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Sarma PP, Rai A, Baruah PK. Recent Advances in the Development of Antibiotics-Coated Gold Nanoparticles to Combat Antimicrobial Resistance. Antibiotics (Basel) 2024; 13:124. [PMID: 38391510 PMCID: PMC10886052 DOI: 10.3390/antibiotics13020124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Antimicrobial resistance (AMR) has become an alarming threat to the successful treatment of rapidly growing bacterial infections due to the abuse and misuse of antibiotics. Traditional antibiotics bear many limitations, including restricted bioavailability, inadequate penetration and the emergence of antimicrobial-resistant microorganisms. Recent advances in nanotechnology for the introduction of nanoparticles with fascinating physicochemical characteristics have been predicted as an innovative means of defence against antimicrobial-resistant diseases. The use of nanoparticles provides several benefits, including improved tissue targeting, better solubility, improved stability, enhanced epithelial permeability and causes minimal side effects. However, except for gold nanoparticles (AuNPs), the biological safety of the majority of metal nanoparticles remains a serious problem. AuNPs appear to be promising for drug delivery and medicinal applications because of their minimal toxicity, biocompatibility, functional flexibility, chemical stability and versatile biological activities, such as their antiviral, antifungal, anti-inflammatory and antimicrobial properties. Hence, we are focusing on the gold nanoparticles possessing antimicrobial activity in this article. This review will cover recent strategies in the preparation of gold nanoparticles, with special emphasis placed on antibiotics-coated AuNPs with enhanced antimicrobial properties and how they fight against disease-causing bacteria and eradicate biofilms, along with their activities and physicochemical properties.
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Affiliation(s)
- Partha Pratim Sarma
- Department of Applied Sciences, GUIST, Gauhati University, Guwahati 781014, Assam, India
| | - Akhilesh Rai
- CNC-Center for Neuroscience and Cell Biology and Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 000-447 Coimbra, Portugal
| | - Pranjal K Baruah
- Department of Applied Sciences, GUIST, Gauhati University, Guwahati 781014, Assam, India
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2
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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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3
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Milani R, Brognara E, Fabbri E, Manicardi A, Corradini R, Finotti A, Gasparello J, Borgatti M, Cosenza LC, Lampronti I, Dechecchi MC, Cabrini G, Gambari R. Targeting miR‑155‑5p and miR‑221‑3p by peptide nucleic acids induces caspase‑3 activation and apoptosis in temozolomide‑resistant T98G glioma cells. Int J Oncol 2019; 55:59-68. [PMID: 31180529 PMCID: PMC6561624 DOI: 10.3892/ijo.2019.4810] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
The present study investigated the effects of the combined treatment of two peptide nucleic acids (PNAs), directed against microRNAs involved in caspase‑3 mRNA regulation (miR‑155‑5p and miR‑221‑3p) in the temozolomide (TMZ)‑resistant T98G glioma cell line. These PNAs were conjugated with an octaarginine tail in order to obtain an efficient delivery to treated cells. The effects of singularly administered PNAs or a combined treatment with both PNAs were examined on apoptosis, with the aim to determine whether reversion of the drug‑resistance phenotype was obtained. Specificity of the PNA‑mediated effects was analyzed by reverse transcription‑quantitative polymerase‑chain reaction, which demonstrated that the effects of R8‑PNA‑a155 and R8-PNA-a221 anti‑miR PNAs were specific. Furthermore, the results obtained confirmed that both PNAs induced apoptosis when used on the temozolomide‑resistant T98G glioma cell line. Notably, co‑administration of both anti‑miR‑155 and anti‑miR‑221 PNAs was associated with an increased proapoptotic activity. In addition, TMZ further increased the induction of apoptosis in T98G cells co‑treated with anti‑miR‑155 and anti‑miR‑221 PNAs.
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Affiliation(s)
- Roberta Milani
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Eleonora Brognara
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I‑143214 Parma, Italy
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I‑143214 Parma, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Lucia Carmela Cosenza
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
| | | | - Giulio Cabrini
- Laboratory of Molecular Pathology, University‑Hospital of Verona, I‑37126 Verona, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, I‑144121 Ferrara, Italy
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4
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Liu Q, Ma K, Wen D, Sun H, Wang Q, Kong J, Qiu Y, Li L, Chen W. BisPNA-assisted Detection of Double-stranded DNA via Electrochemical Impedance Spectroscopy. ELECTROANAL 2018. [DOI: 10.1002/elan.201800611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Qianrui Liu
- School of Environmental and Biological Engineering; Nanjing University of Science and Technology; Nanjing 210094 P. R. China
| | - Kefeng Ma
- School of Environmental and Biological Engineering; Nanjing University of Science and Technology; Nanjing 210094 P. R. China
| | - Dongxiao Wen
- Henan University of Traditional Chinese Medicine Zhengzhou; Henan CN
| | - Haobo Sun
- School of Environmental and Biological Engineering; Nanjing University of Science and Technology; Nanjing 210094 P. R. China
| | - Qiangwei Wang
- School of Environmental and Biological Engineering; Nanjing University of Science and Technology; Nanjing 210094 P. R. China
| | - Jinming Kong
- School of Environmental and Biological Engineering; Nanjing University of Science and Technology; Nanjing 210094 P. R. China
| | - Yunliang Qiu
- Department of Criminal Science and Technology; Nanjing Forest Police College; Nanjing 210023, Jiangsu P. R. China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering; Liaocheng University; Liaocheng 252059 P. R. China
| | - Wuqiao Chen
- Quanzhou Import and Export Commodity Inspection and Quarantine Bureau; Quanzhou 362000 P. R. China
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Prasher P, Sharma M. Medicinal chemistry of acridine and its analogues. MEDCHEMCOMM 2018; 9:1589-1618. [PMID: 30429967 PMCID: PMC6195008 DOI: 10.1039/c8md00384j] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/14/2018] [Indexed: 02/01/2023]
Abstract
'Acridine' along with its functional analogue 'Acridone' is the most privileged pharmacophore in medicinal chemistry with diverse applications ranging from DNA intercalators, endonuclease mimics, ratiometric selective ion sensors, and P-glycoprotein inhibitors in countering the multi-drug resistance, enzyme inhibitors, and reversals of neurodegenerative disorders. Their interaction with DNA and ability of selectively identifying numerous biologically useful ions has cemented exploitability of the acridone nucleus in modern day therapeutics. Additionally, most derivatives and salts of acridine are planar, crystalline, and stable displaying a strong fluorescence which, when coupled with their marked bio selectivity and low cytotoxicity, enables the studying and monitoring of several biochemical, metabolic, and pharmacological processes. In this review, a detailed picture covering the important therapeutic aspects of the acridone nucleus and its functional analogues is discussed.
