1
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Szabat M, Kierzek E, Kierzek R. Modified RNA triplexes: Thermodynamics, structure and biological potential. Sci Rep 2018; 8:13023. [PMID: 30158667 PMCID: PMC6115336 DOI: 10.1038/s41598-018-31387-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022] Open
Abstract
The occurrence of triplexes in vivo has been well documented and is determined by the presence of long homopurine-homopyrimidine tracts. The formation of these structures is the result of conformational changes that occur in the duplex, which allow the binding of a third strand within the major groove of the helix. Formation of these noncanonical forms by introducing synthetic triplex-forming oligonucleotides (TFOs) into the cell may have applications in molecular biology, diagnostics and therapy. This study focused on the formation of RNA triplexes as well as their thermal stability and biological potential in the HeLa cell line. Thermodynamics studies revealed that the incorporation of multiple locked nucleic acid (LNA) and 2-thiouridine (2-thioU) residues increased the stability of RNA triplexes. These data suggest that the number and position of the modified nucleotides within TFOs significantly stabilize the formed structures. Moreover, specificity of the interactions between the modified TFOs and the RNA hairpin was characterized using electrophoretic mobility-shift assay (EMSA), and triplex dissociation constants have been also determined. Finally, through quantitative analysis of GFP expression, the triplex structures were shown to regulate GFP gene silencing. Together, our data provide a first glimpse into the thermodynamic, structural and biological properties of LNA- and 2-thioU modified RNA triplexes.
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Affiliation(s)
- Marta Szabat
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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2
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Singh HN, Rajeswari MR. DNA-triplex Forming Purine Repeat Containing Genes in Acinetobacter baumannii and Their Association with Infection and Adaptation. Front Cell Infect Microbiol 2017; 7:250. [PMID: 28670571 PMCID: PMC5472653 DOI: 10.3389/fcimb.2017.00250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/26/2017] [Indexed: 12/31/2022] Open
Affiliation(s)
- Himanshu N Singh
- Department of Biochemistry, All India Institute of Medical SciencesNew Delhi, India
| | - Moganty R Rajeswari
- Department of Biochemistry, All India Institute of Medical SciencesNew Delhi, India
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3
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Sato T, Sato Y, Nishizawa S. Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA. Chemistry 2017; 23:4079-4088. [PMID: 27897343 DOI: 10.1002/chem.201604676] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 12/24/2022]
Abstract
A series of triplex-forming peptide nucleic acid (TFP) probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found that the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base. Isothermal titration calorimetry experiments revealed that the increased binding affinity resulted from the gain in the binding enthalpy, which could be explained by the enhanced π-stacking interaction between the TO base surrogate and the dsRNA part of the triplex. We expect that these results will provide a molecular basis for designing strong binding tFIT probes for fluorescence sensing of various kinds of purine-rich dsRNAs sequences including those carrying a pyrimidine-purine inversion. The obtained data also offers a new insight into further development of the universal bases incorporated in TFP.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
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4
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Berman CL, Barros SA, Galloway SM, Kasper P, Oleson FB, Priestley CC, Sweder KS, Schlosser MJ, Sobol Z. OSWG Recommendations for Genotoxicity Testing of Novel Oligonucleotide-Based Therapeutics. Nucleic Acid Ther 2016; 26:73-85. [PMID: 26978711 DOI: 10.1089/nat.2015.0534] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Oligonucleotide Safety Working Group subcommittee on genotoxicity testing considers therapeutic oligonucleotides (ONs) unlikely to be genotoxic based on their properties and on the negative results for ONs tested to date. Nonetheless, the subcommittee believes that genotoxicity testing of new ONs is warranted because modified monomers could be liberated from a metabolized ON and incorporated into DNA and could hypothetically cause chain termination, miscoding, and/or faulty replication or repair. The standard test battery as described in Option 1 of International Conference on Harmonisation S2(R1) is generally adequate to assess such potential. However, for the in vitro assay for gene mutations, mammalian cells are considered more relevant than bacteria for most ONs due to their known responsiveness to nucleosides and their greater potential for ON uptake; on the other hand, bacterial assays may be more appropriate for ONs containing non-ON components. Testing is not recommended for ONs with only naturally occurring chemistries or for ONs with chemistries for which there is documented lack of genotoxicity in systems with demonstrated cellular uptake. Testing is recommended for ONs that contain non-natural chemical modifications and use of the complete drug product (including linkers, conjugates, and liposomes) is suggested to provide the most clinically relevant assessment. Documentation of uptake into cells comparable to those used for genotoxicity testing is proposed because intracellular exposure cannot be assumed for these large molecules. ONs could also hypothetically cause mutations through triple helix formation with genomic DNA and no tests are available for detection of such sequence-specific mutations across the entire genome. However, because the potential for triplex formation by therapeutic ONs is extremely low, this potential can be assessed adequately by sequence analysis.
