1
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Zhao Y, Chandrasekaran AR, Rusling DA, Woloszyn K, Hao Y, Hernandez C, Vecchioni S, Ohayon YP, Mao C, Seeman NC, Sha R. The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:3599-3605. [PMID: 36731121 PMCID: PMC10032566 DOI: 10.1021/jacs.2c12667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.
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Affiliation(s)
- Yue Zhao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
| | - David A Rusling
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yudong Hao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Carina Hernandez
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
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2
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Nishizawa S, Tu G, Ogata D, Miyauchi K, Ohkubo A. Development of antiparallel-type triplex-forming oligonucleotides containing quinoline derivatives capable of recognizing a T–A base pair in a DNA duplex. Bioorg Med Chem 2022; 71:116934. [DOI: 10.1016/j.bmc.2022.116934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/02/2022]
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3
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Hennessy J, McGorman B, Molphy Z, Farrell NP, Singleton D, Brown T, Kellett A. A Click Chemistry Approach to Targeted DNA Crosslinking with
cis
‐Platinum(II)‐Modified Triplex‐Forming Oligonucleotides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joseph Hennessy
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
| | - Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical Centre School of Chemical Sciences Dublin City University, Glasnevin Dublin 9 Ireland
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Daniel Singleton
- ATDBio Ltd. School of Chemistry University of Southampton Southampton SO17 1BJ UK
| | - Tom Brown
- ATDBio Ltd. School of Chemistry University of Southampton Southampton SO17 1BJ UK
- Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical Centre School of Chemical Sciences Dublin City University, Glasnevin Dublin 9 Ireland
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4
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Hennessy J, McGorman B, Molphy Z, Farrell NP, Singleton D, Brown T, Kellett A. A Click Chemistry Approach to Targeted DNA Crosslinking with cis-Platinum(II)-Modified Triplex-Forming Oligonucleotides. Angew Chem Int Ed Engl 2021; 61:e202110455. [PMID: 34652881 PMCID: PMC9299770 DOI: 10.1002/anie.202110455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/11/2021] [Indexed: 01/05/2023]
Abstract
Limitations of clinical platinum(II) therapeutics include systemic toxicity and inherent resistance. Modern approaches, therefore, seek new ways to deliver active platinum(II) to discrete nucleic acid targets. In the field of antigene therapy, triplex‐forming oligonucleotides (TFOs) have attracted interest for their ability to specifically recognise extended duplex DNA targets. Here, we report a click chemistry based approach that combines alkyne‐modified TFOs with azide‐bearing cis‐platinum(II) complexes—based on cisplatin, oxaliplatin, and carboplatin motifs—to generate a library of PtII‐TFO hybrids. These constructs can be assembled modularly and enable directed platinum(II) crosslinking to purine nucleobases on the target sequence under the guidance of the TFO. By covalently incorporating modifications of thiazole orange—a known DNA‐intercalating fluorophore—into PtII‐TFOs constructs, enhanced target binding and discrimination between target and off‐target sequences was achieved.
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Affiliation(s)
- Joseph Hennessy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
| | - Daniel Singleton
- ATDBio Ltd., School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- ATDBio Ltd., School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.,Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
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5
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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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6
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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7
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Ohkubo A, Ohnishi T, Nishizawa S, Nishimura Y, Hisamatsu S. The ability of a triplex-forming oligonucleotide to recognize T-A and C-G base pairs in a DNA duplex is enhanced by incorporating N-acetyl-2,7-diaminoquinoline. Bioorg Med Chem 2020; 28:115350. [PMID: 32115336 DOI: 10.1016/j.bmc.2020.115350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/21/2022]
Abstract
A triplex-forming oligonucleotide (TFO) can recognize the homopurine-homopyrimidine sequence in DNA duplexes and inhibit the transcription of targeted mRNAs. Recently, we reported that N-acetyl-2,7-diamino-1,8-naphthyridine (DANac), incorporated into a TFO, has high binding ability and base recognition selectivity for the pyrimidine bases in the purine-rich chain of the DNA duplex at pH 7.4. However, it was found in this study that the difference in the Tm values between the pyrimidine bases and purine bases decreased by more than 4 °C at pH 6.0-7.0. To improve the low base recognition selectivity of the TFO, we designed a new artificial base, DAQac, with a quinoline skeleton. The Tm values of the triplexes containing DAQac:T-A or DAQac:C-G were more than 13 °C higher than those of the triplexes containing DAQac:A-T or DAQac:G-C at pH 7.4. We also observed that under more acidic conditions (pH 6.0-7.0), the base recognition selectivity of DAQac in a triplex was higher than that of DANac, although the binding ability of DAQac in a triplex was similar to that of DANac. Additionally, we found that DAQac, incorporated into the TFO, could accurately recognize the MeC-G base pair in the hairpin DNA, similar to the C-G base pair.
