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Antisense peptide nucleic acids as a potential anti-infective agent. J Microbiol 2019; 57:423-430. [PMID: 31054136 DOI: 10.1007/s12275-019-8635-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/25/2023]
Abstract
Antibiotics have long been used for anti-infective control of bacterial infections, growth promotion in husbandry, and prophylactic protection against plant pathogens. However, their inappropriate use results in the emergence and spread of multiple drug resistance (MDR) especially among various bacterial populations, which limits further administration of conventional antibiotics. Therefore, the demand for novel anti-infective approaches against MDR diseases becomes increasing in recent years. The peptide nucleic acid (PNA)-based technology has been proposed as one of novel anti-infective and/or therapeutic strategies. By definition, PNA is an artificially synthesized nucleic acid mimic structurally similar to DNA or RNA in nature and linked one another via an unnatural pseudo-peptide backbone, rendering to its stability in diverse host conditions. It can bind DNA or RNA strands complimentarily with high affinity and sequence specificity, which induces the target-specific gene silencing by inhibiting transcription and/or translation. Based on these unique properties, PNA has been widely applied for molecular diagnosis as well as considered as a potential anti-infective agent. In this review, we discuss the general features of PNAs and their application to various bacterial pathogens as new anti-infective or antimicrobial agents.
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Malik S, Oyaghire S, Bahal R. Applications of PNA-laden nanoparticles for hematological disorders. Cell Mol Life Sci 2019; 76:1057-1065. [PMID: 30498995 PMCID: PMC11105400 DOI: 10.1007/s00018-018-2979-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/07/2018] [Accepted: 11/23/2018] [Indexed: 12/26/2022]
Abstract
Safe and efficient genome editing has been an unmitigated goal for biomedical researchers since its inception. The most prevalent strategy for gene editing is the use of engineered nucleases that induce DNA damage and take advantage of cellular DNA repair machinery. This includes meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems. However, the clinical viability of these nucleases is marred by their off-target cleavage activity (≥ 50% in RNA-guided endonucleases). In addition, in vivo applications of CRISPR require systemic administration of Cas9 protein, mRNA, or DNA, which presents a significant delivery challenge. The development of nucleic acid probes that can recognize specific double-stranded DNA (dsDNA) regions and activate endogenous DNA repair machinery holds great promise for gene editing applications. Triplex-forming oligonucleotides (TFOs), which were introduced more than 25 years ago, are among the most extensively studied oligomeric dsDNA-targeting agents. TFOs bind duplex DNA to create a distorted helical structure, which can stimulate DNA repair and the exchange of a nearby mutated region-otherwise leading to an undesired phenotype-for a short single-stranded donor DNA that contains the corrective nucleotide sequence. Recombination can be induced within several hundred base-pairs of the TFO binding site and has been shown to depend on triplex-induced initiation of the nucleotide excision repair pathway and engagement of the homology-dependent repair pathway. Since TFOs do not possess any direct nuclease activity, their off-target effects are minimal when compared to engineered nucleases. This review comprehensively covers the advances made in peptide nucleic acid-based TFOs for site-specific gene editing and their therapeutic applications.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Stanley Oyaghire
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA.
