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Wang L, Ling Y, Tian Y, Wang X, Sasaki S, Taniguchi Y. The Development of Non-natural Type Nucleoside to Stabilize Triplex DNA Formation against CG and TA Inversion Site. Curr Med Chem 2024; 31:2663-2686. [PMID: 37183460 DOI: 10.2174/0929867330666230512114130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Based on the sequence-specific recognition of target duplex DNA by triplexforming oligonucleotides (TFOs) at the major groove side, the antigene strategy has been exploited as a gene-targeting tool with considerable attention. Triplex DNA is formed via the specific base triplets by the Hoogsteen or reverse Hoogsteen hydrogen bond interaction between TFOs and the homo-purine strand from the target duplex DNA, leading to the established sequence-specificity. However, the presence of inversion sites, which are known as non-natural nucleosides that can form satisfactory interactions with 2'- deoxythymidine (dT) and 2'-deoxycytidine (dC) in TA and CG base pairs in the target homo-purine DNA sequences, drastically restricts the formation of classically stable base triplets and even the triplex DNA. Therefore, the design of non-natural type nucleosides, which can effectively recognize CG or/and TA inversion sites with satisfactory selectivity, should be of great significance to expanding the triplex-forming sequence. Here, this review mainly provides a comprehensive review of the current development of novel nonnatural nucleosides to recognize CG or/and TA inversion sites in triplex DNA formation against double-strand DNA (dsDNA).
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Affiliation(s)
- Lei Wang
- School of Pharmacy, Nantong University, Nantong, China
| | - Yong Ling
- School of Pharmacy, Nantong University, Nantong, China
| | - Yan Tian
- School of Pharmacy, Nantong University, Nantong, China
| | - Xiao Wang
- School of Pharmacy, Nantong University, Nantong, China
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, Nagasaki City, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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2
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Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:polym15040858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
- Correspondence:
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3
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López-Tena M, Chen SK, Winssinger N. Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits. Bioconjug Chem 2023; 34:111-123. [PMID: 35856656 DOI: 10.1021/acs.bioconjchem.2c00292] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.
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Affiliation(s)
- Miguel López-Tena
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Si-Kai Chen
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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4
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Brodyagin N, Kumpina I, Applegate J, Katkevics M, Rozners E. Pyridazine Nucleobase in Triplex-Forming PNA Improves Recognition of Cytosine Interruptions of Polypurine Tracts in RNA. ACS Chem Biol 2021; 16:872-881. [PMID: 33881836 PMCID: PMC8673316 DOI: 10.1021/acschembio.1c00044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sequence specific recognition of regulatory noncoding RNAs would open new possibilities for fundamental science and medicine. However, molecular recognition of such complex double-stranded RNA (dsRNA) structures remains a formidable problem. Recently, we discovered that peptide nucleic acids (PNAs) form an unusually stable and sequence-specific triple helix with dsRNA. Triplex-forming PNAs could become universal tools for recognition of noncoding dsRNAs but are limited by the requirement of polypurine tracts in target RNAs as only purines form stable Hoogsteen hydrogen bonded base triplets. Herein, we systematically surveyed simple nitrogen heterocycles PN as modified nucleobases for recognition of cytosine in PN*C-G triplets. We found that a 3-pyridazinyl nucleobase formed significantly more stable PN*C-G triplets than other heterocycles including the pyrimidin-2-one previously used by us and others for recognition of cytosine interruptions in polypurine tracts of PNA-dsRNA triplexes. Our results improve triple helical recognition of dsRNA and provide insights for future development of new nucleobases to expand the sequence scope of noncoding dsRNAs that can be targeted by triplex-forming PNAs.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Ilze Kumpina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Justin Applegate
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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5
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Topham CM, Smith JC. Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J Comput Aided Mol Des 2021; 35:355-369. [PMID: 33624202 DOI: 10.1007/s10822-021-00375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 24 Avenue Jacques Besse, 81500, Lavaur, France.