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Affiliation(s)
| | | | | | - Peter Kasper
- 4 Federal Institute for Drugs and Medical Devices (BfArM) , Bonn, Germany
| | | | | | - Kevin S Sweder
- 7 Forensic and National Security Sciences Institute, Syracuse University , Syracuse, New York
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5
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He S, Zhang H, Liu H, Zhu H. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. ACTA ACUST UNITED AC 2014; 31:178-86. [PMID: 25262155 DOI: 10.1093/bioinformatics/btu643] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases and polycomb repressive complexes, which both lack sequence-specific DNA-binding motifs, are recruited by long non-coding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNA-binding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program (LongTarget) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide. AVAILABILITY AND IMPLEMENTATION Website of LongTarget: lncrna.smu.edu.cn, or contact: hao.zhu@ymail.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sha He
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
| | - Hai Zhang
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
| | - Haihua Liu
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China
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6
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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7
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Seio K, Ukawa H, Shohda KI, Sekine M. Computational Evaluation of Intermolecular Interactions of a Universal Base 3-Nitropyrrole in Stacked Dimers and DNA Duplexes. J Biomol Struct Dyn 2012; 22:735-46. [PMID: 15842178 DOI: 10.1080/07391102.2005.10507040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The stacking interactions between a universal base of 3-nitropyrrole (3NP) and four canonical nucleobases were studied by means of ab initio molecular orbital calculations. The stabilities of the complexes are comparable to those of the stacked dimers of canonical bases reported previously. The detailed analysis of the interaction energies revealed the importance of the dipole-dipole interaction included in the Hartree-Fock terms to determine the geometry dependence of the stacking energies. It was also clarified that the dispersion energies included in the electron-correlation terms were essential to obtain adequate stabilities. The contribution of the nitro group was evaluated by the comparative studies of pyrrole and 3NP. The increased molecular dipole moment and surface are expected to account for the enhancement of the stability of the stacked dimers containing 3NP. The force field parameters required for calculation of the molecular mechanics of 3NP were obtained for 3NP on the basis of these molecular orbital calculations. The energy-minimized structures obtained by the molecular mechanics calculations of 3NP accorded with those obtained by the molecular orbital calculations described above. A DNA duplex structure containing 3NP-A, 3NP-T, or 3NP-C was calculated by use of these force field parameters. In the case of 3NP-A, the computationally calculated structure was in good agreement with that previously determined by use of (1)H-NMR except for the orientation of the nitro group.
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Affiliation(s)
- Kohji Seio
- Frontier Collaborative Research Center, Tokyo Institute of Technology, Tokyo, Japan
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8
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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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9
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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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10
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Jain A, Wang G, Vasquez KM. DNA triple helices: biological consequences and therapeutic potential. Biochimie 2008; 90:1117-30. [PMID: 18331847 DOI: 10.1016/j.biochi.2008.02.011] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/08/2008] [Indexed: 01/25/2023]
Abstract
DNA structure is a critical element in determining its function. The DNA molecule is capable of adopting a variety of non-canonical structures, including three-stranded (i.e. triplex) structures, which will be the focus of this review. The ability to selectively modulate the activity of genes is a long-standing goal in molecular medicine. DNA triplex structures, either intermolecular triplexes formed by binding of an exogenously applied oligonucleotide to a target duplex sequence, or naturally occurring intramolecular triplexes (H-DNA) formed at endogenous mirror repeat sequences, present exploitable features that permit site-specific alteration of the genome. These structures can induce transcriptional repression and site-specific mutagenesis or recombination. Triplex-forming oligonucleotides (TFOs) can bind to duplex DNA in a sequence-specific fashion with high affinity, and can be used to direct DNA-modifying agents to selected sequences. H-DNA plays important roles in vivo and is inherently mutagenic and recombinogenic, such that elements of the H-DNA structure may be pharmacologically exploitable. In this review we discuss the biological consequences and therapeutic potential of triple helical DNA structures. We anticipate that the information provided will stimulate further investigations aimed toward improving DNA triplex-related gene targeting strategies for biotechnological and potential clinical applications.