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
| | - Tatsuya Ohnishi
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Yuri Nishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shugo Hisamatsu
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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8
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Sayoh I, Rusling DA, Brown T, Fox KR. DNA Structural Changes Induced by Intermolecular Triple Helix Formation. ACS OMEGA 2020; 5:1679-1687. [PMID: 32010842 PMCID: PMC6990630 DOI: 10.1021/acsomega.9b03776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
DNase I footprints of intermolecular DNA triplexes are often accompanied by enhanced cleavage at the 3'-end of the target site at the triplex-duplex junction. We have systematically studied the sequence dependence of this effect by examining oligonucleotide binding to sites flanked by each base in turn. For complexes with a terminal T.AT triplet, the greatest enhancement is seen with ApC, followed by ApG and ApT, with the weakest enhancement at ApA. Similar DNase I enhancements were observed for a triplex with a terminal C+.GC triplet, though with little difference between the different GpN sites. Enhanced reactivity to diethylpyrocarbonate was observed at As that flank the triplex-duplex junction at AAA or AAC but not AAG or AAT. Fluorescence melting experiments demonstrated that the flanking base affected the stability with a 4 °C difference in T m between a flanking C and G. Sequences that produced the strongest enhancement correlated with those having the lower thermal stability. These results are interpreted in terms of oligonucleotide-induced changes in DNA structure and/or flexibility.
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Affiliation(s)
- Ibrahim Sayoh
- School
of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, U.K.
| | - David A. Rusling
- School
of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Tom Brown
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Keith R. Fox
- School
of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, U.K.
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9
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Klimkowski P, De Ornellas S, Singleton D, El-Sagheer AH, Brown T. Design of thiazole orange oligonucleotide probes for detection of DNA and RNA by fluorescence and duplex melting. Org Biomol Chem 2019; 17:5943-5950. [PMID: 31157811 PMCID: PMC6686645 DOI: 10.1039/c9ob00885c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have synthesised a range of thiazole orange (TO) functionalised oligonucleotides for nucleic acid detection in which TO is attached to the nucleobase or sugar of thymidine. The properties of duplexes between TO-probes and their DNA and RNA targets strongly depend on the length of the linker between TO and the oligonucleotide, the position of attachment of TO to the nucleotide (major or minor groove) and the mode of attachment of thiazole orange (via benzothiazole or quinoline moiety). This information can be used to design probes for detection of target nucleic acids by fluorescence or duplex melting. With cellular imaging in mind we show that 2'-OMe RNA probes with TO at the 5-position of uracil or the 2'-position of the ribose sugar are particularly effective, exhibiting up to 44-fold fluorescence enhancement against DNA and RNA, and high duplex stability. Excellent mismatch discrimination is achieved when the mispaired base is located adjacent to the TO-modified nucleotide rather than opposite to it. The simple design, ease of synthesis and favourable properties of these TO probes suggest applications in fluorescent imaging of DNA and RNA in a cellular context.
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Affiliation(s)
- Piotr Klimkowski
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Sara De Ornellas
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - Daniel Singleton
- ATDBio, School of Chemistry University of Southampton, SO17 1BJ, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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10
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Walsh S, El-Sagheer AH, Brown T. Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above. Chem Sci 2018; 9:7681-7687. [PMID: 30393529 PMCID: PMC6182420 DOI: 10.1039/c8sc02418a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/30/2018] [Indexed: 12/20/2022] Open
Abstract
The instability of DNA triplexes particularly at neutral pH and above severely limits their applications. Here, we demonstrate that the introduction of a thiazole orange (TO) intercalator onto a thymine nucleobase in triplex forming oligonucleotides (TFOs) resolves this problem. The stabilising effects are additive; multiple TO units produce nanomolar duplex binding and triplex stability can surpass that of the underlying duplex. In one example, a TFO containing three TO units increased the triplex melting temperature at pH 7 by a remarkable 50 °C relative to the unmodified triplex. Notably, TO intercalation promotes TFO binding to target sequences other than pure polypurine tracts by the use of 5-(1-propynyl)cytosine (pC) against C:G inversions. By overcoming the instability of triplexes across a broad range of pH and sequence contexts, these very simple 'TOTFO' probes could expand triplex applications into many areas including diagnostics and cell imaging.
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Affiliation(s)
- Sarah Walsh
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
- ATDBio Ltd. , Oxford Science Park , Oxford , UK
| | - Afaf Helmy El-Sagheer
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
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11
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Ito Y, Masaki Y, Kanamori T, Ohkubo A, Seio K, Sekine M. Synthesis of 5-[3-(2-aminopyrimidin-4-yl)aminopropyn-1-yl]uracil derivative that recognizes Ade-Thy base pairs in double-stranded DNA. Bioorg Med Chem Lett 2016; 26:194-6. [PMID: 26602276 DOI: 10.1016/j.bmcl.2015.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/28/2022]
Abstract
5-[3-(2-Aminopyrimidin-4-yl)aminopropyn-1-yl]uracil (Ura(Pyr)) was designed as a new nucleobase to recognize Ade-Thy base pair in double-stranded DNA. We successfully synthesized the dexoynucleoside phosphoramidite having Ura(Pyr) and incorporated it into triplex forming oligonucleotides (TFOs). Melting temperature analysis revealed that introduction of Ura(Pyr) into TFOs could effectively stabilize their triplex structures without loss of base recognition capabilities.
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Affiliation(s)
- Yu Ito
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan.
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan.
