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Huber HF, Jaberi-Douraki M, DeVader S, Aparicio-Lopez C, Nava-Chavez J, Xu X, Millagaha Gedara NI, Gaudreault NN, Delong RK. Targeting SARS-CoV-2 Variants with Nucleic Acid Therapeutic Nanoparticle Conjugates. Pharmaceuticals (Basel) 2021; 14:1012. [PMID: 34681236 PMCID: PMC8539335 DOI: 10.3390/ph14101012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of SARS-CoV-2 variants is cause for concern, because these may become resistant to current vaccines and antiviral drugs in development. Current drugs target viral proteins, resulting in a critical need for RNA-targeted nanomedicines. To address this, a comparative analysis of SARS-CoV-2 variants was performed. Several highly conserved sites were identified, of which the most noteworthy is a partial homopurine palindrome site with >99% conservation within the coding region. This sequence was compared among recently emerged, highly infectious SARS-CoV-2 variants. Conservation of the site was maintained among these emerging variants, further contributing to its potential as a regulatory target site for SARS-CoV-2. RNAfold was used to predict the structures of the highly conserved sites, with some resulting structures being common among coronaviridae. An RNA-level regulatory map of the conserved regions of SARS-CoV-2 was produced based on the predicted structures, with each representing potential target sites for antisense oligonucleotides, triplex-forming oligomers, and aptamers. Additionally, homopurine/homopyrimidine sequences within the viral genome were identified. These sequences also demonstrate appropriate target sites for antisense oligonucleotides and triplex-forming oligonucleotides. An experimental strategy to investigate these is summarized along with potential nanoparticle types for delivery, and the advantages and disadvantages of each are discussed.
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Affiliation(s)
- Hanah F. Huber
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Majid Jaberi-Douraki
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Sarah DeVader
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Cesar Aparicio-Lopez
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Juliet Nava-Chavez
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Xuan Xu
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Nuwan Indika Millagaha Gedara
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA;
| | - Robert K. Delong
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
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Yamada K, Abe Y, Nagatsugi F. Synthesis of RNA Crosslinking Oligonucleotides Modified with 2-Amino-7-Deaza-7-Propynyl-6-Vinylpurine. ACTA ACUST UNITED AC 2019; 77:e79. [PMID: 30860656 DOI: 10.1002/cpnc.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article describes procedures to synthesize 2'-OMe-RNA modified with cross-linkable 2-amino-7-deaza-7-propynyl-6-vinylpurine (ADpVP) and preparation of the RNA-crosslinking experiment in vitro. All synthesis steps yield the desired compound in moderate or high yield without expensive chemical reagents or specific devices. The crosslink-active form of modified RNA can also be purified by commonly used reversed-phase HPLC, can be stored at -80°C after lyophilization for a few days, and is ready to use for crosslinking experiments. This crosslink-active RNA can efficiently form covalent bonds with complementary RNA in a sequence-specific manner. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai-shi, Japan
| | - Yusuke Abe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai-shi, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai-shi, Japan
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Mojžíšek M. Triplex Forming Oligonucleotides – Tool for Gene Targeting. ACTA MEDICA (HRADEC KRÁLOVÉ) 2019. [DOI: 10.14712/18059694.2018.82] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This review deals with the antigene strategy whereby an oligonucleotide binds to the major or minor groove of double helical DNA where it forms a local triple helix. Preoccupation of this article is triplex-forming oligonucleotides (TFO). These are short, synthetic single-stranded DNAs that recognize polypurine:polypyrimidine regions in double stranded DNA in a sequence-specific manner and form triplex. Therefore, the mechanisms for DNA recognition by triple helix formation are discussed, together with main characteristics of TFO and also major obstacles that remain to be overcome are highlighted. TFOs can selectively inhibit gene expression at the transcriptional level or repair genetic defect by direct genome modification in human cells. These qualities makes TFO potentially powerful therapeutic tool for gene repair and/or expression regulation.