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
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6
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Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA. Methods Mol Biol 2021; 2105:157-172. [PMID: 32088869 DOI: 10.1007/978-1-0716-0243-0_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the important roles noncoding RNAs play in gene expression, their sequence-specific recognition is important for both fundamental science and the pharmaceutical industry. However, most noncoding RNAs fold in complex helical structures that are challenging problems for molecular recognition. Herein, we describe a method for sequence-specific recognition of double-stranded RNA using peptide nucleic acids (PNAs) that form triple helices in the major grove of RNA under physiologically relevant conditions. We also outline methods for solid-phase conjugation of PNA with cell-penetrating peptides and fluorescent dyes. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.
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7
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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8
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Li Y, Dong Q, Xie Q, Tang P, Zhang M, Qin Y. Enantioselective Synthesis of ABCF Tetracyclic Framework of Daphniphyllum Alkaloid Calyciphylline N. Org Lett 2018; 20:5053-5057. [PMID: 30091930 DOI: 10.1021/acs.orglett.8b02202] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yunfei Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Qiuyan Dong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Qinxia Xie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Pei Tang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Min Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yong Qin
- Sichuan Engineering Laboratory for Plant-Sourced Drug and Research Center for Drug Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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9
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Hari Y, Akabane M, Obika S. 2′,4′-BNA bearing a chiral guanidinopyrrolidine-containing nucleobase with potent ability to recognize the CG base pair in a parallel-motif DNA triplex. Chem Commun (Camb) 2013; 49:7421-3. [DOI: 10.1039/c3cc44030c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Kolganova NA, Shchyolkina AK, Chudinov AV, Zasedatelev AS, Florentiev VL, Timofeev EN. Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides. Nucleic Acids Res 2012; 40:8175-85. [PMID: 22641847 PMCID: PMC3439883 DOI: 10.1093/nar/gks410] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/14/2022] Open
Abstract
Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.
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Affiliation(s)
| | | | | | | | | | - E. N. Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991, Russia
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12
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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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13
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Gupta P, Zengeya T, Rozners E. Triple helical recognition of pyrimidine inversions in polypurine tracts of RNA by nucleobase-modified PNA. Chem Commun (Camb) 2011; 47:11125-7. [PMID: 21909545 DOI: 10.1039/c1cc14706d] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids containing 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E) heterocycles recognized C-G and U-A inversions in a polypurine tract of double helical RNA with high affinity and sequence selectivity at pH 6.25. E-modified PNA bound strongly to bacterial A-site RNA, while no binding was observed to the human A-site RNA.
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Affiliation(s)
- Pankaj Gupta
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, USA
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14
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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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15
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Hari Y, Akabane M, Hatanaka Y, Nakahara M, Obika S. A 4-[(3R,4R)-dihydroxypyrrolidino]pyrimidin-2-one nucleobase for a CG base pair in triplex DNA. Chem Commun (Camb) 2011; 47:4424-6. [PMID: 21390385 DOI: 10.1039/c1cc10138b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to expand target sequences in triplex DNA formation, the development of a nucleobase that recognizes a CG base pair in dsDNA was attempted. A 4-[(3R,4R)-dihydroxypyrrolidino]pyrimidin-2-one nucleobase was found to recognize a CG base pair with high sequence-selectivity.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan.
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16
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Zengeya T, Li M, Rozners E. PNA containing isocytidine nucleobase: synthesis and recognition of double helical RNA. Bioorg Med Chem Lett 2011; 21:2121-4. [PMID: 21333533 DOI: 10.1016/j.bmcl.2011.01.130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 01/25/2011] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
Abstract
Peptide nucleic acid (PNA1) containing a 5-methylisocytidine (iC) nucleobase has been synthesized. Triple helix formation between PNA1 and RNA hairpins having variable base pairs interacting with iC was studied using isothermal titration calorimetry. The iC nucleobase recognized the proposed target, C-G inversion in polypurine tract of RNA, with slightly higher affinity than the natural nucleobases, though the sequence selectivity of recognition was low. Compared to non-modified PNA, PNA1 had lower affinity for its RNA target.