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Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India . ;
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
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6
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Wera M, Storoniak P, Serdiuk IE, Zadykowicz B. Structural considerations on acridine/acridinium derivatives: Synthesis, crystal structure, Hirshfeld surface analysis and computational studies. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Mitra P, Pal U, Chandra Maiti N, Ghosh A, Bhunia A, Basu S. Identification of modes of interactions between 9-aminoacridine hydrochloride hydrate and serum proteins by low and high resolution spectroscopy and molecular modeling. RSC Adv 2016. [DOI: 10.1039/c6ra04140j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Photophysical studies on binding interactions of 9-aminoacridine hydrochloride hydrate (9AA-HCl) with serum proteins using low and high resolution spectroscopic techniques in conjunction with molecular modeling.
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Affiliation(s)
- Piyali Mitra
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Uttam Pal
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Nakul Chandra Maiti
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Anirban Ghosh
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
| | - Anirban Bhunia
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
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8
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Lundin KE, Gissberg O, Smith CE. Oligonucleotide Therapies: The Past and the Present. Hum Gene Ther 2015; 26:475-85. [PMID: 26160334 PMCID: PMC4554547 DOI: 10.1089/hum.2015.070] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/04/2015] [Indexed: 12/19/2022] Open
Abstract
In this review we address the development of oligonucleotide (ON) medicines from a historical perspective by listing the landmark discoveries in this field. The various biological processes that have been targeted and the corresponding ON interventions found in the literature are discussed together with brief updates on some of the more recent developments. Most ON therapies act through antisense mechanisms and are directed against various RNA species, as exemplified by gapmers, steric block ONs, antagomirs, small interfering RNAs (siRNAs), micro-RNA mimics, and splice switching ONs. However, ONs binding to Toll-like receptors and those forming aptamers have completely different modes of action. Similar to other novel medicines, the path to success has been lined with numerous failures, where different therapeutic ONs did not stand the test of time. Since the first ON drug was approved for clinical use in 1998, the therapeutic landscape has changed considerably, but many challenges remain until the expectations for this new form of medicine are met. However, there is room for cautious optimism.
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Affiliation(s)
- Karin E. Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Olof Gissberg
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - C.I. Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
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9
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Bohländer PR, Vilaivan T, Wagenknecht HA. Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids. Org Biomol Chem 2015. [PMID: 26223770 DOI: 10.1039/c5ob01273b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The so-called acpcPNA system bears a peptide backbone consisting of 4'-substituted proline units with (2'R,4'R) configuration in an alternating combination with (2S)-amino-cyclopentane-(1S)-carboxylic acids. acpcPNA forms exceptionally stable hybrids with complementary DNA. We demonstrate herein (i) strand displacements by single-stranded DNA from acpcPNA-DNA hybrids, and by acpcPNA strands from DNA duplexes, and (ii) strand invasions by acpcPNA into double-stranded DNA. These processes were studied in vitro using synthetic oligonucleotides and by means of our concept of wavelength-shifting fluorescent nucleic acid probes, including fluorescence lifetime measurements that allow quantifying energy transfer efficiencies. The strand displacements of preannealed 14mer acpcPNA-7mer DNA hybrids consecutively by 10mer and 14mer DNA strands occur with rather slow kinetics but yield high fluorescence color ratios (blue : yellow or blue : red), fluorescence intensity enhancements, and energy transfer efficiencies. Furthermore, 14mer acpcPNA strands are able to invade into 30mer double-stranded DNA, remarkably with quantitative efficiency in all studied cases. These processes can also be quantified by means of fluorescence. This remarkable behavior corroborates the extraordinary versatile properties of acpcPNA. In contrast to conventional PNA systems which require 3 or more equivalents PNA, only 1.5 equivalents acpcPNA are sufficient to get efficient double duplex invasion. Invasions also take place even in the presence of 250 mM NaCl which represents an ionic strength nearly twice as high as the physiological ion concentration. These remarkable results corroborate the extraordinary properties of acpcPNA, and thus acpcPNA represents an eligible tool for biological analytics and antigene applications.
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Affiliation(s)
- Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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10
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Mitra P, Chakraborty PK, Saha P, Ray P, Basu S. Antibacterial efficacy of acridine derivatives conjugated with gold nanoparticles. Int J Pharm 2014; 473:636-43. [DOI: 10.1016/j.ijpharm.2014.07.051] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/25/2014] [Accepted: 07/26/2014] [Indexed: 01/23/2023]
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Abstract
Chiral open-chain PNAs have been shown to have improved properties in terms of control of helical handedness, DNA affinity, sequence selectivity, and cellular uptake. They can be synthesized either using preformed chiral monomers or by means of a submonomeric strategy. The former is preferred when only a stereogenic center is present at C-5, whereas for PNA-bearing substituents at C-2, the submonomeric approach is preferred, since racemization, generally occurring during the solid-phase synthesis, can be minimized by this procedure. Here we describe the protocols for the synthesis of PNA oligomers containing C-2- or C-5- (or both) modified monomers and a GC method for checking the optical purity of C-2-modified PNAs.
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12
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Englund EA, Gupta P, Micklitsch CM, Onyshchenko MI, Remeeva E, Neumann RD, Panyutin IG, Appella DH. PPG peptide nucleic acids that promote DNA guanine quadruplexes. Chembiochem 2014; 15:1887-90. [PMID: 25044379 DOI: 10.1002/cbic.201402224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Indexed: 12/11/2022]
Abstract
Recent studies have shown that guanine-rich (G-rich) sequences with the potential to form quadruplexes might play a role in normal transcription as well as overexpression of oncogenes. Chemical tools that allow examination of the specific roles of G-quadruplex formation in vivo, and their association with gene regulation will be essential to understanding the functions of these quadruplexes and might lead to beneficial therapies. Properly designed peptide nucleic acids (PNAs) can invade G-rich DNA duplexes and induce the formation of a G-quadruplex in the free DNA strand. Replacing guanines in the PNA sequence with pyrazolo[3,4-d]pyrimidine guanine (PPG) nucleobases eliminates G-quadruplex formation with PNA and promotes invasion of the target DNA.
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Affiliation(s)
- Ethan A Englund
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, DHHS, 8 Center Drive, Bethesda, MD 20892 (USA)
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Xia X, Piao X, Bong D. Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J Am Chem Soc 2014; 136:7265-8. [PMID: 24796374 DOI: 10.1021/ja5032584] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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14
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Kumar R, Kaur M, Bahia MS, Silakari O. Synthesis, cytotoxic study and docking based multidrug resistance modulator potential analysis of 2-(9-oxoacridin-10(9H)-yl)-N-phenyl acetamides. Eur J Med Chem 2014; 80:83-91. [PMID: 24769346 DOI: 10.1016/j.ejmech.2014.04.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
Abstract
The present study describes the synthesis of fifteen 2-(9-oxoacridin-10(9H)-yl)-N-phenyl acetamide derivatives (13a-o) through condensation of 2-chloro-N-phenyl acetamides (12a-o) with acridone molecule (10). All the synthesized compounds were screened for their anti-cancer activity against three diverse cell lines including breast (MCF-7), cervical (HeLa) and lung adenocarcinoma (A-549) employing standard MTT assay. Among synthesized molecules, 13k and 13l showed good cytotoxicity activity against considered three cancer cell lines. Additionally, in silico studies of multidrug resistance modulator (MDR) effects of these compounds was performed by docking simulation in the ATP binding site of P-gp. The results of docking simulation displayed important interactions of these molecules in the active site of this protein and predicted their MDR modulator behavior.