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Shigi N, Mizuno Y, Kunifuda H, Matsumura K, Komiyama M. Promotion of Single-Strand Invasion of PNA to Double-Stranded DNA by Pseudo-Complementary Base Pairing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Narumi Shigi
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yuki Mizuno
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Materials Science & Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Hiroko Kunifuda
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Kazunari Matsumura
- Department of Materials Science & Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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Karmakar S, Horrocks T, Gibbons BC, Guenther DC, Emehiser R, Hrdlicka PJ. Synthesis and biophysical characterization of oligonucleotides modified with O2'-alkylated RNA monomers featuring substituted pyrene moieties. Org Biomol Chem 2019; 17:609-621. [PMID: 30575837 DOI: 10.1039/c8ob02764a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past three decades, a wide range of pyrene-functionalized oligonucleotides have been developed and explored for potential applications in material science and nucleic acid diagnostics. Our efforts have focused on their possible use as components of Invader probes, i.e., DNA duplexes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides. We have previously demonstrated that Invader probes based on 2'-O-(pyren-1-yl)methyl-RNA monomers are energetically activated for sequence-unrestricted recognition of chromosomal DNA targets under non-denaturing conditions. As part of ongoing efforts towards delineating structure-property relationships and optimizing Invader probes, we report the synthesis and biophysical characterization of oligodeoxyribonucleotides (ONs) modified with 2'-O-(7-neo-pentylpyren-1-yl)methyl-uridine monomer V and 2'-O-(7-tert-butyl-1-methoxypyren-5-yl)methyl-uridine monomer Y. ONs modified with monomer V display increased DNA affinity (ΔTm up to +10.5 °C), while Y-modified ONs display lower DNA affinity and up to 22-fold increases in fluorescence emission upon RNA binding. Although these monomers display limited potential as building blocks for Invader probes, their photophysical properties render them of interest for diagnostic RNA-targeting applications.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
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Tadimety A, Zhang Y, Kready KM, Palinski TJ, Tsongalis GJ, Zhang JXJ. Design of peptide nucleic acid probes on plasmonic gold nanorods for detection of circulating tumor DNA point mutations. Biosens Bioelectron 2019; 130:236-244. [PMID: 30769288 DOI: 10.1016/j.bios.2019.01.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/06/2019] [Accepted: 01/19/2019] [Indexed: 01/06/2023]
Abstract
Here we present a gold nanorod-based platform for the sequence-specific detection of circulating tumor DNA (ctDNA) point mutations without the need for amplification or fluorescence labeling. Peptide nucleic acid probes complimentary to the G12V mutation in the KRAS gene were conjugated to gold nanorods, and the localized surface plasmon resonance absorbance through the sample was measured after exposure to synthetic ctDNA at various concentrations. Each step of the reaction was thoroughly controlled, starting from reagent concentrations and including conjugation, sonication, and incubation time. The platform was evaluated in both buffer and spiked healthy patient serum, demonstrating a linear working range below 125 nanograms of ctDNA per milliliter solution, and an effective limit of detection of 2 nanograms of ctDNA per milliliter. A clear distinction between mutant and wild type synthetic ctDNA was also found using this platform. In order to improve upon the selectivity of the sensor, a DNA hybridization simulation was performed to understand how the addition of mutations to the peptide nucleic acid probe could enhance the selectivity for capture of mutant over wild type sequences. The top candidate from the simulations, which had an additional mutation two base pairs away from the mutation of interest, had a significant impact on the selectivity between mutant and wild type capture. This paper provides a framework for sequence-specific capture of ctDNA, and a method of improving selectivity for desired point mutations through careful probe design.
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Affiliation(s)
- Amogha Tadimety
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Yichen Zhang
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Kasia M Kready
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Timothy J Palinski
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Gregory J Tsongalis
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA
| | - John X J Zhang
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA.
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Hibino M, Aiba Y, Watanabe Y, Shoji O. Peptide Nucleic Acid Conjugated with Ruthenium-Complex Stabilizing Double-Duplex Invasion Complex Even under Physiological Conditions. Chembiochem 2018; 19:1601-1604. [PMID: 29797750 DOI: 10.1002/cbic.201800256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 02/03/2023]
Abstract
Peptide nucleic acid (PNA) can form a stable duplex with DNA, and, accordingly, directly recognize double-stranded DNA through the formation of a double-duplex invasion complex, wherein a pair of complementary PNA strands form two PNA/DNA duplexes. Because invasion does not require prior denaturation of DNA, PNA holds great potential for in cellulo or in vivo applications. To broaden the applicability of PNA invasion, we developed a new conjugate of PNA with a ruthenium complex. This Ru-PNA conjugate exhibits higher DNA-binding affinity, which results in enhanced invasion efficiency, even under physiological conditions.