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Affiliation(s)
- Aklank Jain
- Department of Carcinogenesis, University of Texas, M.D. Anderson Cancer Center, Science Park--Research Division, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957, USA
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11
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Timofeev EN, Goryaeva BV, Florentiev VL. Recognition of base pair inversions in duplex by chimeric (alpha,beta) triplex-forming oligonucleotides. J Biomol Struct Dyn 2006; 24:183-8. [PMID: 16928141 DOI: 10.1080/07391102.2006.10507111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
DNA recognition by triplex-forming oligonucleotides (TFOs) is usually limited by homopurine-homopyrimidine sequence in duplexes. Modifications of the third strand may overcome this limitation. Chimeric alpha-beta TFOs are expected to form triplex DNA upon binding to non-regular sequence duplexes. In the present study we describe binding properties of chimeric alpha-beta oligodeoxynucleotides in the respect to short DNA duplexes with one, three, and five base pair inversions. Non-natural chimeric TFO's contained alpha-thymidine residues inside (GT) or (GA) core sequences. Modified residues were addressed to AT/TA inversions in duplexes. It was found in the non-denaturing gel-electrophoresis experiments that single or five adjacent base pair inversions in duplexes may be recognized by chimeric alpha-beta TFO's at 10 degrees C and pH 7.8. Three dispersed base pair inversions in the double stranded DNA prevented triplex formation by either (GT) or (GA) chimeras. Estimation of thermal stability of chimeric alpha-beta triplexes showed decrease in T(m) values as compared with unmodified complexes.
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Affiliation(s)
- Edward N Timofeev
- W.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia.
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12
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Géci I, Filichev VV, Pedersen EB. Synthesis of twisted intercalating nucleic acids possessing acridine derivatives. Thermal stability studies. Bioconjug Chem 2006; 17:950-7. [PMID: 16848402 DOI: 10.1021/bc060058o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twisted intercalating nucleic acids (TINA) possessing acridine derivatives have been synthesized via the postsynthetic modifications of oligonucleotides possessing insertions of (R)-1-O-(4-iodobenzyl)glycerol (8) or (R)-1-O-(4-ethynylbenzyl)glycerol (9) at the 5'-end or in the middle as a bulge. In the first postsynthetic step, oligonucleotides 8 and 9 on the CPG support were treated with a Sonogashira coupling reaction mixture containing 9-chloro-2-ethynylacridine or 9-chloro-2-iodoacridine, respectively. After the postsynthetic step, treatment of the oligonucleotides with 32% aq ammonia or 50% ethanolic solution of tris(2-aminoethyl)amine led to the substitution of chloride on acridine concurrent with deprotection of the bases and cleavage of the oligonucleotides from CPG. Molecular modeling of the parallel triplex with a bulged insertion of the monomer (R)-3-O-[4-(9-aminoacridin-2-ylethynyl)benzyl]glycerol in the triplex-forming oligonucleotide (TFO) showed that the acridine moiety was stacking between the bases of the duplex, while phenyl was placed between the bases of the TFO. Thermal denaturation studies and fluorescence properties of TINA-acridine oligonucleotide duplexes and triplexes are discussed.
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Affiliation(s)
- Imrich Géci
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
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13
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Ueno Y, Mikawa M, Hoshika S, Matsuda A. Nucleosides and nucleotides. 208. Alternate-strand triple-helix formation by the 3'-3'-linked oligodeoxynucleotides with the anthraquinonyl group at the junction point. Bioconjug Chem 2001; 12:635-42. [PMID: 11459470 DOI: 10.1021/bc010023i] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The synthesis of 3'-3'-linked oligodeoxynucleotides (ODNs) with the anthraquinonyl group at the junction point is described. The ODNs were synthesized on a DNA synthesizer using a controlled pore glass (CPG) carrying pentaerythritol that has an intercalator at one of the four hydroxymethyl groups. Stability of the triplexes with the target duplexes was studied by thermal denaturation. The 3'-3'-linked ODNs with the anthraquinonyl group enhanced the thermal stability of the triplexes when compared with those without the intercalator and the unmodified nonamer 10. It was found that the ODNs 12 and 13 carrying the anthraquinonyl groups can form thermally stable triplexes by skipping two or three extra base pairs between two binding domains of the target duplexes. The ability of the 3'-3'-linked ODNs to inhibit cleavage of the target DNA 22 by the restriction enzyme Hind III was tested. It was found that the 3'-3'-linked ODN 16 with the anthraquinonyl group at the junction point inhibited the cleavage by the enzyme more effectively than the nonamer 14 and the 3'-3'-linked ODN 15 without the intercalator.