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Affiliation(s)
- Thomas Zengeya
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
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17
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Hari Y, Nakahara M, Pang J, Akabane M, Kuboyama T, Obika S. Synthesis and triplex-forming ability of oligonucleotides bearing 1-substituted 1H-1,2,3-triazole nucleobases. Bioorg Med Chem 2010; 19:1162-6. [PMID: 21256033 DOI: 10.1016/j.bmc.2010.12.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 11/19/2022]
Abstract
Using the copper(I)-catalyzed alkyne-azide 1,3-dipolar cycloaddition, a post-elongation modification of 1-ethynyl substituted nucleobases has been employed to construct 18 variations of oligonucleotides from a common oligonucleotide precursor. The triplex-forming ability of each oligonucleotide with dsDNA was evaluated by the UV melting experiment. It was found that triazole nucleobases generally tend to exhibit binding affinities in the following order: CG>TA>AT, GC base pairs. Among the triazole nucleobases examined, a 1-(4-ureidophenyl)triazole provided the best result with regard to affinity and selectivity for the CG base pair.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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18
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Malnuit V, Duca M, Benhida R. Targeting DNA base pair mismatch with artificial nucleobases. Advances and perspectives in triple helix strategy. Org Biomol Chem 2010; 9:326-36. [PMID: 21046036 DOI: 10.1039/c0ob00418a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review, divided into three sections, describes the contribution of the chemists' community to the development and application of triple helix strategy by using artificial nucleic acids, particularly for the recognition of DNA sequences incorporating base pair inversions. Firstly, the development of nucleobases that recognise CG inversion is surveyed followed secondly by specific recognition of TA inverted base pair. Finally, we point out in the last section recent perspectives and applications, driven from knowledge in nucleic acids interactions, in the growing field of nanotechnology and supramolecular chemistry at the border area of physics, chemistry and molecular biology.
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Affiliation(s)
- Vincent Malnuit
- Laboratoire de Chimie des Molécules Bioactives et des Arômes, LCMBA, UMR 6001, Institut de Chimie de Nice, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
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19
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Semenyuk A, Darian E, Liu J, Majumdar A, Cuenoud B, Miller PS, MacKerell AD, Seidman MM. Targeting of an interrupted polypurine:polypyrimidine sequence in mammalian cells by a triplex-forming oligonucleotide containing a novel base analogue. Biochemistry 2010; 49:7867-78. [PMID: 20701359 PMCID: PMC2935506 DOI: 10.1021/bi100797z] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The DNA triple helix consists of a third strand of nucleic acid lying in the major groove of an intact DNA duplex. The most stable triplexes form on polypurine:polypyrimidine sequences, and pyrimidine interruptions in the purine strand are destabilizing. Sequence stringency is imparted by specific Hoogsteen hydrogen bonds between third strand bases and the purine bases in the duplex. Appropriate base and sugar modifications of triple helix-forming oligonucleotides (TFOs) confer chromosome targeting activity in living cells. However, broad utilization of TFOs as gene targeting reagents in mammalian cells has been limited by the requirement for homopurine target sequences. Although there have been a number of base analogues described that appear to be promising as candidates for triplex target expansion, none has been examined in a biological system. We have employed a postsynthetic strategy to prepare a collection of TFOs with base analogues at a defined position. Following assessment of affinity for a triplex target with a single C:G inversion, TFOs with a second generation of analogues were synthesized. One of these, TFO-5a, with 2'-OMe-guanidinylethyl-5-methylcytosine at the position corresponding to the C:G interruption in the target sequence, was further modified to confer bioactivity. The activity of this TFO, linked to psoralen, was measured in a mammalian cell line that was engineered by directed sequence conversion to carry a triplex target with a single C:G interruption. TFO-5a was active against this target and inactive against the corresponding target with an uninterrupted polypurine:polypyrimidine sequence.