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Affiliation(s)
- Rajesh Kumar
- Pharmaceutical Chemistry Division, Shivalik College of Pharmacy, Nangal, Punjab 140126, India; Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Maninder Kaur
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Malkeet Singh Bahia
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India.
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15
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Novopashina DS, Siniakov AN, Riabinin VA, Perrouault L, Giovannangeli C, Venyaminova AG, Butorin AS. [Oligo(2'-O-Methylribonucleotides) and their derivatives: IV. Conjugates of oligo(2'-O-methylribonucleotides) with minor groove binders and intercalators: synthesis, properties and application]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:159-74. [PMID: 23964516 DOI: 10.1134/s1068162013010081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conjugates of pyrimidine triplex forming 3'-protected oligo(2'-O-methylribonucleotides) with minor groove binders (MGB) and triplex specific intercalator benzoindoloquinoline (BIQ) at 5'-terminus were synthesized. The conjugates formed stable complexes with target dsDNA by simultaneous binding both in its minor and major grooves and BIQ intercalation. The dissociation constants and thermal stability of the conjugate complexes with model dsDNA corresponding to polypurine tract (PPT) of genes nef and pol from HIV proviral genome were determined. Conjugation of oligo(2'-O-methylribonucleotides) with MGB and intercalator increased the stability of the triple complexes with dsDNA at pH 7.2 and 37 degrees C. Intercalator introduction accelerates the process of complex formation. Dose-dependent arrest of the in vitro transcription was demonstrated when a 780 b.p. DNA fragment containing the polypurine tract was transcribed under the control of T7 promoter in the presence of different concentrations of conjugates of oligo(2'-O-methylribonucleotides) containing MGB and BIQ intercalator.
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16
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Li P, Zhan C, Zhang S, Ding X, Guo F, He S, Yao J. Alkali metal cations control over nucleophilic substitutions on aromatic fused pyrimidine-2,4-[1H,3H]-diones: towards new PNA monomers. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Ramesh C, Lei PM, Janreddy D, Kavala V, Kuo CW, Yao CF. Synthesis of indolylquinolines, indolylacridines, and indolylcyclopenta[b]quinolines from the Baylis-Hillman adducts: an in situ [1,3]-sigmatropic rearrangement of an indole nucleus to access indolylacridines and indolylcyclopenta[b]quinolines. J Org Chem 2012; 77:8451-64. [PMID: 22967265 DOI: 10.1021/jo301313m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A simple and easy route to the synthesis of a variety of structurally diverse indolylquinolines, indolylacridines, and indolylcyclopenta[b]quinoline derivatives via the reductive cyclization of C-alkylated indole derivatives, derived from acyclic as well as cyclic Baylis-Hillman adducts with indoles, is described. An unusual in situ [1,3]-sigmatropic rearrangement of the indole nucleus was observed during the reductive cyclicization of α-regioselective B-H adducts containing indoles to produce indolylacridines and indolylcyclopenta[b]quinoline derivatives.
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Affiliation(s)
- Chintakunta Ramesh
- Department of Chemistry, National Taiwan Normal University, 88, Section 4, Tingchow Road, Taipei, Taiwan 116, Republic of China
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18
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Manivannan C, Renganathan R. Spectroscopic investigation on the interaction of 9-aminoacridine with certain dyes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 95:685-692. [PMID: 22584125 DOI: 10.1016/j.saa.2012.04.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/12/2012] [Accepted: 04/18/2012] [Indexed: 05/31/2023]
Abstract
The fluorescence quenching of 9-Aminoacridine (9-AA) by various dyes were probed in aqueous medium using steady state and time resolved fluorescence spectroscopic techniques. From these techniques, we had rationalized the interaction of 9-AA with various dyes via ground state complex formation. The binding constant (K) and number of binding sites (n) were calculated from the relevant fluorescence quenching data. The fluorescence emission of 9-Aminoacridine was quenched by the dyes through static quenching followed by the mechanism of energy transfer. The static quenching mechanism was confirmed by lifetime measurements. The thermodynamic parameters such as free energy change (ΔG), enthalpy change (ΔH) and entropy change (ΔS), were calculated by thermodynamic equations. The results showed that Van der Waals interaction or hydrogen bond formation played a major role in the binding of 9-AA with these dyes.
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Affiliation(s)
- C Manivannan
- School of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
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19
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Avitabile C, Moggio L, Malgieri G, Capasso D, Di Gaetano S, Saviano M, Pedone C, Romanelli A. γ Sulphate PNA (PNA S): highly selective DNA binding molecule showing promising antigene activity. PLoS One 2012; 7:e35774. [PMID: 22586450 PMCID: PMC3346730 DOI: 10.1371/journal.pone.0035774] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/21/2012] [Indexed: 11/18/2022] Open
Abstract
Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. γ PNAs, PNA derivatives having a substituent in the γ position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the γ position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.
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Affiliation(s)
- Concetta Avitabile
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Loredana Moggio
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Domenica Capasso
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | | | | | - Carlo Pedone
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
- Istituto di Biostrutture e Bioimmagini (CNR), Napoli, Italy
| | - Alessandra Romanelli
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
- Istituto di Biostrutture e Bioimmagini (CNR), Napoli, Italy
- * E-mail:
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20
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Investigations on photoinduced interaction of 9-aminoacridine with certain catechols and rutin. J Fluoresc 2012; 22:1113-25. [PMID: 22477060 DOI: 10.1007/s10895-012-1050-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
Abstract
The fluorescence quenching of 9-aminoacridine by certain biologically important catechols and rutin was investigated using absorption, steady state and time resolved fluorescence measurements. The in vitro-antioxidant activities of the above compounds were studied using deoxyribose degradation assay and nitric oxide scavenging assay. The experimental results showed that the fluorescence of 9-aminoacridine was quenched by quencher molecules via forming ground state complex. The bimolecular quenching rate constant k(q), binding constant (K) and number of binding sites (n) were calculated at different temperatures from relevant fluorescence data. Static quenching mechanism was supported by lifetime measurement. The free energy change (ΔG(et)) for electron transfer process was calculated by Rehm-Weller equation. The binding distance of 4-nitrocatechol with 9-aminoacridine was obtained according to Forster's non-radiative energy transfer theory. Nature of binding forces and their interactions was probed based on thermodynamic parameters.
