analogs, suggest that specificity depends on a combination of steric and electrostatic contacts by the peptide linker in the floor of the major groove. CONCLUSIONS In view of the modular nature and facile synthesis of our NDI-based polyintercalators, such structural knowledge can be used to improve or alter the specificity of the compounds and design longer polyintercalators that recognize correspondingly longer DNA sequences with alternating access to both DNA grooves.
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Affiliation(s)
- V Guelev
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 78722, USA
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10
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Krylov AS, Zasedateleva OA, Prokopenko DV, Rouviere-Yaniv J, Mirzabekov AD. Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res 2001; 29:2654-60. [PMID: 11410675 PMCID: PMC55728 DOI: 10.1093/nar/29.12.2654] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A generic hexadeoxyribonucleotide microchip has been applied to test the DNA-binding properties of HU histone-like bacterial protein, which is known to have a low sequence specificity. All 4096 hexamers flanked within 8mers by degenerate bases at both the 3'- and 5'-ends were immobilized within the 100 x 100 x 20 mm polyacrylamide gel pads of the microchip. Single-stranded immobilized oligonucleotides were converted in some experiments to the double-stranded form by hybridization with a specified mixture of 8mers. The DNA interaction with HU was characterized by three type of measurements: (i) binding of FITC-labeled HU to microchip oligonucleotides; (ii) melting curves of complexes of labeled HU with single-stranded microchip oligonucleotides; (iii) the effect of HU binding on melting curves of microchip double-stranded DNA labeled with another fluorescent dye, Texas Red. Large numbers of measurements of these parameters were carried out in parallel for all or many generic microchip elements in real time with a multi-wavelength fluorescence microscope. Statistical analysis of these data suggests some preference for HU binding to G/C-rich single-stranded oligonucleotides. HU complexes with double-stranded microchip 8mers can be divided into two groups in which HU binding either increased the melting temperature (T(m)) of duplexes or decreased it. The stabilized duplexes showed some preference for presence of the sequence motifs AAG, AGA and AAGA. In the second type of complex, enriched with A/T base pairs, the destabilization effect was higher for longer stretches of A/T duplexes. Binding of HU to labeled duplexes in the second type of complex caused some decrease in fluorescence. This decrease also correlates with the higher A/T content and lower T(m). The results demonstrate that generic microchips could be an efficient approach in analysis of sequence specificity of proteins.
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Affiliation(s)
- A S Krylov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
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Schmidt M, Hoffmann G, Wissler M, Lemke N, Müssig A, Glimm H, Williams DA, Ragg S, Hesemann CU, von Kalle C. Detection and direct genomic sequencing of multiple rare unknown flanking DNA in highly complex samples. Hum Gene Ther 2001; 12:743-9. [PMID: 11339891 DOI: 10.1089/104303401750148649] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
By identifying the sequence of retro- and lentiviral integration sites in peripheral blood leukocytes, the clonal composition and fate of genetically modified hematopoietic progenitor and stem cells could be mapped in vitro and in vivo. Previously available methods have been limited to the analysis of mono- or oligoclonal integration sites present in high copy numbers. Here, we perform characterization of multiple rare retroviral and lentiviral integration sites in highly complex DNA samples. The reliability of this method results from nontarget DNA removal via magnetic extension primer tag selection (EPTS) preceding solid-phase ligation-mediated PCR. EPTS/LM-PCR allowed the simultaneous direct genomic sequencing of multiple proviral LTR-flanking sequences of retro- and lentiviral vectors even if only 1 per 100 to 1000 cells contained the provirus. A primer walking "around" the integration locus demonstrated the adaptability of EPTS/LM-PCR to study unknown flanking DNA regions unrelated to proviruses. The technique is fast, inexpensive, and sensitive in minimal samples. It enables studies of retro- and lentiviral integration, viral vector tracking in gene therapy, insertional mutagenesis, transgene integration, and direct genomic sequencing that until now have been difficult or impossible to perform.
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Affiliation(s)
- M Schmidt
- Department I of Internal Medicine, University of Freiburg, 79106 Freiburg, Germany
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12
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Cogoi S, Suraci C, Del Terra E, Diviacco S, van der Marel G, van Boom J, Quadrifoglio F, Xodo L. Downregulation of c-Ki-ras promoter activity by triplex-forming oligonucleotides endogenously generated in human 293 cells. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:283-95. [PMID: 10984122 DOI: 10.1089/108729000421466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Exogenous triplex-forming oligodeoxynucleotides (TFO) have the capacity to modulate in vivo the expression of individual genes. As the administration of TFO to cells is not without problems, we analyzed the possibility of generating them directly in the cell, using specific expression vectors. We constructed three vectors, mU6-GA, mU6-CA, and mU6-CT, that direct the synthesis in human 293 cells of 76-mer CU, GU, and AG motif TFO (rTFO) potentially capable of binding to a critical poly (R x Y) sequence contained in the promoter of the Ki-ras proto-oncogene. The ability of the CU, GU, and AG motif rTFO to interact with the double helix of the c-Ki-ras target was investigated in vitro by footprinting and band-shift experiments, using both synthetic and endogenously synthesized oligoribonucleotides. The human 293 cells were transfected with DNA mixtures containing a plasmid, which bears the reporter chloramphenicol acetyltransferase (CAT) gene downstream from the c-Ki-ras promoter (pKRS-413), as well as an rTFO-generating vector (mU6-GA, mU6-CA, or mU6-CT). As control, the cells were transfected with DNA mixtures containing vector mU6-C1 or mU6-C2. These generated transcripts unable to form triple helices with the poly (R x Y) sequence of the c-Ki-ras promoter. Intracellular synthesis of the 76-mer CU, GU, and AG rTFO by mU6-GA, mU6-CA, and mU6-CT was checked by Northern blot hybridization. Through beta-gal and CAT ELISA immunoassays, we found that the 293 cells transfected with either mU6-GA, mU6-CA, or mU6-CT showed a significant inhibition of CAT expression compared with cells transfected with control plasmids mU6-C1 or mU6-C2. The results of five separate transient transfection experiments showed that endogenous GU and AG rTFO, generated by mU6-CA and mU6-CT, produce, respectively, 40% (+/- 4% SE) and 47% (+/- 8% SE) CAT inhibition, whereas CU rTFO, generated by mU6-GA, produces 38% (+/- 7% SE) CAT inhibition. In conclusion, this study suggests that it is possible to downregulate the expression of an individual gene through the use of recombinant vectors encoding the information for the intracellular synthesis of short triplex-forming RNA strands.
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Affiliation(s)
- S Cogoi
- Department of Biomedical Sciences and Technologies, School of Medicine, Udine, Italy
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