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Affiliation(s)
- A. Semenyuk
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - E. Darian
- School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - J. Liu
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - A. Majumdar
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - B. Cuenoud
- Merck Serono S.A., Chemin des mines 9, 1202 Geneva, Switzerland
| | - P. S. Miller
- Bloomberg School of Public Health, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - A. D. MacKerell
- School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - M. M. Seidman
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
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20
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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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Hari Y, Matsugu S, Inohara H, Hatanaka Y, Akabane M, Imanishi T, Obika S. 2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA. Org Biomol Chem 2010; 8:4176-80. [PMID: 20648389 DOI: 10.1039/c004895j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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22
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Ohkubo A, Sakaue T, Tsunoda H, Seio K, Sekine M. Synthesis and Hybridization Properties of Oligonucleotides Incorporating Bi- and Tricyclic Cytosine Derivatives. CHEM LETT 2010. [DOI: 10.1246/cl.2010.726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 665] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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Gerrard SR, Edrees MM, Bouamaied I, Fox KR, Brown T. CG base pair recognition within DNA triple helices by modified N-methylpyrrolo-dC nucleosides. Org Biomol Chem 2010; 8:5087-96. [DOI: 10.1039/c0ob00119h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ben Gaied N, Zhao Z, Gerrard SR, Fox KR, Brown T. Potent triple helix stabilization by 5',3'-modified triplex-forming oligonucleotides. Chembiochem 2009; 10:1839-51. [PMID: 19554592 DOI: 10.1002/cbic.200900232] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Anthraquinone and pyrene analogues attached to the 3' and/or 5' termini of triplex-forming oligonucleotides (TFOs) by various linkers increased the stability of parallel triple helices. The modifications are simple to synthesize and can be introduced during standard solid-phase oligonucleotide synthesis. Potent triplex stability was achieved by using doubly modified TFOs, which in the most favourable cases gave an increase in melting temperature of 30 degrees C over the unmodified counterparts and maintained their selectivity for the correct target duplex. Such TFOs can produce triplexes with melting temperatures of 40 degrees C at pH 7 even though they do not contain any triplex-stabilizing base analogues. These studies have implications for the design of triplex-forming oligonucleotides for use in biology and nanotechnology.
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Affiliation(s)
- Nouha Ben Gaied
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
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Campbell MA, Miller PS. Cross-linking to an interrupted polypurine sequence with a platinum-modified triplex-forming oligonucleotide. J Biol Inorg Chem 2009; 14:873-81. [PMID: 19350290 DOI: 10.1007/s00775-009-0499-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) can bind specifically to polypurine sequences in double-stranded DNA. A single interruption of this polypurine tract can greatly destabilize triplex formation. The stability of triplexes can be significantly enhanced by covalently linking the TFO to its DNA target with reactive functional groups conjugated to the TFO. Covalently cross-linked TFOs are effective inhibitors of transcription of the target DNA sequence. We have designed a TFO with a platinum-modified base that can interact with and cross-link to a cytosine interruption in the polypurine tract of a target DNA duplex. The TFO contains an N(4)-(aminoalkyl)cytosine derivatized with cis-diamminediaquaplatinum(II) or trans-diamminediaquaplatinum(II). When bound to its target, the tethered platinum of the TFO can reach across the major groove and form an adduct with the guanine N7 of the interrupting C.G base pair. The optimal tether length is five methylene groups, and cross-linking is most efficient when the tether is modified with trans-diamminediaquaplatinum(II). Cross-linking requires that the TFO is bound to its designated DNA target. Addition of cyanide to the cross-linked TFO product reversed the cross-link, behavior that is consistent with the presence of a platinum-guanine adduct. The kinetics of the cross-linking reaction were studied and the half-life of the cross-linking reaction was approximately 3 h. Our results demonstrate that platinum-conjugated TFOs can be designed to cross-link with DNA targets that contain a single pyrimidine interruption. Modifications of this type may prove useful for expanding the DNA sequences that can be targeted by TFOs and increasing the stability of the resulting triplexes.