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12
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Bahal R, Gupta A, Glazer PM. Precise Genome Modification Using Triplex Forming Oligonucleotides and Peptide Nucleic Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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13
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Ohkubo A, Yamada K, Ito Y, Yoshimura K, Miyauchi K, Kanamori T, Masaki Y, Seio K, Yuasa H, Sekine M. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs. Nucleic Acids Res 2015; 43:5675-86. [PMID: 26013815 PMCID: PMC4499124 DOI: 10.1093/nar/gkv496] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/03/2015] [Indexed: 11/28/2022] Open
Abstract
A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (dgC) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2’-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2’-OMegC), 2’-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2’-OMegCs), dgC and 4S-(2-guanidoethyl)-4-thiothymidine (gsT). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine (DANac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing DANac, dgC, 2’-OMe-2-thiothymidine (2’-OMesT) and 2’-OMe-8-thioxoadenosine (2’-OMesA) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions.
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kenji Yamada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Yu Ito
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kiichi Yoshimura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Koichiro Miyauchi
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
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14
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Semioshkin A, Ilinova A, Lobanova I, Bregadze V, Paradowska E, Studzińska M, Jabłońska A, Lesnikowski ZJ. Synthesis of the first conjugates of 5-ethynyl-2′-deoxyuridine with closo-dodecaborate and cobalt-bis-dicarbollide boron clusters. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.06.100] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Sau SP, Kumar P, Sharma PK, Hrdlicka PJ. Fluorescent intercalator displacement replacement (FIDR) assay: determination of relative thermodynamic and kinetic parameters in triplex formation--a case study using triplex-forming LNAs. Nucleic Acids Res 2012; 40:e162. [PMID: 22855561 PMCID: PMC3505983 DOI: 10.1093/nar/gks729] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Triplex forming oligonucleotides (TFOs) are the most commonly used approach for site-specific targeting of double stranded DNA (dsDNA). Important parameters describing triplex formation include equilibrium binding constants (K(eq)) and association/dissociation rate constants (k(on) and k(off)). The 'fluorescent intercalator displacement replacement' (FIDR) assay is introduced herein as an operationally simple approach toward determination of these parameters for triplexes involving TC-motif TFOs. Briefly described, relative rate constants are determined from fluorescence intensity changes upon: (i) TFO-mediated displacement of pre-intercalated and fluorescent ethidium from dsDNA targets (triplex association) and (ii) Watson-Crick complement-mediated displacement of the TFO and replacement with ethidium (triplex dissociation). The assay is used to characterize triplexes between purine-rich dsDNA targets and TC-motif TFOs modified with six different locked nucleic acid (LNA) monomers, i.e. conventional and C5-alkynyl-functionalized LNA and α-L-LNA pyrimidine monomers. All of the studied monomers increase triplex stability by decreasing the triplex dissociation rate. LNA-modified TFOs form more stable triplexes than α-L-LNA-modified counterparts owing to slower triplex dissociation. Triplexes modified with C5-(3-aminopropyn-1-yl)-LNA-U monomer Z are particularly stable. The study demonstrates that three affinity-enhancing features can be combined into one high-affinity TFO monomer: conformational restriction of the sugar ring, expansion of the pyrimidine π-stacking surface and introduction of an exocyclic amine.
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Affiliation(s)
- Sujay P Sau
- Department of Chemistry, University of Idaho, PO Box 442343, Moscow, ID 83844-2343, USA
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16
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Shibata A, Ueno Y, Iwata M, Wakita H, Matsuda A, Kitade Y. Double-stranded oligonucleotides containing 5-aminomethyl-2'-deoxyuridine form thermostable anti-parallel triplexes with single-stranded DNA or RNA. Bioorg Med Chem Lett 2012; 22:2681-3. [PMID: 22460027 DOI: 10.1016/j.bmcl.2012.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/28/2012] [Accepted: 03/05/2012] [Indexed: 11/15/2022]
Abstract
This Letter describes the synthesis and properties of double-stranded antisense oligonucleotides connected with a pentaerythritol linker. We found that double-stranded antisense oligonucleotides with aminomethyl residues have high affinity for single-stranded DNA or RNA in buffer solutions with and without MgCl(2). Thus, these oligonucleotides would be useful as antisense oligonucleotides for targeting single-stranded RNA through triplex formation.
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Affiliation(s)
- Aya Shibata
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu, Japan
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17
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Hari Y, Obika S, Imanishi T. Towards the Sequence-Selective Recognition of Double-Stranded DNA Containing Pyrimidine-Purine Interruptions by Triplex-Forming Oligonucleotides. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101821] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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18
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Cardew AS, Brown T, Fox KR. Secondary binding sites for heavily modified triplex forming oligonucleotides. Nucleic Acids Res 2011; 40:3753-62. [PMID: 22180535 PMCID: PMC3333850 DOI: 10.1093/nar/gkr1119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In order to enhance DNA triple helix stability synthetic oligonucleotides have been developed that bear amino groups on the sugar or base. One of the most effective of these is bis-amino-U (B), which possesses 5-propargylamino and 2′-aminoethoxy modifications. Inclusion of this modified nucleotide not only greatly enhances triplex stability, but also increases the affinity for related sequences. We have used a restriction enzyme protection, selection and amplification assay (REPSA) to isolate sequences that are bound by the heavily modified 9-mer triplex-forming oligonucleotide B6CBT. The isolated sequences contain An tracts (n = 6), suggesting that the 5′-end of this TFO was responsible for successful triplex formation. DNase I footprinting with these sequences confirmed triple helix formation at these secondary targets and demonstrated no interaction with similar oligonucleotides containing T or 5-propargylamino-dU.