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21
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Zeng Y, Pratumyot Y, Piao X, Bong D. Discrete Assembly of Synthetic Peptide–DNA Triplex Structures from Polyvalent Melamine–Thymine Bifacial Recognition. J Am Chem Soc 2011; 134:832-5. [PMID: 22201288 DOI: 10.1021/ja2099326] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yingying Zeng
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Yaowalak Pratumyot
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Xijun Piao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Dennis Bong
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
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22
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Manivannan C, Renganathan R. An investigation on the fluorescence quenching of 9-aminoacridine by certain pyrimidines. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 82:475-480. [PMID: 21839670 DOI: 10.1016/j.saa.2011.07.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 05/31/2023]
Abstract
The fluorescence quenching of 9-aminoacridine by certain substituted uracils in water was studied using absorption, steady state and time resolved measurements. The bimolecular quenching rate constants (k(q)), binding constant K and number of binding sites (n) were calculated based on the fluorescence quenching data. The free energy change (ΔG(et)) for electron transfer process was calculated by Rehm-Weller equation. From lifetime measurement we observed that the quenching was mainly due to static mechanism involving ground state complex formation.
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Affiliation(s)
- C Manivannan
- School of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
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23
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Rapireddy S, Bahal R, Ly DH. Strand invasion of mixed-sequence, double-helical B-DNA by γ-peptide nucleic acids containing G-clamp nucleobases under physiological conditions. Biochemistry 2011; 50:3913-8. [PMID: 21476606 PMCID: PMC3092786 DOI: 10.1021/bi2002554] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acids (PNAs) make up the only class of nucleic acid mimics developed to date that has been shown to be capable of invading double-helical B-form DNA. Recently, we showed that sequence limitation associated with PNA recognition can be relaxed by utilizing conformationally preorganized γ-peptide nucleic acids (γPNAs). However, like all the previous studies, with the exception of triplex binding, DNA strand invasion was performed at relatively low salt concentrations. When physiological ionic strengths were used, little to no binding was observed. On the basis of this finding, it was not clear whether the lack of binding is due to the lack of base pair opening or the lack of binding free energy, either of which would result in no productive binding. In this work, we show that it is the latter. Under simulated physiological conditions, the DNA double helix is sufficiently dynamic to permit strand invasion by the designer oligonucleotide molecules provided that the required binding free energy can be met. This finding has important implications for the design oligonucleotides for recognition of B-DNA via direct Watson-Crick base pairing.
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Affiliation(s)
- Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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24
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Jensen NM, Dalsgaard T, Jakobsen M, Nielsen RR, Sørensen CB, Bolund L, Jensen TG. An update on targeted gene repair in mammalian cells: methods and mechanisms. J Biomed Sci 2011; 18:10. [PMID: 21284895 PMCID: PMC3042377 DOI: 10.1186/1423-0127-18-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 02/02/2011] [Indexed: 11/10/2022] Open
Abstract
Transfer of full-length genes including regulatory elements has been the preferred gene therapy strategy for clinical applications. However, with significant drawbacks emerging, targeted gene alteration (TGA) has recently become a promising alternative to this method. By means of TGA, endogenous DNA repair pathways of the cell are activated leading to specific genetic correction of single-base mutations in the genome. This strategy can be implemented using single-stranded oligodeoxyribonucleotides (ssODNs), small DNA fragments (SDFs), triplex-forming oligonucleotides (TFOs), adeno-associated virus vectors (AAVs) and zinc-finger nucleases (ZFNs). Despite difficulties in the use of TGA, including lack of knowledge on the repair mechanisms stimulated by the individual methods, the field holds great promise for the future. The objective of this review is to summarize and evaluate the different methods that exist within this particular area of human gene therapy research.
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Affiliation(s)
- Nanna M Jensen
- Institute of Human Genetics, The Bartholin Building, University of Aarhus, 8000 Aarhus C, Denmark
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25
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Wang M, Holmes-Davis R, Rafinski Z, Jedrzejewska B, Choi KY, Zwick M, Bupp C, Izmailov A, Paczkowski J, Warner B, Koshinsky H. Accelerated photobleaching of a cyanine dye in the presence of a ternary target DNA, PNA probe, dye catalytic complex: a molecular diagnostic. Anal Chem 2010; 81:2043-52. [PMID: 19231844 DOI: 10.1021/ac702519k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In many settings, molecular testing is needed but unavailable due to complexity and cost. Simple, rapid, and specific DNA detection technologies would provide important alternatives to existing detection methods. Here we report a novel, rapid nucleic acid detection method based on the accelerated photobleaching of the light-sensitive cyanine dye, 3,3'-diethylthiacarbocyanine iodide (DiSC(2)(3) I(-)), in the presence of a target genomic DNA and a complementary peptide nucleic acid (PNA) probe. On the basis of the UV-vis, circular dichroism, and fluorescence spectra of DiSC(2)(3) with PNA-DNA oligomer duplexes and on characterization of a product of photolysis of DiSC(2)(3) I(-), a possible reaction mechanism is proposed. We propose that (1) a novel complex forms between dye, PNA, and DNA, (2) this complex functions as a photosensitizer producing (1)O(2), and (3) the (1)O(2) produced promotes photobleaching of dye molecules in the mixture. Similar cyanine dyes (DiSC(3)(3), DiSC(4)(3), DiSC(5)(3), and DiSC(py)(3)) interact with preformed PNA-DNA oligomer duplexes but do not demonstrate an equivalent accelerated photobleaching effect in the presence of PNA and target genomic DNA. The feasibility of developing molecular diagnostic assays based on the accelerated photobleaching (the smartDNA assay) that results from the novel complex formed between DiSC(2)(3) and PNA-DNA is under way.
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Affiliation(s)
- M Wang
- Investigen Inc., Hercules, California, USA
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26
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Hansen ME, Bentin T, Nielsen PE. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers. Nucleic Acids Res 2009; 37:4498-507. [PMID: 19474349 PMCID: PMC2715256 DOI: 10.1093/nar/gkp437] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
While sequence-selective dsDNA targeting by triplex forming oligonucleotides has been studied extensively, only very little is known about the properties of PNA–dsDNA triplexes—mainly due to the competing invasion process. Here we show that when appropriately modified using pseudoisocytosine substitution, in combination with (oligo)lysine or 9-aminoacridine conjugation, homopyrimidine PNA oligomers bind complementary dsDNA targets via triplex formation with (sub)nanomolar affinities (at pH 7.2, 150 mM Na+). Binding affinity can be modulated more than 1000-fold by changes in pH, PNA oligomer length, PNA net charge and/or by substitution of pseudoisocytosine for cytosine, and conjugation of the DNA intercalator 9-aminoacridine. Furthermore, 9-aminoacridine conjugation also strongly enhanced triplex invasion. Specificity for the fully matched target versus one containing single centrally located mismatches was more than 150-fold. Together the data support the use of homopyrimidine PNAs as efficient and sequence selective tools in triplex targeting strategies under physiological relevant conditions.