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Affiliation(s)
- Y Ueno
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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14
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Loakes D. Survey and summary: The applications of universal DNA base analogues. Nucleic Acids Res 2001; 29:2437-47. [PMID: 11410649 PMCID: PMC55727 DOI: 10.1093/nar/29.12.2437] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2001] [Revised: 04/18/2001] [Accepted: 04/18/2001] [Indexed: 11/13/2022] Open
Abstract
A universal base analogue forms 'base pairs' with each of the natural DNA/RNA bases with little discrimination between them. A number of such analogues have been prepared and their applications as biochemical tools investigated. Most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex DNA by stacking interactions. This review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discussed.
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Affiliation(s)
- D Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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15
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Zhang BP, Egholm M, Paul N, Pingle M, Bergstrom DE. Peptide nucleic acid-DNA duplexes containing the universal base 3-nitropyrrole. Methods 2001; 23:132-40. [PMID: 11181032 DOI: 10.1006/meth.2000.1114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A peptide nucleic acid (PNA) monomer containing the universal base 3-nitropyrrole was synthesized by coupling 1-carboxymethyl-3-nitropyrrole to ethyl N-[2-(tert-butoxycarbonylamino)ethyl]glycinate. The PNA sequence H-TGTACGTXACAACTA-NH2 (X = 3-nitropyrrole and C) and DNA sequence 5'-TGTACGTXACAACTA-3' were synthesized and thermal melting studies with the complementary DNA sequence 5'-TAGTTGTYACGTACA-3' (Y = A,C, G, T) compared. The T(m) data show that 3-nitropyrrole pairs indiscriminately with all four natural nucleobases as a constituent of either DNA or PNA. However, 3-nitropyrrole-containing PNA-DNA (average T(m) value = 51.1 degrees C) is significantly more thermally stable than 3-nitropyrrole-containing DNA-DNA (average T(m) value = 39.6 degrees C). From circular dichroism measurements, it is apparent that 3-nitropyrrole in the PNA strand causes a significant change in duplex structure.
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Affiliation(s)
- B P Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, USA
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16
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Chen DL, McLaughlin LW. Use of pK(a) differences to enhance the formation of base triplets involving C-G and G-C base pairs. J Org Chem 2000; 65:7468-74. [PMID: 11076604 DOI: 10.1021/jo000754w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two C-nucleosides are employed for the recognition of dC-dG base pairs. Both derivatives are related to dC but lack the O2-carbonyl. The absence of the carbonyl should eliminate any unfavorable steric interactions at this site. One of the derivatives contains a 2-aminopyridine heterocycle (d2APy) while the second contains a 2-aminopyrimidine heterocycle (d2APm). The former with a pK(a) of 6. 8 functions better for the recognition of dG-dC base pairs than it does in the binding to dC-dG base pairs. The d2APm derivative with a pK(a) of 3.3 functions better to form base triplets with dC-dG base pairs than with dG-dC targets. Triplex T(m)'s in both cases are compared with the sequence containing the native dC residue. The dC analogues appear to make two hydrogen bonds to a target dG base residue, one of which requires protonation of the ring nitrogen. Recognition of a target dC residue appears to require the formation of a single hydrogen bond to the C-nucleoside and having that nitrogen largely in the unprotonated state facilitates its formation.
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Affiliation(s)
- D L Chen
- Department of Chemistry, Merkert Chemistry Center, 2609 Beacon Street, Boston College, Chestnut Hill, Massachusetts 02467, USA
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17
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Asanuma H, Liang X, Yoshida T, Yamazawa A, Komiyama M. Photocontrol of Triple-Helix Formation by Using Azobenzene-Bearing Oligo(thymidine). Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000403)112:7<1372::aid-ange1372>3.0.co;2-e] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Gianolio DA, McLaughlin LW. Selective Recognition of a dC−dG Base Pair by Oligonucleotide-Directed Triplex Formation Using a dC Residue Tethering an Intercalator. J Am Chem Soc 1999. [DOI: 10.1021/ja990799i] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Diego A. Gianolio
- Department of Chemistry, Merkert Chemistry Center Boston College, Chestnut Hill, Massachusetts 02167
| | - Larry W. McLaughlin
- Department of Chemistry, Merkert Chemistry Center Boston College, Chestnut Hill, Massachusetts 02167
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