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Yamada K, Abe Y, Murase H, Ida Y, Hagihara S, Nagatsugi F. Synthesis and Properties of 2′-OMe-RNAs Modified with Cross-Linkable 7-Deazaguanosine Derivatives. J Org Chem 2018; 83:8851-8862. [DOI: 10.1021/acs.joc.8b01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Yusuke Abe
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Hirotaka Murase
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Yuta Ida
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
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Yamada K, Ishiyama S, Onizuka K, Nagatsugi F. Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.01.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Lin SB, Wu CM, Lin WC, Kan LS. The Formation of Triple Stranded Helix of Oligodeoxyribonucleotides Containing 8-Oxo-2′-deoxyadenosine. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199900095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Seela F, Jiang D, Budow S. Triplexes with 8-Aza-2'-deoxyisoguanosine replacing protonated dC: probing third strand stability with a fluorescent nucleobase targeting duplex DNA. Chembiochem 2010; 11:1443-50. [PMID: 20544775 DOI: 10.1002/cbic.201000162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The fluorescent 8-aza-2'-deoxyisoguanosine (4) as well as the parent 2'-deoxyisoguanosine (1) were used as protonated dCH(+) surrogates in the third strand of oligonucleotide triplexes. Stable triplexes were formed by Hoogsteen base pairing. In contrast to dC, triplexes containing nucleoside 1 or 4 in place of dCH(+) are already formed under neutral conditions or even at alkaline pH values. Triplex melting can be monitored separately from duplex dissociation in cases in which the third strand contains the fluorescent nucleoside 4. Third-strand binding of oligonucleotides with 4, opposite to dG, was selective as demonstrated by hybridisation experiments studying mismatch discrimination. Third-strand binding is more efficient when the stability of the DNA duplex is reduced by mismatches, giving third-strand binding more flexibility.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster Germany
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Ye Z, Houssein HSH, Mahato RI. Bioconjugation of oligonucleotides for treating liver fibrosis. Oligonucleotides 2008; 17:349-404. [PMID: 18154454 DOI: 10.1089/oli.2007.0097] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Liver fibrosis results from chronic liver injury due to hepatitis B and C, excessive alcohol ingestion, and metal ion overload. Fibrosis culminates in cirrhosis and results in liver failure. Therefore, a potent antifibrotic therapy is urgently needed to reverse scarring and eliminate progression to cirrhosis. Although activated hepatic stellate cells (HSCs) remain the principle cell type responsible for liver fibrosis, perivascular fibroblasts of portal and central veins as well as periductular fibroblasts are other sources of fibrogenic cells. This review will critically discuss various treatment strategies for liver fibrosis, including prevention of liver injury, reduction of inflammation, inhibition of HSC activation, degradation of scar matrix, and inhibition of aberrant collagen synthesis. Oligonucleotides (ODNs) are short, single-stranded nucleic acids, which disrupt expression of target protein by binding to complementary mRNA or forming triplex with genomic DNA. Triplex forming oligonucleotides (TFOs) provide an attractive strategy for treating liver fibrosis. A series of TFOs have been developed for inhibiting the transcription of alpha1(I) collagen gene, which opens a new area for antifibrotic drugs. There will be in-depth discussion on the use of TFOs and how different bioconjugation strategies can be utilized for their site-specific delivery to HSCs or hepatocytes for enhanced antifibrotic activities. Various insights developed in individual strategy and the need for multipronged approaches will also be discussed.
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Affiliation(s)
- Zhaoyang Ye
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Nagatsugi F, Sasaki S. Chemical tools for targeted mutagenesis of DNA based on triple helix formation. Biol Pharm Bull 2004; 27:463-7. [PMID: 15056848 DOI: 10.1248/bpb.27.463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The development of methods for targeted mutagenesis shows promise as an alternative form of gene therapy. Triple helix-forming oligonucleotides (TFOs) provide an attractive strategy for inducing mutations. Especially, alkylation of nucleobases with functionalized TFOs would have potential for site-directed mutation. Several studies have demonstrated that treatment of mammalian cells with TFOs can be exploited to introduce desired sequence changes and point mutations. This review summarizes targeted mutagenesis using reactive TFOs, including studies with photo reactive psolaren derivatives as well as a new reactive derivative recently developed by our group.