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Affiliation(s)
- Mads E Hansen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200-N, Denmark
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27
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Fadeyi OO, Adamson ST, Myles EL, Okoro CO. Novel fluorinated acridone derivatives. Part 1: Synthesis and evaluation as potential anticancer agents. Bioorg Med Chem Lett 2008; 18:4172-6. [PMID: 18541426 DOI: 10.1016/j.bmcl.2008.05.078] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Affiliation(s)
- Olugbeminiyi O Fadeyi
- Department of Chemistry, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN 37209-1561, USA
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28
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Rapireddy S, He G, Roy S, Armitage BA, Ly DH. Strand invasion of mixed-sequence B-DNA by acridine-linked, gamma-peptide nucleic acid (gamma-PNA). J Am Chem Soc 2007; 129:15596-600. [PMID: 18027941 DOI: 10.1021/ja074886j] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acid (PNA) is a synthetic mimic of DNA and RNA that can recognize double-stranded B-DNA through direct Watson-Crick base-pairing. Although promising, PNA recognition is presently limited to mostly purine- and pyrimidine-rich targets, because mixed-sequence PNA, in general, does not have sufficient binding free energy to invade B-DNA. In this Article, we show that conformationally preorganized gamma-peptide nucleic acid (gamma-PNA) containing an acridine moiety covalently linked at the C-terminus can invade mixed-sequence B-DNA in a sequence-specific manner. Recognition occurs through direct Watson-Crick base-pairing. This finding is significant because it demonstrates that the same principles that guide the recognition of single-stranded DNA and RNA can also be applied to double-stranded B-DNA.
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Affiliation(s)
- Srinivas Rapireddy
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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29
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Bentin T, Hansen GI, Nielsen PE. Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes. Nucleic Acids Res 2006; 34:5790-9. [PMID: 17053099 PMCID: PMC1635314 DOI: 10.1093/nar/gkl736] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Sequence-selective recognition of double-stranded (ds) DNA by homopyrimidine peptide nucleic acid (PNA) oligomers can occur by major groove triplex binding or by helix invasion via triplex P-loop formation. We have compared the binding of a decamer, a dodecamer and a pentadecamer thymine–cytosine homopyrimidine PNA oligomer to a sequence complementary homopurine target in duplex DNA using gel-shift and chemical probing analyses. We find that all three PNAs form stable triplex invasion complexes, and also conventional triplexes with the dsDNA target. Triplexes form with much faster kinetics than invasion complexes and prevail at lower PNA concentrations and at shorter incubation times. Furthermore, increasing the ionic strength strongly favour triplex formation over invasion as the latter is severely inhibited by cations. Whereas a single triplex invasion complex is formed with the decameric PNA, two structurally different target-specific invasion complexes were characterized for the dodecameric PNA and more than five for the pentadecameric PNA. Finally, it is shown that isolated triplex complexes can be converted to specific invasion complexes without dissociation of the Hoogsteen base-paired triplex PNA. These result demonstrate a clear example of a ‘triplex first’ mechanism for PNA helix invasion.
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Affiliation(s)
| | | | - Peter E. Nielsen
- To whom correspondence should be addressed. Tel: +45 35327762/61; Fax: +45 35396042;
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30
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Shiraishi T, Bendifallah N, Nielsen PE. Cellular delivery of polyheteroaromate-peptide nucleic acid conjugates mediated by cationic lipids. Bioconjug Chem 2006; 17:189-94. [PMID: 16417268 DOI: 10.1021/bc050246z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the search of facile and efficient methods for PNA cellular delivery, we have tested a series of PNA conjugates based on (hetero) aromatic, lipophilic compounds such as 9-aminoacridine, benzimidazoles, carbazole, anthraquinone, porphyrine, psoralen, pyrene, and phenyl-bis-benzimidazole ("Hoechst"). These chemically modified PNAs were delivered to cultured pLuc705HeLa cells mediated by cationic liposomes (LipofectAMINE or LiofectAMINE2000), and their nuclear delivery was inferred from induced luciferase activity as a consequence of pre-mRNA splicing correction by the antisense-PNA. PNAs modified with 9-aminoacridine, "Hoechst", or acetyl-"Hoechst" showed highest antisense activities (while unmodified PNA failed to show any significant antisense activity). In particular, bis-acridine-conjugated PNA showed nearly 60% splicing correction at 250 nM concentration in combination with LipofectAMINE2000. Interestingly, relative differences between the derivatives were observed when LipofectAMINE was used as compared to LipofectAMINE2000, but in general the latter yielded the higher antisense activity. The most active modifications of these PNA constructs were further tested for antisense down-regulation of luciferase in p53R cells in order to evaluate the cytoplasmic activity (uptake) of the PNAs. A dose-dependent down regulation of luciferase was demonstrated also in this system. The PNA conjugated to acetyl-Hoechst caused a reduction of luciferase activity to less than 40% of the control at a concentration of 1 muM. These results indicate that conjugation of (hetero) polyaromatic compounds to PNA can dramatically improve liposome-mediated cellular delivery both to cytoplasm as well as to the nucleus. However, no clear structure/activity relations are apparent from the present results, except that both 9-aminoacridine and "Hoechst" are also nucleic acid binding ligands.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
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31
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Zhilina ZV, Ziemba AJ, Nielsen PE, Ebbinghaus SW. PNA-nitrogen mustard conjugates are effective suppressors of HER-2/neu and biological tools for recognition of PNA/DNA interactions. Bioconjug Chem 2006; 17:214-22. [PMID: 16417271 DOI: 10.1021/bc0502964] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptide nucleic acids (PNAs) are promising tools for gene regulation. One of the challenges of using PNAs as gene regulators is the need to optimize the efficiency of interaction with critical sequences of DNA. To improve the efficiency of binding between PNAs and the HER-2/neu promoter, mono- and bis-pyrimidine-rich PNAs were conjugated to a nitrogen mustard at either the amino or carboxy terminus. Gel shift analysis demonstrated that conjugation to an alkylating agent slowed PNA binding and favored PNA:DNA:DNA triplex helix formation while preserving a high binding affinity. Sites of DNA alkylation were visualized by piperidine cleavage and showed PNA binding first by Hoogsteen bond formation with the target duplex to form a stable PNA:DNA:DNA triplex structure which is later converted to a PNA:DNA:PNA triple helix by strand invasion and Watson-Crick base pairing by a second PNA molecule. In this way, PNA-directed DNA alkylation was used to deduce the mode of PNA binding. Transient transfection experiments demonstrated that the PNA-nitrogen mustard conjugates suppressed HER-2/neu expression by up to 80%. In comparison with an unmodified mono-PNA or a bis-PNA, these results indicate that the covalent adducts stabilized PNA binding in cells and suggest that the conjugation of PNAs to nitrogen mustards is a robust strategy for developing antigene PNA oligonucleotides to prevent transcription.