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Affiliation(s)
- Antonia S Cardew
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton SO17 1BJ, UK
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19
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Jain ML, Bruice PY, Szabó IE, Bruice TC. Incorporation of positively charged linkages into DNA and RNA backbones: a novel strategy for antigene and antisense agents. Chem Rev 2011; 112:1284-309. [PMID: 22074477 DOI: 10.1021/cr1004265] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Moti L Jain
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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20
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Abstract
Triple-helical nucleic acids are formed by binding an oligonucleotide within the major groove of duplex DNA. These complexes offer the possibility of designing oligonucleotides which bind to duplex DNA with considerable sequence specificity. However, triple-helix formation with natural nucleotides is limited by (i) the requirement for low pH, (ii) the requirement for homopurine target sequences, and (iii) their relatively low affinity. We have prepared modified oligonucleotides to overcome these limitations, including the addition of positive charges to the sugar and/or base, the inclusion of cytosine analogues, the development of nucleosides for recognition of pyrimidine interruptions and the attachment of one or more cross-linking groups. By these means we are able to generate triplexes which have high affinities at physiological pH at sequences that contain pyrimidine interruptions.
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21
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Mukherjee A, Vasquez KM. Triplex technology in studies of DNA damage, DNA repair, and mutagenesis. Biochimie 2011; 93:1197-208. [PMID: 21501652 DOI: 10.1016/j.biochi.2011.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 04/01/2011] [Indexed: 12/18/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms of DNA repair, recombination, and mutagenesis. In addition, TFO targeting of specific genes has been exploited in the development of therapeutic strategies to modulate DNA structure and function. In this review, we discuss advances made in studies of DNA damage, DNA repair, recombination, and mutagenesis by using triplex technology to target specific DNA sequences.
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Affiliation(s)
- Anirban Mukherjee
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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22
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Ohkubo A, Nishino Y, Yokouchi A, Ito Y, Noma Y, Kakishima Y, Masaki Y, Tsunoda H, Seio K, Sekine M. Stable triplex formation using the strong stacking effect of consecutive thionucleoside moieties. Chem Commun (Camb) 2011; 47:12556-8. [DOI: 10.1039/c1cc14339e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Park SM, Nam SJ, Jeong HS, Kim WJ, Kim BH. The effects of the 4-(4-Methylpiperazine)phenyl group on nucleosides and oligonucleotides: cellular delivery, detection, and stability. Chem Asian J 2010; 6:487-92. [PMID: 21254426 DOI: 10.1002/asia.201000574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Indexed: 11/11/2022]
Abstract
As drug candidates, one promising way to improve the cellular delivery efficacy of oligonucleotides is to introduce a cationic group. By introducing a cationic moiety into the oligonucleotide structure, they become capable of approaching the cell surface and also of crossing the cellular membrane. In an effort to develop cell-permeable oligonucleotides, we examined the piperazinephenyl-bearing 2'-deoxyuridine ((PP)U), which can be not only cationic but also fluorescent as a cationic monomer for cationic oligonucleotides. Several modified DNA oligonucleotides with different numbers of (PP)U building blocks were synthesized and evaluated for the effect on thermal stability and conformation by the introduction of (PP)U. The cellular delivery of modified oligonucleotides was different depending on the number of (PP)U building blocks. Furthermore, these (PP)U-modified oligonucleotides had sufficient fluorescence that we were able to identify the delivery results without the use of conventional fluorescent tags. They were predominantly localized in the cell cytoplasm. In addition, they were stable enough after 3 hours in the presence of nuclease. These results showed that a piperazinephenyl moiety that is conjugated with nucleobase is able to deliver and detect the oligonucleotides, which suggests that this concept of 'dual-function oligonucleotides' might be utilized in diagnostics, therapeutics, and as a convenient biological tool for probing the activity of oligonucleotides inside cells.
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Affiliation(s)
- Sun Min Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Republic of Korea
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24
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Lou C, Xiao Q, Brennan L, Light ME, Vergara-Irigaray N, Atkinson EM, Holden-Dye LM, Fox KR, Brown T. Synthesis and properties of triplex-forming oligonucleotides containing 2'-O-(2-methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine. Bioorg Med Chem 2010; 18:6389-97. [PMID: 20674370 DOI: 10.1016/j.bmc.2010.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 07/01/2010] [Accepted: 07/06/2010] [Indexed: 10/19/2022]
Abstract
2'-O-(2-Methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine phosphoramidite (MEPU) has been synthesized from d-ribose and 5-iodouracil and incorporated into triplex-forming oligonucleotides (TFOs) by automated solid-phase oligonucleotide synthesis. The TFOs gave very high triplex stability with their target duplexes as measured by ultraviolet/fluorescence melting and DNase I footprinting. The incorporation of MEPU into TFOs renders them resistant to degradation by serum nucleases.