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Affiliation(s)
- Masaki Hibino
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
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Abstract
Peptide nucleic acids (PNAs) can bind duplex DNA in a sequence-targeted manner, forming a triplex structure capable of inducing DNA repair and producing specific genome modifications. Since the first description of PNA-mediated gene editing in cell free extracts, PNAs have been used to successfully correct human disease-causing mutations in cell culture and in vivo in preclinical mouse models. Gene correction via PNAs has resulted in clinically-relevant functional protein restoration and disease improvement, with low off-target genome effects, indicating a strong therapeutic potential for PNAs in the treatment or cure of genetic disorders. This review discusses the progress that has been made in developing PNAs as an effective, targeted agent for gene editing, with an emphasis on recent in vivo, nanoparticle-based strategies.
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58
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D'Souza AD, Belotserkovskii BP, Hanawalt PC. A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:158-166. [PMID: 29357316 PMCID: PMC5820110 DOI: 10.1016/j.bbagrm.2017.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 01/01/2023]
Abstract
The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription.
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Affiliation(s)
- Alicia D D'Souza
- Department of Biology, Stanford University, Stanford, CA 94305-5020, United States
| | | | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, CA 94305-5020, United States.
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59
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Abstract
An impressive array of antigene approaches has been developed for recognition of double helical DNA over the past three decades; however, few have exploited the 'Watson-Crick' base-pairing rules for establishing sequence-specific recognition. One approach employs peptide nucleic acid as a molecular reagent and strand invasion as a binding mode. However, even with integration of the latest conformationally-preorganized backbone design, such an approach is generally confined to sub-physiological conditions due to the lack of binding energy. Here we report the use of a class of shape-selective, bifacial nucleic acid recognition elements, namely Janus bases, for targeting double helical DNA or RNA. Binding occurs in a highly sequence-specific manner under physiologically relevant conditions. The work may provide a foundation for the design of oligonucleotides for targeting the secondary and tertiary structures of nucleic acid biopolymers.
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60
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Karmakar S, Guenther DC, Gibbons BC, Hrdlicka PJ. Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2'-triphenylene- and coronene-functionalized RNA monomers. Org Biomol Chem 2017; 15:9362-9371. [PMID: 29090304 PMCID: PMC5700769 DOI: 10.1039/c7ob01920c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Development of hybridization-based probes that enable recognition of specific mixed-sequence double-stranded DNA (dsDNA) regions is of considerable interest due to their potential applications in molecular biology, biotechnology, and medicine. We have recently demonstrated that nucleic acid duplexes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl RNA monomers are inherently activated for recognition of mixed-sequence dsDNA targets, including chromosomal DNA. In the present work, we follow up on our previous structure-activity relationship studies and explore if the dsDNA-recognition efficiency of these so-called Invader probes can be improved by using larger intercalators than pyrene. Oligodeoxyribonucleotides modified with 2'-O-(triphenylen-2-yl)methyl-uridine monomer X and 2'-O-(coronen-1-yl)methyl-uridine monomer Z form extraordinarily stabilized duplexes with complementary DNA (ΔTm's per modification of up to 13 °C and 20 °C, respectively). Invader probes based on X- and Z-monomers are shown to recognize model dsDNA targets with exceptional binding specificity, but are less efficient than reference probes modified with 2'-O-(pyren-1-yl)methyl-uridine monomer Y. The insight from this study will inform further optimization of Invader probes.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
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61
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Applications of PNA-Based Artificial Restriction DNA Cutters. Molecules 2017; 22:molecules22101586. [PMID: 28934140 PMCID: PMC6151779 DOI: 10.3390/molecules22101586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022] Open
Abstract
More than ten years ago, artificial restriction DNA cutters were developed by combining two pseudo-complementary peptide nucleic acid (pcPNA) strands with either Ce(IV)/EDTA or S1 nuclease. They have remarkably high site-specificity and can cut only one predetermined site in the human genome. In this article, recent progress of these man-made tools have been reviewed. By cutting the human genome site-selectively, desired fragments can be clipped from either the termini of chromosomes (telomeres) or from the middle of genome. These fragments should provide important information on the biological functions of complicated genome system. DNA/RNA hybrid duplexes, which are formed in living cells, are also site-selectively hydrolyzed by these cutters. In order to further facilitate the applications of the artificial DNA cutters, various chemical modifications have been attempted. One of the most important successes is preparation of PNA derivatives which can form double-duplex invasion complex even under high salt conditions. This is important for in vivo applications, since the inside of living cells is abundant of metal ions. Furthermore, site-selective DNA cutters which require only one PNA strand, in place of a pair of pcPNA strands, are developed. This progress has opened a way to new fields of PNA-based biochemistry and biotechnology.