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Affiliation(s)
- Zhanna V Zhilina
- Arizona Cancer Center, University of Arizona, 1515 North Campbell, 85724, Tucson, Arizona, USA
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32
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Goodman CM, Chari NS, Han G, Hong R, Ghosh P, Rotello VM. DNA-binding by functionalized gold nanoparticles: mechanism and structural requirements. Chem Biol Drug Des 2006; 67:297-304. [PMID: 16629827 DOI: 10.1111/j.1747-0285.2006.00372.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A family of nanoparticles featuring surfaces of varying hydrophobicity was synthesized. The efficiency of DNA-binding was determined, demonstrating in a fivefold modulation in binding a 37-mer DNA strand. Nanoparticle-binding causes a reversible conformational change in the DNA structure, as demonstrated by circular dichroism and fluorescence experiments. Furthermore, the affinity of the nanoparticle for the DNA can be regulated by external agents, though stability of the complex is observed at relatively high ionic strengths.
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Affiliation(s)
- Catherine M Goodman
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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33
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Rasmussen FW, Bendifallah N, Zachar V, Shiraishi T, Fink T, Ebbesen P, Nielsen PE, Koppelhus U. Evaluation of transfection protocols for unmodified and modified peptide nucleic acid (PNA) oligomers. Oligonucleotides 2006; 16:43-57. [PMID: 16584294 DOI: 10.1089/oli.2006.16.43] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We have compared the efficacy of different transfection protocols reported for peptide nucleic acid (PNA) oligomers. A precise evaluation of uptake efficacy was achieved by using a positive readout assay based on the ability of a PNA oligomer to correct aberrant splicing of a recombinant luciferase gene. The study comprised transfection of PNA conjugated to acridine, adamantyl, decanoic acid, and porphyrine (acr-PNA, ada-PNA, deca-PNA, and por-RNA, respectively) and unmodified PNA partially hybridized to a DNA oligomer (PNA/DNA cotransfection). Furthermore, the effect of conjugation to a nuclear localization signal (NLS) was evaluated as part of the PNA/DNA cotransfection protocol. Transfection of the tested PNAs was systematically optimized. PNA/DNA cotransfection was found to produce the highest luciferase activity, but only after careful selection of the DNA oligonucleotide. Both a cationic lipid, Lipofectamine, and a nonliposomal cationic polymer, polyethylenimine (PEI, ExGen 500), were efficient transfection reagents for the PNA/DNA complex. However, Lipofectamine, in contrast to PEI, showed severe side effects, such as cytotoxicity. acr-PNA, ada-PNA, and por-PNA were transfectable with efficacies between 5 and 10 times lower than that seen with PNA/DNA cotransfection. Conjugation of PNA to NLS had no effect on PNA/DNA cotransfection efficacy. An important lesson from the study was the finding that because of uncontrollable biologic variations, even optimal transfection conditions differed to a certain extend from experiment to experiment in an unpredictable way.
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34
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Lundin KE, Good L, Strömberg R, Gräslund A, Smith CIE. Biological activity and biotechnological aspects of peptide nucleic acid. ADVANCES IN GENETICS 2006; 56:1-51. [PMID: 16735154 DOI: 10.1016/s0065-2660(06)56001-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the latest decades a number of different nucleic acid analogs containing natural nucleobases on a modified backbone have been synthesized. An example of this is peptide nucleic acid (PNA), a DNA mimic with a noncyclic peptide-like backbone, which was first synthesized in 1991. Owing to its flexible and neutral backbone PNA displays very good hybridization properties also at low-ion concentrations and has subsequently attracted large interest both in biotechnology and biomedicine. Numerous modifications have been made, which could be of value for particular settings. However, the original PNA does so far perform well in many diverse applications. The high biostability makes it interesting for in vivo use, although the very limited diffusion over lipid membranes requires further modifications in order to make it suitable for treatment in eukaryotic cells. The possibility to use this nucleic acid analog for gene regulation and gene editing is discussed. Peptide nucleic acid is now also used for specific genetic detection in a number of diagnostic techniques, as well as for site-specific labeling and hybridization of functional molecules to both DNA and RNA, areas that are also discussed in this chapter.
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Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center Karolinska Institutet, Karolinska University Hospital, Huddinge 141 86 Stockholm, Sweden
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35
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Tedeschi T, Sforza S, Dossena A, Corradini R, Marchelli R. Lysine-based peptide nucleic acids (PNAs) with strong chiral constraint: control of helix handedness and DNA binding by chirality. Chirality 2005; 17 Suppl:S196-204. [PMID: 15952136 DOI: 10.1002/chir.20128] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Two enantiomeric chiral PNAs bearing three adjacent D- or L-lysine-based residues in the middle of the strand ("chiral box" PNAs, sequence H-GTAGA(Lys)T(Lys)C(Lys)ACT-NH2) have been used as models in order to comprehensively study the effects of the stereogenic centers on PNA conformation and on PNA binding properties to complementary PNA and DNA strands. The binding properties of the two enantiomeric PNAs and of their homologous achiral PNA have been extensively studied by UV and CD spectroscopy and by mass spectrometry, both in the antiparallel and in the parallel mode with complementary PNA and DNA strands. In the antiparallel PNA:PNA duplexes, L-Lys PNA were found to form left-handed, and D-Lys PNA right handed helices, while in parallel duplexes, the reversed helicities were observed. Correspondingly, the preferred mode of binding and the best mismatch recognition of the D-Lys containing PNA with (right handed) DNA was found to be in the antiparallel orientation, while that of L-Lys PNA was found to be in the parallel mode. A rationale which correlates the preferred handedness of the PNA-PNA duplexes to the directionality of the binding to complementary DNA duplexes has been devised according to structural data and considering the "retro-inverso" concept widely used for peptides.
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Affiliation(s)
- Tullia Tedeschi
- Dipartimento di Chimica Organica e Industriale, Università di Parma, Parma, Italy
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Nielsen PE, Frederiksen K, Behrens C. Extended target sequence specificity of PNA-minor-groove binder conjugates. Chembiochem 2005; 6:66-8. [PMID: 15593115 DOI: 10.1002/cbic.200400251] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Peter E Nielsen
- Department of Medical Biochemistry and Genetics, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, Copenhagen N 2200, Denmark.