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Affiliation(s)
- Chenguang Lou
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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25
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Morvan F, Debart F, Vasseur JJ. From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers 2010; 7:494-535. [PMID: 20232324 DOI: 10.1002/cbdv.200900220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université Montpellier 1 and Université Montpellier 2, Place Eugène Bataillon, CC1704, FR-34095 Montpellier cedex 5, France
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26
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Sau SP, Kumar TS, Hrdlicka PJ. Invader LNA: efficient targeting of short double stranded DNA. Org Biomol Chem 2010; 8:2028-36. [PMID: 20401378 DOI: 10.1039/b923465a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Despite progress with triplex-forming oligonucleotides or helix-invading peptide nucleic acids (PNAs), there remains a need for probes facilitating sequence-unrestricted targeting of double stranded DNA (dsDNA) at physiologically relevant conditions. Invader LNA probes, i.e., DNA duplexes with "+1 interstrand zipper arrangements" of intercalator-functionalized 2'-amino-alpha-l-LNA monomers, are demonstrated herein to recognize short mixed sequence dsDNA targets. This approach, like pseudo-complementary PNA (pcPNA), relies on relative differences in stability between probe duplexes and the corresponding probe:target duplexes for generation of a favourable thermodynamic gradient. Unlike pcPNA, Invader LNA probes take advantage of the "nearest neighbour exclusion principle", i.e., intercalating units of Invader LNA monomers are poorly accommodated in probe duplexes but extraordinarily well tolerated in probe-target duplexes (DeltaT(m)/modification up to +11.5 degrees C). Recognition of isosequential dsDNA-targets occurs: a) at experimental temperatures much lower than the thermal denaturation temperatures (T(m)'s) of Invader LNAs or dsDNA-targets, b) at a wide range of ionic strengths, and c) with good mismatch discrimination. Recognition of dsDNA is monitored in real-time using inherent pyrene-pyrene excimer signals of Invader LNA probes, which provides insights into reaction kinetics and enables rational design of probes. These properties render Invader LNAs as promising probes for biomedical applications entailing sequence-unrestricted recognition of dsDNA.
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Affiliation(s)
- Sujay P Sau
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA
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27
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Sau SP, Kumar P, Anderson BA, Østergaard ME, Deobald L, Paszczynski A, Sharma PK, Hrdlicka PJ. Optimized DNA-targeting using triplex forming C5-alkynyl functionalized LNA. Chem Commun (Camb) 2009:6756-8. [PMID: 19885469 DOI: 10.1039/b917312a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triplex forming oligonucleotides (TFOs) modified with C5-alkynyl functionalized LNA (locked nucleic acid) monomers display extraordinary thermal affinity toward double stranded DNA targets, excellent discrimination of Hoogsteen-mismatched targets, and high stability against 3?-exonucleases.
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Affiliation(s)
- Sujay P Sau
- Dept. of Chemistry, Univ. of Idaho, ID-83844, USA
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28
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Rusling DA, Rachwal PA, Brown T, Fox KR. The stability of triplex DNA is affected by the stability of the underlying duplex. Biophys Chem 2009; 145:105-10. [PMID: 19819611 DOI: 10.1016/j.bpc.2009.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/16/2009] [Accepted: 09/16/2009] [Indexed: 11/16/2022]
Abstract
We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C(+).GC and T.AT triplets) at pH 5.0 the T(m) is more than 10 degrees C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the T(m) is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogues.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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29
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Bergstrom DE. Unnatural nucleosides with unusual base pairing properties. ACTA ACUST UNITED AC 2009; Chapter 1:1.4.1-1.4.32. [PMID: 19488968 DOI: 10.1002/0471142700.nc0104s37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.
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30
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Rusling DA, Peng G, Srinivasan N, Fox KR, Brown T. DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine. Nucleic Acids Res 2009; 37:1288-96. [PMID: 19139069 PMCID: PMC2651792 DOI: 10.1093/nar/gkn1060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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31
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Ends free and self-quenched molecular beacon with pyrene labeled pyrrolocytidine in the middle of the stem. Tetrahedron 2009. [DOI: 10.1016/j.tet.2008.10.093] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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32
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Li H, Miller PS, Seidman MM. Selectivity and affinity of DNA triplex forming oligonucleotides containing the nucleoside analogues 2'-O-methyl-5-(3-amino-1-propynyl)uridine and 2'-O-methyl-5-propynyluridine. Org Biomol Chem 2008; 6:4212-7. [PMID: 18972052 DOI: 10.1039/b810709b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triplex forming oligonucleotides (TFOs) containing the nucleoside analogues 2'-O-methyl-5-propynyluridine (1) and 2'-O-methyl-5-(3-amino-1-propynyl)uridine (2) were synthesized. The affinity and selectivity of triplex formation by these TFOs were studied by gel shift analysis, T(m) value measurement, and association rate assays. The results show that the introduction of 1 and 2 into TFOs can improve the stability of the triplexes under physiological conditions. Optimized distribution of 1 or 2 in the TFOs combined with a cluster of contiguous nucleosides with 2'-aminoethoxy sugars resulted in formation of triplexes with further enhanced stability and improved selectivity.
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Affiliation(s)
- Hong Li
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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33
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Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB. The triple helix: 50 years later, the outcome. Nucleic Acids Res 2008; 36:5123-38. [PMID: 18676453 PMCID: PMC2532714 DOI: 10.1093/nar/gkn493] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.