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Pabon-Martinez YV, Xu Y, Villa A, Lundin KE, Geny S, Nguyen CH, Pedersen EB, Jørgensen PT, Wengel J, Nilsson L, Smith CIE, Zain R. LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures. Sci Rep 2017; 7:11043. [PMID: 28887512 PMCID: PMC5591256 DOI: 10.1038/s41598-017-09147-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/20/2017] [Indexed: 12/19/2022] Open
Abstract
The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures. Particularly, we investigated the role played by the position and number of locked nucleic acid (LNA) substitutions in the ON when targeting a c-MYC or FXN (Frataxin) sequence. We found that LNA-containing single strand TFOs are conformationally pre-organized for major groove binding. Reduced content of LNA at consecutive positions at the 3'-end of a TFO destabilizes the triplex structure, whereas the presence of Twisted Intercalating Nucleic Acid (TINA) at the 3'-end of the TFO increases the rate and extent of triplex formation. A triplex-specific intercalating benzoquinoquinoxaline (BQQ) compound highly stabilizes LNA-containing triplex structures. Moreover, LNA-substitution in the duplex pyrimidine strand alters the double helix structure, affecting x-displacement, slide and twist favoring triplex formation through enhanced TFO major groove accommodation. Collectively, these findings should facilitate the design of potent anti-gene ONs.
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Affiliation(s)
- Y Vladimir Pabon-Martinez
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Sylvain Geny
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Chi-Hung Nguyen
- Institut Curie, PSL Research University, UMR 9187-U 1196, CNRS-Institut Curie, INSERM, Centre Universitaire, Orsay, France
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
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Sugiyama T, Hasegawa G, Niikura C, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A. PNA monomers fully compatible with standard Fmoc-based solid-phase synthesis of pseudocomplementary PNA. Bioorg Med Chem Lett 2017; 27:3337-3341. [PMID: 28610975 DOI: 10.1016/j.bmcl.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 11/18/2022]
Abstract
Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase. The new PNA monomers reported here would facilitate a wide range of applications, such as antigene PNAs and DNA nanotechnologies.
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Affiliation(s)
- Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Genki Hasegawa
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Chie Niikura
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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Solé A, Delagoutte E, Ciudad CJ, Noé V, Alberti P. Polypurine reverse-Hoogsteen (PPRH) oligonucleotides can form triplexes with their target sequences even under conditions where they fold into G-quadruplexes. Sci Rep 2017; 7:39898. [PMID: 28067256 PMCID: PMC5220335 DOI: 10.1038/srep39898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 11/28/2016] [Indexed: 02/03/2023] Open
Abstract
Polypurine reverse-Hoogsteen (PPRH) oligonucleotides are non-modified DNA molecules composed of two mirror-symmetrical polypurine stretches linked by a five-thymidine loop. They can fold into reverse-Hoogsteen hairpins and bind to their polypyrimidine target sequence by Watson-Crick bonds forming a three-stranded structure. They have been successfully used to knockdown gene expression and to repair single-point mutations in cells. In this work, we provide an in vitro characterization (UV and fluorescence spectroscopy, gel electrophoresis and nuclease assays) of the structure and stability of two repair-PPRH oligonucleotides and of the complexes they form with their single-stranded targets. We show that one PPRH oligonucleotide forms a hairpin, while the other folds, in potassium, into a guanine-quadruplex (G4). However, the hairpin-prone oligonucleotide does not form a triplex with its single-stranded target, while the G4-prone oligonucleotide converts from a G4 into a reverse-Hoogsteen hairpin forming a triplex with its target sequence. Our work proves, in particular, that folding of a PPRH oligonucleotide into a G4 does not necessarily impair sequence-specific DNA recognition by triplex formation. It also illustrates an original example of DNA structural conversion of a G4 into a reverse-Hoogsteen hairpin driven by triplex formation; this kind of conversion might occur at particular loci of genomic DNA.