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Affiliation(s)
- Fumi Nagatsugi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Zozulya V, Blagoi Y, Dubey I, Fedoryak D, Makitruk V, Ryazanova O, Shcherbakova A. Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue. Biopolymers 2003; 72:264-73. [PMID: 12833481 DOI: 10.1002/bip.10403] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
UV absorption and fluorescence techniques with a thermal denaturation procedure were used in studies of the anchorage of an oligonucleotide hybridization by a covalently tethered nucleoside analogue of an intercalating imidazophenazine derivative (Pzn). The formation by the (dT)(10)Pzn conjugate of the duplex complex with (dA)(15) and the triplex complex with (dA)(15) or poly(dA).poly(dT) was studied in buffered solutions with 0.11 and/or 1M sodium ions at the oligomer strand concentration of 10 microM. Because of the Pzn emission sensitivity to the interaction with adenine bases, a fluorescence technique was found to be effective in the detection of melting transitions. The attached Pzn substantially enhanced the thermal stability of complexes formed by (dT)(10) because of the intercalation mechanism, which increased the temperature of half-dissociation of the duplex by 10-12 degrees C and of the triplexes by approximately 13 degrees C. With the assumption of a two-state model of transition, the thermodynamic parameters for duplex formations were derived. The investigated variant of conjugation has a certain advantage over the widely used attachment via a flexible linker, consisting of a predetermined location of the Pzn chromophore in target sequences that makes it useful as a fluorescent reporter of the hybridization correctness. Molecular modeling was used to construct the geometries of the intercalation sites that turned out to be in conformity with the behavior of the Pzn fluorescence.
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Affiliation(s)
- V Zozulya
- Institute for Low Temperature Physics and Engineering, NAS of Ukraine, 47 Lenin Avenue, Kharkov, 61103, Ukraine
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11
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Uil TG, Haisma HJ, Rots MG. Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Res 2003; 31:6064-78. [PMID: 14576293 PMCID: PMC275457 DOI: 10.1093/nar/gkg815] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Designer molecules that can specifically target pre-determined DNA sequences provide a means to modulate endogenous gene function. Different classes of sequence-specific DNA-binding agents have been developed, including triplex-forming molecules, synthetic polyamides and designer zinc finger proteins. These different types of designer molecules with their different principles of engineered sequence specificity are reviewed in this paper. Furthermore, we explore and discuss the potential of these molecules as therapeutic modulators of endogenous gene function, focusing on modulation by stable gene modification and by regulation of gene transcription.
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Affiliation(s)
- Taco G Uil
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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12
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Abstract
Triplex-forming oligonucleotides (TFOs) can bind to polypurine/polypyrimidine regions in DNA in a sequence-specific manner. The specificity of this binding raises the possibility of using triplex formation for directed genome modification, with the ultimate goal of repairing genetic defects in human cells. Several studies have demonstrated that treatment of mammalian cells with TFOs can provoke DNA repair and recombination, in a manner that can be exploited to introduce desired sequence changes. This review will summarize recent advances in this field while also highlighting major obstacles that remain to be overcome before the application of triplex technology to therapeutic gene repair can be achieved.