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Affiliation(s)
- Maria Duca
- LCMBA CNRS UMR6001, University of Nice-Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France
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34
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Brennan L, Peng G, Srinivasan N, Fox KR, Brown T. 2'-o-dimethylaminoethoxyuridine and 5-dimethylaminopropargyl deoxyuridine for at base pair recognition in triple helices. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1283-6. [PMID: 18066769 DOI: 10.1080/15257770701530525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The nucleoside analogues 2'-O-dimethylaminoethoxy uridine and 5-dimethylaminopropargyl deoxyuridine have been synthesised and incorporated into oligonucleotides. Their triplex-stabilising properties have been determined in fluorescence melting experiments.
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Affiliation(s)
- Lavinia Brennan
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom.
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35
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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: 18] [Impact Index Per Article: 1.1] [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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36
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Deglane G, Morvan F, Debart F, Vasseur JJ. 5-Propynylamino alpha-deoxyuridine promotes DNA duplex stabilization of anionic and neutral but not cationic alpha-oligonucleotides. Bioorg Med Chem Lett 2006; 17:951-4. [PMID: 17157020 DOI: 10.1016/j.bmcl.2006.11.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 11/14/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Incorporation of 5-propynylamino and 5-propynyl alpha-2'-deoxyuridine into alpha-oligonucleotides (alpha-ON) allows high-affinity targeting of complementary DNA for alpha-ON with anionic and neutral backbone but not for cationic alpha-ON, revealing clues on the role of the amino group of the propynylamino on the formation of DNA duplexes.
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Affiliation(s)
- Gaëlle Deglane
- LCOBS, UMR 5625 CNRS-UM II, Université Montpellier II, 34095 Montpellier, France
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37
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Deglane G, Abes S, Michel T, Prévot P, Vives E, Debart F, Barvik I, Lebleu B, Vasseur JJ. Impact of the guanidinium group on hybridization and cellular uptake of cationic oligonucleotides. Chembiochem 2006; 7:684-92. [PMID: 16518865 DOI: 10.1002/cbic.200500433] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The grafting of cationic groups to synthetic oligonucleotides (ONs) in order to reduce the charge repulsion between the negatively charged strands of a duplex or triplex, and consequently to increase a complex's stability, has been extensively studied. Guanidinium groups, which are highly basic and positively charged over a wide pH range, could be an efficient ON modification to enhance their affinity for nucleic acid targets and to improve cellular uptake. A straightforward post-synthesis method to convert amino functions attached to ONs (on sugar, nucleobase or backbone) into guanidinium tethers has been perfected. In comparison to amino groups, such cationic groups anchored to alpha-oligonucleotide phosphoramidate backbones play important roles in duplex stability, particularly with RNA targets. This high affinity could be explained by dual recognition resulting from Watson-Crick or Hoogsteen base pairing combined with cationic/anionic backbone recognition between strands involving H-bond formation and salt bridging. Molecular-dynamics simulations corroborate interactions between the cationic backbones of the alpha-ONs and the anionic backbones of the nucleic acid targets. Moreover, ONs with guanidinium modification increased cellular uptake relative to negatively charged ONs. The cellular localization of these new cationic phosphoramidate ONs is mainly cytoplasmic. The uptake of these ON analogues might occur through endocytosis.
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Affiliation(s)
- Gaëlle Deglane
- LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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38
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Ozaki H, Mine M, Ogawa Y, Sawai H. Effect of the terminal amino group of a linker arm and its length at the C5 position of a pyrimidine nucleoside on the thermal stability of DNA duplexes. Bioorg Chem 2005; 29:187-97. [PMID: 16256691 DOI: 10.1006/bioo.2001.1212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2000] [Indexed: 11/22/2022]
Abstract
2'-Deoxyuridine derivatives bearing a substituent at the C5-position, which has a different chain length and a different functional group (methyl or amino), were synthesized and incorporated into oligodeoxyribonucleotides. The effect of the substituent groups in the major groove on the stability of the duplexes was investigated by UV melting experiments. It was found that the stabilization of these duplexes by a terminal amino group depended on the length of a linker arm.
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Affiliation(s)
- H Ozaki
- Department of Chemistry, Faculty of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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39
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Rusling DA, Le Strat L, Powers VEC, Broughton-Head VJ, Booth J, Lack O, Brown T, Fox KR. Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH. FEBS Lett 2005; 579:6616-20. [PMID: 16293248 DOI: 10.1016/j.febslet.2005.10.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 10/12/2005] [Accepted: 10/27/2005] [Indexed: 10/25/2022]
Abstract
We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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40
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Michel T, Debart F, Heitz F, Vasseur JJ. Highly stable DNA triplexes formed with cationic phosphoramidate pyrimidine alpha-oligonucleotides. Chembiochem 2005; 6:1254-62. [PMID: 15912553 DOI: 10.1002/cbic.200400436] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ability of cationic phosphoramidate pyrimidine alpha-oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in alpha-ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate alpha-TFO (triplex-forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic alpha-TFO through Hoogsteen base pairing is highly sequence-specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic alpha-oligonucleotides and duplex targets.