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Affiliation(s)
- Anna Solé
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Emmanuelle Delagoutte
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Carlos J. Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Patrizia Alberti
- Structure et Instability of Genomes, Sorbonne Universités, Muséum National d’Histoire Naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France
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65
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Pyrrolidinyl peptide nucleic acid terminally labeled with fluorophore and end-stacking quencher as a probe for highly specific DNA sequence discrimination. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.10.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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66
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Tanaka M, Shigi N, Komiyama M. Ribonuclease A as Effective Promoter for Unimolecular Invasion of Peptide Nucleic Acid to Double-stranded DNA. CHEM LETT 2016. [DOI: 10.1246/cl.160340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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67
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Asanuma H, Niwa R, Akahane M, Murayama K, Kashida H, Kamiya Y. Strand-invading linear probe combined with unmodified PNA. Bioorg Med Chem 2016; 24:4129-4137. [PMID: 27394693 DOI: 10.1016/j.bmc.2016.06.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022]
Abstract
Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration.
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Affiliation(s)
- Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Rie Niwa
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mariko Akahane
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yukiko Kamiya
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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68
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Futai K, Sumaoka J, Komiyama M. Fabrication of DNA/RNA Hybrids Through Sequence-Specific Scission of Both Strands by pcPNA-S1 Nuclease Combination. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:233-44. [PMID: 27057646 DOI: 10.1080/15257770.2015.1131294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
By combining two strands of pseudo-complementary peptide nucleic acid (pcPNA) with S1 nuclease, a tool for site-selective and dual-strand scission of DNA/RNA hybrids has been developed. Both of the DNA and the RNA strands in the hybrids are hydrolyzed at desired sites to provide unique sticky ends. The scission fragments are directly ligated with other DNA/RNA hybrids by using T4 DNA ligase, resulting in the formation of desired recombinant DNA/RNA hybrids.
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69
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Anderson BA, Hrdlicka PJ. Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes. J Org Chem 2016; 81:3335-46. [PMID: 26998918 PMCID: PMC4836393 DOI: 10.1021/acs.joc.6b00369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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The development of molecular strategies
that enable recognition
of specific double-stranded DNA (dsDNA) regions has been a longstanding
goal as evidenced by the emergence of triplex-forming oligonucleotides,
peptide nucleic acids (PNAs), minor groove binding polyamides, and—more
recently—engineered proteins such as CRISPR/Cas9. Despite this
progress, an unmet need remains for simple hybridization-based probes
that recognize specific mixed-sequence dsDNA regions under physiological
conditions. Herein, we introduce pseudocomplementary Invader probes as a step in this direction. These double-stranded probes
are chimeras between pseudocomplementary DNA (pcDNA) and Invader probes,
which are activated for mixed-sequence dsDNA-recognition through the
introduction of pseudocomplementary base pairs comprised of 2-thiothymine
and 2,6-diaminopurine, and +1 interstrand zipper arrangements of intercalator-functionalized
nucleotides, respectively. We demonstrate that certain pseudocomplementary
Invader probe designs result in very efficient and specific recognition
of model dsDNA targets in buffers of high ionic strength. These chimeric
probes, therefore, present themselves as a promising strategy for
mixed-sequence recognition of dsDNA targets for applications in molecular
biology and nucleic acid diagnostics.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, University of Idaho , Moscow, Idaho 83844-2343, United States
| | - Patrick J Hrdlicka
- Department of Chemistry, University of Idaho , Moscow, Idaho 83844-2343, United States
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70