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Affiliation(s)
- Michael M Seidman
- Department of Therapeutic Radiology, Yale University School of Medicine, P.O. Box 208040, New Haven, Connecticut 06520-8040, USA
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13
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Cassidy RA, Puri N, Miller PS. Effect of DNA target sequence on triplex formation by oligo-2'-deoxy- and 2'-O-methylribonucleotides. Nucleic Acids Res 2003; 31:4099-108. [PMID: 12853627 PMCID: PMC165951 DOI: 10.1093/nar/gkg436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The interactions of pyrimidine deoxyribo- or 2'-O-methylribo-psoralen-conjugated, triplex-forming oligonucleotides, psTFOs, with a 17-bp env-DNA whose purine tract is 5'-AGAGAGAAAAAAGAG-3', or an 18-bp gag-DNA whose purine tract is 5'-AGG GGGAAAGAAAAAA-3', were studied over the pH range 6.0-7.5. The stability of the triplex formed by a deoxy-env-psTFO containing 5-methylcytosines and thymines decreased with increasing pH (T(m) = 56 degrees C at pH 6.0; 27 degrees C at pH 7.5). Replacement of 5-methylcytosines with 8-oxo-adenines reduced the pH dependence, but lowered triplex stability. A 2'-O-methyl-env-psTFO containing uracil and cytosine did not form a triplex at pH 7.5. Surprisingly, replacement of the cytosines in this oligomer with 5-methylcytosines dramatically increased triplex stability (T(m) = 25 degrees C at pH 7.5), and even greater stability was achieved by selective replacement of uracils with thymines (T(m) = 37 degrees C at pH 7.5). Substitution of the contiguous 5-methylcytosines of the deoxy-gag-psTFO with 8-oxo-adenines significantly reduced pH dependence and increased triplex stability. In contrast to the behavior of env-specific TFOs, triplexes formed by 2'-O-methyl-gag-psTFOs did not show enhanced stability. Replacement of the 3'-terminal phosphodiester of the TFO with a methylphosphonate group significantly increased the resistance of both deoxy- and 2'-O-methyl-TFOs to degradation by 3'-exonucleases, while maintaining triplex stability.
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Affiliation(s)
- Rachel A Cassidy
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
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Rao JE, Craig NL. Selective recognition of pyrimidine motif triplexes by a protein encoded by the bacterial transposon Tn7. J Mol Biol 2001; 307:1161-70. [PMID: 11292332 DOI: 10.1006/jmbi.2001.4553] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The bacterial transposon Tn7 is distinguished among mobile genetic elements by its targeting abilities. Recently, we reported that Tn7 is able to selectively insert adjacent to triple-helical DNA. The binding of TnsC, a Tn7-encoded protein, to the triplex DNA target leads to the specific transposition of Tn7 adjacent to both inter- and intramolecular pyrimidine motif triplexes. Here, we further probe how Tn7 targets triplex DNA. We report that TnsC discriminates between different types of triplexes, showing binding preference for pyrimidine but not for purine motif intermolecular triplex DNA. The binding preferences of TnsC and the Tn7 insertion profiles were obtained using psoralenated, triplex- forming oligonucleotides annealed to plasmid DNAs. Although the presence of psoralen is not required for targeting nor is it alone able to attract TnsC, we show that the location of psoralen within the pyrimidine motif triplex does alter the position of Tn7 insertion relative to the triplex. Comparison between the triplex-targeting pathway and the highly site-specific targeting pathway mediated by the binding of the Tn7-encoded protein, TnsD, to the unique site attTn7, suggests that similar structural features within each target DNA are recognized by TnsC, leading to site-specific transposition. This work demonstrates that a prokaryotic protein involved in the targeting and regulation of Tn7 translocation, TnsC, can selectively recognize pyrimidine motif triplexes.
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Affiliation(s)
- J E Rao
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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Liu J, Xu R, Jin Y, Wang D. Triplex targeting of human PDGF-B (c-sis, proto-oncogene) promoter specifically inhibits factors binding and PDGF-B transcription. Nucleic Acids Res 2001; 29:783-91. [PMID: 11160902 PMCID: PMC30399 DOI: 10.1093/nar/29.3.783] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human c-sis/PDGF-B proto-oncogene has been shown to be overexpressed in a large percentage of human tumor cells establishing a growth-promoting, autocrine growth circuit. Triplex forming oligonucleotides (TFOs) can recognize and bind sequences in duplex DNA, and have received considerable attention because of their potential for targeting specific genomic sites. The c-sis/PDGF-B promoter contains a unique homopurine/homopyrimidine sequence (SIS proximal element, SPE), which is crucial for binding nuclear factors that provoke transcription. In order to develop specific transcriptional inhibitors of the human c-sis/PDGF-B proto-oncogene, 20 potential TFOs targeting part or all of the SPE were screened by gel mobility analysis. DNase I footprinting shows that the TFOs we designed can form a sequence-specific triplex with the target. Protein binding assays demonstrate that triplex formation inhibits nuclear factors binding the c-sis/PDGF-B promoter. Both transient and stable transfection experiments demonstrate that the transcriptional activity of the promoter is considerably inhibited by the TFOs. We propose that TFOs represent a therapeutic potential to specifically diminish the expression of c-sis/PDGF-B proto-oncogene in various pathologic settings where constitutive expression of this gene has been observed.