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Affiliation(s)
- Thibaut Michel
- LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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41
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Rusling DA, Powers VEC, Ranasinghe RT, Wang Y, Osborne SD, Brown T, Fox KR. Four base recognition by triplex-forming oligonucleotides at physiological pH. Nucleic Acids Res 2005; 33:3025-32. [PMID: 15911633 PMCID: PMC1137030 DOI: 10.1093/nar/gki625] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 04/29/2005] [Accepted: 05/12/2005] [Indexed: 11/29/2022] Open
Abstract
We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, (Me)P (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while (A)PP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, (Me)P and (A)PP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA.
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Affiliation(s)
- David A. Rusling
- School of Biological Sciences, University of SouthamptonBassett Crescent East, Southampton SO16 7PX, UK
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Vicki E. C. Powers
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Rohan T. Ranasinghe
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Yang Wang
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Sadie D. Osborne
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Keith R. Fox
- To whom correspondence should be addressed. Tel: +44 23 8059 4374; Fax: +44 23 8059 4459;
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Mayer A, Häberli A, Leumann CJ. Synthesis and triplex forming properties of pyrrolidino pseudoisocytidine containing oligodeoxynucleotides. Org Biomol Chem 2005; 3:1653-8. [PMID: 15858646 DOI: 10.1039/b502799c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pyrrolidino pseudo-C-nucleosides are isosteres of natural deoxynucleosides which are protonated at the pyrrolidino ring nitrogen under physiological conditions. As constituents of a triplex forming oligodeoxynucleotide (TFO), the positive charge is expected to stabilise DNA triple helices via electrostatic interactions with the phosphodiester backbone of the target DNA. We describe the synthesis of the pyrrolidino isocytidine pseudonucleoside and the corresponding phosphoramidite building block and its incorporation into TFOs. Such TFOs show substantially increased DNA affinity compared to unmodified oligodeoxynucleotides. The increase in affinity is shown to be due to the positive charge at the pyrrolidino subunit.
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Affiliation(s)
- Alain Mayer
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
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43
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Brazier JA, Shibata T, Townsley J, Taylor BF, Frary E, Williams NH, Williams DM. Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2'-deoxyuridines and their application in DNA triplex formation. Nucleic Acids Res 2005; 33:1362-71. [PMID: 15745996 PMCID: PMC552953 DOI: 10.1093/nar/gki254] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The incorporation of C5-amino-modified 2′-deoxyuridine analogues into DNA have found application in nucleic acid labelling, the stabilization of nucleic acid structures, functionalization of nucleic acid aptamers and catalysts, and the investigation of sequence-specific DNA bending. In this study, we describe the physicochemical properties of four different C5-amino-modified 2′-deoxyuridines in which the amino group is tethered to the base via a 3-carbon alkyl, Z- or E-alkenyl or alkynyl linker. Conformational parameters of the nucleosides and their pKa values were deduced using 1H NMR. All of them display the expected anti-conformation of the nucleoside with 2′-endo sugar puckers for the deoxyribose ring. A preference for the cisoid conformation for the Z-alkenyl analogue is found, while the E-alkenyl analogue exists exclusively as its transoid conformation. The pKa values range from 10.0 for the analogue with an aliphatic propyl linker to 8.5 for the propargylamino analogue. The analogues have been used for the synthesis of triple-helix forming oligonucleotides (TFOs) in which they replace thymidine in the natural sequence. Oligonucleotides containing the propargylamino analogue display the highest stability especially at low pH, while those containing analogues with propyl and especially Z-alkenyl linkers are destabilized to a great extent. TFOs containing the analogue with the E-alkenyl linker have stability similar to the unmodified structures. The chemical synthesis of TFOs containing the analogue, 5-(3-hydroxyprop-1-ynyl)-2′-deoxyuridine that possesses a neutral but polar side chain show a remarkable stability, which is higher than that of all TFOs containing the alkylamino or alkenylamino analogues and only slightly lower than that of TFOs containing the propargylamino analogue. Both the hydroxyl and propargylamino substitutions impart enhanced triple-helix stability relative to the analogous sequences containing C5-propynyl-2′-deoxyuridine. Furthermore, a similar dependence of stability on pH is found between TFOs containing the hydroxypropynyl modifications and those containing the propargylamino side chains. This suggests that the major factor responsible for stabilizing such triple helices is due to the presence of the alkyne with an attached electronegative group.
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Affiliation(s)
| | | | | | | | | | | | - David M. Williams
- To whom correspondence should be addressed. Tel: +44 114 222 9502; Fax: +44 114 222 9346;
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Osborne SD, Powers VEC, Rusling DA, Lack O, Fox KR, Brown T. Selectivity and affinity of triplex-forming oligonucleotides containing 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA. Nucleic Acids Res 2004; 32:4439-47. [PMID: 15317869 PMCID: PMC516051 DOI: 10.1093/nar/gkh776] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have used DNase I footprinting, fluorescence and ultraviolet (UV) melting experiments and circular dichroism to demonstrate that, in the parallel triplex binding motif, 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) has very high affinity for AT relative to all other Watson-Crick base pairs in DNA. Complexes containing two or more substitutions with this nucleotide analogue are stable at pH 7.0, even though they contain several C.GC base triplets. These modified triplex-forming oligonucleotides retain exquisite sequence specificity, with enhanced discrimination against YR base pairs (especially CG). These properties make BAU a useful base analogue for the sequence-specific creation of stable triple helices at pH 7.0.