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Pereira RV, Garcia Ferreira AP, Gehlen MH. Excited-State Intramolecular Charge Transfer in 9-Aminoacridine Derivative. J Phys Chem A 2005; 109:5978-83. [PMID: 16833932 DOI: 10.1021/jp044704x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new fluorochromic dye was obtained from the reaction of 9-aminoacridine with ethyl-2-cyano-3-ethoxyacrylate. It displays complex fluorescence that is ascribed to normal emission from the acridine chromophore in addition to excited-state intramolecular charge transfer (ESICT) formed upon light excitation. The analysis of the fluorescence decays in different solvents reveals two short-lived components in the range of 80-450 ps and 0.7-3.2 ns, ascribed to the formation and decay of the intramolecular charge transfer (ICT) state, in addition to a third component of about 9.0 ns, which is related to the normal emission from the acridine singlet excited state, probably in an enol-imine tautomeric form. The ICT emission is readily quenched by water addition to polar solvents, and this effect is ascribed to changes in the keto-amine/enol-imine equilibrium of this fluorochromic dye.
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Affiliation(s)
- Robson Valentim Pereira
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-590, São Carlos SP, Brazil
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38
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Whitney AM, Ladame S, Balasubramanian S. Templated ligand assembly by using G-quadruplex DNA and dynamic covalent chemistry. Angew Chem Int Ed Engl 2005; 43:1143-6. [PMID: 14983458 PMCID: PMC2195892 DOI: 10.1002/anie.200353069] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The recognition of cellular nucleic acids by synthetic oligonucleotides is a versatile strategy for regulating biological processes. The vast majority of published studies have focused on antisense oligonucleotides that target mRNA, but it is also possible to design antigene oligonucleotides that are complementary to chromosomal DNA. Antigene oligomers could be used to inhibit the expression of any gene or analyze promoter structure and the mechanisms governing gene regulation. Other potential applications of antigene oligomers include activation of expression of chosen genes or the introduction of mutations to correct genetic disease. Peptide nucleic acid (PNA) is a nonionic DNA/RNA mimic that possesses outstanding potential for recognition of duplex DNA. Here we describe properties of PNAs and the challenges for their development as robust antigene agents.
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Affiliation(s)
- Kunihiro Kaihatsu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 USA
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40
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Nielsen PE. The many faces of PNA. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-005-4860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Abstract
Peptide nucleic acids (PNAs) are synthetic oligonucleotides with chemically modified backbones. PNAs can bind to both DNA and RNA targets in a sequence-specific manner to form PNA/DNA and PNA/RNA duplex structures. When bound to double-stranded DNA (dsDNA) targets, the PNA molecule replaces one DNA strand in the duplex by strand invasion to form a PNA/DNA/PNA [or (PNA)2/DNA] triplex structure and the displaced DNA strand exists as a single-stranded D-loop. PNA has been used in many studies as research tools for gene regulation and gene targeting. The D-loops generated from the PNA binding have also been demonstrated for its potential in initiating transcription and inducing gene expression. PNA provides a powerful tool to study the mechanism of transcription and an innovative strategy to regulate target gene expression. An understanding of the PNA-mediated gene regulation will have important clinical implications in treatment of many human diseases including genetic, cancerous, and age-related diseases.
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Affiliation(s)
- Gan Wang
- Institute of Environmental Health Sciences, Wayne State University, 2727 Second Avenue, Detroit, MI 48201, USA.
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42
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Abstract
Peptide nucleic acids (PNA) are deoxyribonucleic acid (DNA) mimics with a pseudopeptide backbone. PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion. Therefore, these molecules are of interest in many areas of chemistry, biology, and medicine, including drug discovery, genetic diagnostics, molecular recognition, and the origin of life. Recent progress in studies of PNA properties and applications is reviewed.
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Affiliation(s)
- Peter E Nielsen
- Center for Biomolecular Recognition, IMBG, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK-2200N, Denmark.
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Basavaiah D, Rao JS, Reddy RJ. Simple, Facile, and One-Pot Conversion of the Baylis−Hillman Adducts into Functionalized 1,2,3,4-Tetrahydroacridines and Cyclopenta[b]quinolines. J Org Chem 2004; 69:7379-82. [PMID: 15471499 DOI: 10.1021/jo0489871] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple, facile, and one-pot synthesis of functionalized 1,2,3,4-tetrahydroacridines and cyclopenta[b]quinolines from the Baylis-Hillman alcohols, i.e., 2-[hydroxy(2-nitroaryl)methyl]cycloalk-2-enones, is described.
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Affiliation(s)
- Deevi Basavaiah
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India.
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Kuhn H, Cherny DI, Demidov VV, Frank-Kamenetskii MD. Inducing and modulating anisotropic DNA bends by pseudocomplementary peptide nucleic acids. Proc Natl Acad Sci U S A 2004; 101:7548-53. [PMID: 15136738 PMCID: PMC419643 DOI: 10.1073/pnas.0308756101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA bending is significant for various DNA functions in the cell. Here, we demonstrate that pseudocomplementary peptide nucleic acids (pcPNAs) represent a class of versatile, sequence-specific DNA-bending agents. The occurrence of anisotropic DNA bends induced by pcPNAs is shown by gel electrophoretic phasing analysis. The magnitude of DNA bending is determined by circular permutation assay and by electron microscopy, with good agreement of calculated mean values between both methods. Binding of a pair of 10-meric pcPNAs to its target DNA sequence results in moderate DNA bending with a mean value of 40-45 degrees, while binding of one self-pc 8-mer PNA to target DNA yields a somewhat larger average value of the induced DNA bend. Both bends are found to be in phase when the pcPNA target sites are separated by distances of half-integer numbers of helical turns of regular duplex DNA, resulting in an enhanced DNA bend with an average value in the range of 80-90 degrees. The occurrence of such a sharp bend within the DNA double helix is confirmed and exploited through efficient formation of 170-bp-long DNA minicircles by means of dimerization of two bent DNA fragments. The pcPNAs offer two main advantages over previously designed classes of nonnatural DNA-bending agents: they have very mild sequence limitations while targeting duplex DNA and they can easily be designed for a chosen target sequence, because their binding obeys the principle of complementarity. We conclude that pcPNAs are promising tools for inducing bends in DNA at virtually any chosen site.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
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45
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Bentin T, Larsen HJ, Nielsen PE. Combined triplex/duplex invasion of double-stranded DNA by "tail-clamp" peptide nucleic acid. Biochemistry 2004; 42:13987-95. [PMID: 14636067 DOI: 10.1021/bi0351918] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
"Tail-clamp" PNAs composed of a short (hexamer) homopyrimidine triplex forming domain and a (decamer) mixed sequence duplex forming extension have been designed. Tail-clamp PNAs display significantly increased binding to single-stranded DNA compared with PNAs lacking a duplex-forming extension as determined by T(m) measurements. Binding to double-stranded (ds) DNA occurred by combined triplex and duplex invasion as analyzed by permanganate probing. Furthermore, C(50) measurements revealed that tail-clamp PNAs consistently bound the dsDNA target more efficiently, and kinetics experiments revealed that this was due to a dramatically reduced dissociation rate of such complexes. Increasing the PNA net charge also increased binding efficiency, but unexpectedly, this increase was much more pronounced for tailless-clamp PNAs than for tail-clamp PNAs. Finally, shortening the tail-clamp PNA triplex invasion moiety to five residues was feasible, but four bases were not sufficient to yield detectable dsDNA binding. The results validate the tail-clamp PNA concept and expand the applications of the P-loop technology.