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Affiliation(s)
- Meghan A Campbell
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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28
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Sniady A, Durham A, Morreale MS, Marcinek A, Szafert S, Lis T, Brzezinska KR, Iwasaki T, Ohshima T, Mashima K, Dembinski R. Zinc-Catalyzed Cycloisomerizations. Synthesis of Substituted Furans and Furopyrimidine Nucleosides. J Org Chem 2008; 73:5881-9. [PMID: 18597532 DOI: 10.1021/jo8007995] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Adam Sniady
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Audrey Durham
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Marco S. Morreale
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Andrzej Marcinek
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Slawomir Szafert
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadeusz Lis
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Krystyna R. Brzezinska
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Takanori Iwasaki
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Takashi Ohshima
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kazushi Mashima
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Roman Dembinski
- Department of Chemistry, Oakland University, 2200 N. Squirrel Rd., Rochester, Michigan 48309-4477, Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland, Department of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland, Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Seela F, Sirivolu VR. Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azide-alkyne "click" reaction. Org Biomol Chem 2008; 6:1674-87. [PMID: 18421402 DOI: 10.1039/b719459e] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-(Octa-1,7-diynyl)-2'-deoxyuridine was converted into the furano-dU derivative 7 by copper-catalyzed cyclization; the pyrolodC-derivative 3 was formed upon ammonolysis. The bicyclic nucleosides 3 and 7 as well as the corresponding non-cyclic precursors 4 and 6 all containing terminal C[triple bond]C bonds were conjugated with the non-fluorescent 3-azido-7-hydroxycoumarin 5 employing the copper(I)-catalyzed Huisgen-Sharpless-Meldal cycloaddition "click reaction". Strongly fluorescent 1H-1,2,3-triazole conjugates (30-33) are formed incorporating two fluorescent reporters-the pyrdC nucleoside and the coumarin moiety. Oligonucleotides incorporating 6-alkynyl and 6-alkyl 7H-pyrrolo[2,3-d]pyrimidin-2(3H)-one nucleosides (3 and 2f) have been prepared by solid-phase synthesis using the phosphoramidite building blocks 10 and 13 ; the pyrrolo-dC oligonucleotides are formed during ammonia treatment. The duplex stability of oligonucleotides containing 3 and related derivatives was studied. Oligonucleotides with terminal triple bonded nucleosides such as 3 are more stabilizing than those lacking a side chain with terminal unsaturation; open-chain derivatives (4) are even more efficient. The click reaction was also performed on oligonucleotides containing the pyrdC-derivative and the fluorescence properties of nucleosides, oligonucleotides and their coumarin conjugates were studied.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 4814, Münster, Germany.
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30
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Gerrard SR, Srinivasan N, Fox KR, Brown T. CG base pair recognition within DNA triple helices using N-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one nucleoside analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1363-7. [PMID: 18066784 DOI: 10.1080/15257770701533958] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Triplex-mediated recognition of Py.Pu base pairs in DNA is a greater challenge than for Pu.Py base pairs as fewer hydrogen bonds are presented for binding in the major groove. Initial studies on m-aminophenyl-modified analogues of the bicyclic nucleoside N-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7 H)-one suggest that selective recognition of the CG base pair is possible.
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Affiliation(s)
- Simon R Gerrard
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
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Abstract
The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.
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Affiliation(s)
- Alexander J A Cobb
- School of Pharmacy, University of Reading, Whiteknights, Reading, Berks RG6 6AD, UK.
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Mayer A, Leumann CJ. Pyrrolidino DNA with Bases Corresponding to the 2-Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex-Forming Properties. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700217] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Filichev VV, Gaber H, Olsen TR, Jørgensen PT, Jessen CH, Pedersen EB. Twisted Intercalating Nucleic Acids – Intercalator Influence on Parallel Triplex Stabilities. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600168] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Buchini S, Leumann CJ. 2′-O-Aminoethyl Oligoribonucleotides Containing Novel Base Analogues: Synthesis and Triple-Helix Formation At Pyrimidine/Purine Inversion Sites. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600182] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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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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: 111] [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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