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Affiliation(s)
- Sadie D Osborne
- School of Chemistry, University of Southampton, Highfield, Southampton SC17 1BJ, UK
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45
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Keppler MD, James PL, Neidle S, Brown T, Fox KR. DNA sequence specificity of triplex-binding ligands. ACTA ACUST UNITED AC 2004; 270:4982-92. [PMID: 14653824 DOI: 10.1046/j.1432-1033.2003.03901.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have examined the ability of naphthylquinoline, a 2,7-disubstituted anthraquinone and BePI, a benzo[e]pyridoindole derivative, to stabilize parallel DNA triplexes of different base composition. Fluorescence melting studies, with both inter- and intramolecular triplexes, show that all three ligands stabilize triplexes that contain blocks of TAT triplets. Naphthylquinoline has no effect on triplexes formed with third strands composed of (TC)n or (CCT)n, but stabilizes triplexes that contain (TTC)n. In contrast, BePI slightly destabilizes the triplexes that are formed at (TC)n (CCT)n and (TTC)n. 2,7-Anthraquinone stabilizes (TC)n (CCT)n and (TTC)n, although it has the greatest effect on the latter. DNase I footprinting studies confirm that triplexes formed with (CCT)n are stabilized by the 2,7-disubstituted amidoanthraquinone but not by naphthylquinoline. Both ligands stabilize the triplex formed with (CCTT)n and neither affects the complex with (CT)n. We suggest that BePI and naphthylquinoline can only bind between adjacent TAT triplets, while the anthraquinone has a broader sequence of selectivity. These differences may be attributed to the presence (naphthylquinoline and BePI) or absence (anthraquinone) of a positive charge on the aromatic portion of the ligand, which prevents intercalation adjacent to C+GC triplets. The most stable structures are formed when the stacked rings (bases or ligand) alternate between charged and uncharged species. Triplexes containing alternating C+GC and TAT triplets are not stabilized by ligands as they would interrupt the alternating pattern of charged and uncharged residues.
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Affiliation(s)
- Melanie D Keppler
- Division of Biochemistry & Molecular Biology, School of Biological Sciences, University of Southampton, UK
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46
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Booth J, Cummins WJ, Brown T. An analogue of adenine that forms an “A:T” base pair of comparable stability to G:C. Chem Commun (Camb) 2004:2208-9. [PMID: 15467875 DOI: 10.1039/b409155h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The heterocyclic base 7-aminopropargyl-7-deaza-2,6-diaminopurine (D) has been incorporated into oligodeoxynucleotides. D:T has similar thermodynamic stability to G:C and is a stable analogue of A:T.
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Affiliation(s)
- James Booth
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
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47
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Michel T, Martinand-Mari C, Debart F, Lebleu B, Robbins I, Vasseur JJ. Cationic phosphoramidate alpha-oligonucleotides efficiently target single-stranded DNA and RNA and inhibit hepatitis C virus IRES-mediated translation. Nucleic Acids Res 2003; 31:5282-90. [PMID: 12954764 PMCID: PMC203318 DOI: 10.1093/nar/gkg733] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2003] [Revised: 07/24/2003] [Accepted: 07/24/2003] [Indexed: 12/29/2022] Open
Abstract
A potential means to improve the efficacy of steric-blocking antisense oligonucleotides (ON) is to increase their affinity for a target RNA. The grafting of cationic amino groups to the backbone of the ON is one way to achieve this, as it reduces the electrostatic repulsion between the ON and its target. We have examined the duplex stabilising effects of introducing cationic phosphoramidate internucleoside linkages into ON with a non-natural alpha-anomeric configuration. Cationic alpha-ON bound with high affinity to single-stranded DNA and RNA targets. Duplex stabilisation was proportional to the number of cationic modifications, with fully cationic ON having particularly high thermal stability. The average stabilisation was greatly increased at low ionic strength. The duplex formed between cationic alpha-ON and their RNA targets were not substrates for RNase H. The penalty in T(m) inflicted by a single mismatch, however, was high; suggesting that they are well suited as sequence-specific, steric-blocking, antisense agents. Using a well-described target sequence in the internal ribosome entry site of the human hepatitis C virus, we have confirmed this potential in a cell-free translation assay as well as in a whole cell assay. Interestingly, no vectorisation was necessary for the cationic alpha-ON in cell culture.
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Affiliation(s)
- Thibaut Michel
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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48
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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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49
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Michel T, Debart F, Vasseur JJ. Efficient guanidination of the phosphate linkage towards cationic phosphoramidate oligonucleotides. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)01694-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Held HA, Roychowdhury A, Benner SA. C-5 modified nucleosides: direct insertion of alkynyl-thio functionality in pyrimidines. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:391-404. [PMID: 12885121 DOI: 10.1081/ncn-120022030] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A route is presented to append, in a single step, alkynyl thioesters to the 5-position of a pyrimidine ring of a nucleoside that is unprotected. These products should be useful to support in vitro selection experiments with functionalized DNA.
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Affiliation(s)
- Heike A Held
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA
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