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Affiliation(s)
- Thomas Bentin
- Center for Biomolecular Recognition, IMBG, Department B, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
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Kaihatsu K, Shah RH, Zhao X, Corey DR. Extending recognition by peptide nucleic acids (PNAs): binding to duplex DNA and inhibition of transcription by tail-clamp PNA-peptide conjugates. Biochemistry 2004; 42:13996-4003. [PMID: 14636068 DOI: 10.1021/bi035194k] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide nucleic acids (PNAs) are a powerful tool for recognition of double-stranded DNA. Strand invasion is most efficient when pyrimidine PNAs are linked to form a bisPNA in which one strand binds by Watson-Crick base pairing while the other binds by Hoogsteen base pairing to the newly formed PNA-DNA duplex. Within many genes, however, polypyrimidine target sequences may not be located in optimal positions relative to transcription factor binding sites, and this deficiency may complicate attempts to identify potent antigene PNAs. To increase the versatility of strand invasion by PNAs, we have synthesized bisPNAs and bisPNA-peptide conjugates containing a mixed base extension of the Watson-Crick polypyrimidine strand. We find that these tail-clamp PNAs (TC-PNAs) bind duplex DNA and inhibit transcription. DNA recognition occurs with single-stranded or TC-bisPNAs and requires attachment of positively charged amino acids. Association rate constants, k(a), for binding to DNA by TC-PNAs are as high as 35000 M(-1) s(-1) and are usually only a fewfold lower than for analogous PNAs that lack mixed base extensions. The ability to bind duplex DNA is not always necessary for inhibition of transcription, possibly because PNAs can bind to accessible DNA within the transcription bubble created by RNA polymerase. These results, together with similar findings independently obtained by Nielsen and colleagues [Bentin, T., Larsen, H. J., and Nielsen, P. E. (2003) Biochemistry 42, 13987-13995], expand the range of sequences within duplex DNA that are accessible to PNAs and suggest that TC-PNA-peptide conjugates are good candidates for further testing as antigene agents.
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Affiliation(s)
- Kunihiro Kaihatsu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9041, USA
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Veldhuyzen WF, Pande P, Rokita SE. A transient product of DNA alkylation can be stabilized by binding localization. J Am Chem Soc 2004; 125:14005-13. [PMID: 14611237 DOI: 10.1021/ja036943o] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 9-aminoacridine conjugate of a silyl-protected bis(acetoxymethyl)phenol (bisQMP) was synthesized and evaluated as an inducible cross-linking agent of DNA to test our ability to harness the chemistry of reactive quinone methide intermediates (QM). The acridine component was chosen for its ability to delivery an appendage to the major groove of DNA, and the silyl-protected component was chosen for its ability to generate two quinone methide equivalents in tandem upon addition of fluoride. This design created competition between reaction of (1) the 2-amino group of guanine that reacts irreversibly to form a stable QM adduct and (2) the more nucleophilic N7 group of guanine that reacts more efficiently but reversibly to form a labile QM adduct. This lability was apparently compensated by co-localization of the N7 group and QM in the major groove since the N7 adduct appeared to dominate the profile of products formed by duplex DNA. The controlling influence of acridine was also expressed in the sensitivity of the conjugate to ionic strength. High salt concentration inhibited covalent reaction just as it inhibits intercalation of the cationic acridine. As expected for QM formation, the presence of fluoride was indeed necessary for initiating reaction, and no direct benzylic substitution was observed. The conjugate also cross-linked DNA with high efficiency, forming one cross-link for every four alkylation events. Both alkylation and cross-linking products formed by duplex DNA were labile to hot piperidine treatment which led to approximately 40% strand scission and approximately 50% reversion to a material with an electrophoretic mobility equivalent to the parent DNA. All guanines exhibited at least some reactivity including those which were recalcitrant to cross-linking by an oligonucleotide-bisQMP conjugate designed for triplex formation [Zhou, G.; Pande, P.; Johnson, A. E.; Rokita, S. E. Bioorg. Med. Chem. 2001, 9, 2347-2354].
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Affiliation(s)
- Willem F Veldhuyzen
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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48
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Shiraishi T, Nielsen PE. Down-regulation of MDM2 and activation of p53 in human cancer cells by antisense 9-aminoacridine-PNA (peptide nucleic acid) conjugates. Nucleic Acids Res 2004; 32:4893-902. [PMID: 15371552 PMCID: PMC519114 DOI: 10.1093/nar/gkh820] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A series of peptide nucleic acid (PNA) oligomers targeting the mdm2 oncogene mRNA has been tested for the ability to inhibit the growth of JAR cells. The effect of these PNAs on the cells was also reflected in reduced levels of the MDM2 protein and increased levels of the p53 tumor suppressor protein, which is negatively regulated by MDM2. Initially, PNA oligomers were delivered as DNA complexes with lipofectamine, but it was discovered that PNA conjugated to the DNA intercalator 9-aminoacridine (Acr) (Acr-PNA) could be effectively delivered to JAR cells (as well as to HeLa pLuc705 cells) even in the absence of a DNA carrier. Using such lipofectamine-delivered Acr-PNA conjugates, one PNA targeting a cryptic AUG initiation site was identified that at a concentration of 2 microM caused a reduction of MDM2 levels to approximately 20% (but no reduction in mdm2 mRNA levels) and a 3-fold increase in p53 levels, whereas a 2-base mismatch control had no such effects. Furthermore, transcriptional activation by p53 was also increased (6-fold), and cell viability was reduced to 80%. Finally, this PNA acted cooperatively with camptothecin treatment both with regard to p53 activity induction as well as cell viability. Using this novel cell delivery system, we have identified a target on the mdm2 mRNA that appears sensitive to antisense inhibition by PNA and therefore could be used as a lead for further development of mdm2-targeted antisense (PNA and other) gene therapeutic anticancer drugs.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
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49
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Affiliation(s)
- Andrew Dodd
- Molecular Genetics and Development Group, School of Biological Sciences, University of Auckland, Auckland 1001, New Zealand
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50
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