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Affiliation(s)
- J Liu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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16
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Rao JE, Miller PS, Craig NL. Recognition of triple-helical DNA structures by transposon Tn7. Proc Natl Acad Sci U S A 2000; 97:3936-41. [PMID: 10737770 PMCID: PMC18120 DOI: 10.1073/pnas.080061497] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have found that the bacterial transposon Tn7 can recognize and preferentially insert adjacent to triple-helical nucleic acid structures. Both synthetic intermolecular triplexes, formed through the pairing of a short triplex-forming oligonucleotide on a plasmid DNA, and naturally occurring mirror repeat sequences known to form intramolecular triplexes or H-form DNA are preferential targets for Tn7 insertion in vitro. This target site selectivity depends upon the recognition of the triplex region by a Tn7-encoded ATP-using protein, TnsC, which controls Tn7 target site selection: the interaction of TnsC with the triplex region results in recruitment and activation of the Tn7 transposase. Recognition of a nucleic acid structural motif provides both new information into the factors that influence Tn7's target site selection and broadens its targeting capabilities.
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Affiliation(s)
- J E Rao
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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17
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Guzzo-Pernell N, Tregear GW, Haralambidis J, Lawlor JM. The Design and Synthesis ofN4-Anthraniloyl-2′-dC, the Improved Syntheses ofN4-Carbamoyl-andN4-Ureidocarbamoyl-2′-dC, Incorporation into Oligonucleotides and Triplex Formation Testing. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/07328319808004232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Zozulya VN, Blagoi YP, Dubey IY, Fedoryak OD, Shcherbakova AS, Fedoryak DM. Stabilization of duplex and triplex complexes of oligothymidylate by covalently linked imidazophenazine glycoside. ACTA ACUST UNITED AC 1998. [DOI: 10.7124/bc.0004b9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- V. N. Zozulya
- B. I. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
| | - Yu. P. Blagoi
- B. I. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
| | - I. Y. Dubey
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine
| | - O. D. Fedoryak
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine
| | - A. S. Shcherbakova
- B. I. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine
| | - D. M. Fedoryak
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine
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19
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Faruqi AF, Krawczyk SH, Matteucci MD, Glazer PM. Potassium-resistant triple helix formation and improved intracellular gene targeting by oligodeoxyribonucleotides containing 7-deazaxanthine. Nucleic Acids Res 1997; 25:633-40. [PMID: 9016606 PMCID: PMC146453 DOI: 10.1093/nar/25.3.633] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Triple helix formation by purine-rich oligonucleotides in the anti-parallel motif is inhibited by physiological concentrations of potassium. Substitution with 7-deazaxanthine (c7X) has been suggested as a strategy to overcome this effect. We have tested this by examining triple helix formation both in vitro and in vivo by a series of triple helix-forming oligonucleotides (TFOs) containing guanine plus either adenine, thymine, or c7X. The TFOs were conjugated to psoralen at the 5'end and were designed to bind to a portion of the supF mutation reporter gene. Using in vitro gel mobility shift assays, we found that triplex formation by the c7X-substituted TFOs was relatively resistant to the presence of 140 mM K+. The c7X-containing TFOs were also superior in gene targeting experiments in mammalian cells, yielding 4- to 5-fold higher mutation frequencies in a shuttle vector-based mutagenesis assay designed to detect mutations induced by third strand-directed psoralen adducts. When the phosphodiester backbone was replaced by a phosphorothioate one, the in vitro binding of the c7X-TFOs was not affected, but the efficiency of in vivo triple helix formation was reduced. These results indicate the utility of the c7X substitution for in vivo gene targeting experiments, and they show that the feasibility of the triplex anti-gene strategy can be significantly enhanced by advances in nucleotide chemistry.
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Affiliation(s)
- A F Faruqi
- Department of Therapeutic Radiology, Yale University School of Medicine, PO Box 208040, New Haven, CT 06520-8040, USA
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