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Geny S, Moreno PMD, Krzywkowski T, Gissberg O, Andersen NK, Isse AJ, El-Madani AM, Lou C, Pabon YV, Anderson BA, Zaghloul EM, Zain R, Hrdlicka PJ, Jørgensen PT, Nilsson M, Lundin KE, Pedersen EB, Wengel J, Smith CIE. Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes. Nucleic Acids Res 2016; 44:2007-19. [PMID: 26857548 PMCID: PMC4797291 DOI: 10.1093/nar/gkw021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson–Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson–Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2′-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
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Affiliation(s)
- Sylvain Geny
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden INEB-Instituto de Engenharia Biomedica, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Tomasz Krzywkowski
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Olof Gissberg
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Nicolai K Andersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Abdirisaq J Isse
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Amro M El-Madani
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Chenguang Lou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Y Vladimir Pabon
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | | | - Eman M Zaghloul
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | | | - Per T Jørgensen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Erik B Pedersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
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71
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Guenther DC, Karmakar S, Hrdlicka PJ. Bulged Invader probes: activated duplexes for mixed-sequence dsDNA recognition with improved thermodynamic and kinetic profiles. Chem Commun (Camb) 2015; 51:15051-4. [PMID: 26314212 PMCID: PMC4589525 DOI: 10.1039/c5cc06264k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Double-stranded oligonucleotides with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides are energetically activated for recognition of mixed-sequence double-stranded DNA. Incorporation of nonyl (C9) bulges at specific positions of these probes, results in more highly affine (>5-fold), faster (>4-fold) and more persistent dsDNA recognition relative to conventional Invader probes.
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Affiliation(s)
- Dale C Guenther
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, Moscow, ID 83844-2343, USA.
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72
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Bahal R, Quijano E, McNeer NA, Liu Y, Bhunia DC, Lopez-Giraldez F, Fields RJ, Saltzman WM, Ly DH, Glazer PM. Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition. Curr Gene Ther 2015; 14:331-42. [PMID: 25174576 DOI: 10.2174/1566523214666140825154158] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 01/13/2023]
Abstract
Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peter M Glazer
- Yale School of Medicine, Dept. of Therapeutic Radiology, P.O. Box 208040, New Haven, Connecticut 06520-8040, USA.
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73
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Anderson BA, Hrdlicka PJ. Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine. Bioorg Med Chem Lett 2015; 25:3999-4004. [PMID: 26254942 PMCID: PMC4540677 DOI: 10.1016/j.bmcl.2015.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 01/11/2023]
Abstract
Pyrene-functionalized oligonucleotides are intensively explored for applications in materials science and diagnostics. Here, we describe a short synthetic route to 2'-S-(pyren-1-yl)methyl-2'-thiouridine monomer S, its incorporation into oligodeoxyribonucleotides (ONs), and biophysical characterization thereof. Pseudorotational analysis reveals that the furanose ring of this monomer has a slight preference for South-type conformations. ONs modified with monomer S display high cDNA affinity but decreased binding specificity. Hybridization is associated with bathochromic shifts of pyrene absorption bands and quenching of pyrene fluorescence consistent with an intercalative binding mode of the pyrene moiety. Monomer S was also evaluated as a building block for mixed-sequence recognition of double-stranded DNA via the Invader strategy. However, probes with +1 interstrand arrangements of monomer S were found to be less efficient than Invader probes based on 2'-O-(pyren-1-yl)methyluridine or 2'-N-(pyren-1-yl)methyl-2'-N-methyl-2'-aminouridine.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, United States
| | - Patrick J Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, United States.
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74
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Guenther DC, Anderson GH, Karmakar S, Anderson BA, Didion BA, Guo W, Verstegen JP, Hrdlicka PJ. Invader probes: Harnessing the energy of intercalation to facilitate recognition of chromosomal DNA for diagnostic applications. Chem Sci 2015; 6:5006-5015. [PMID: 26240741 PMCID: PMC4521421 DOI: 10.1039/c5sc01238d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/10/2015] [Indexed: 01/01/2023] Open
Abstract
Development of probes capable of recognizing specific regions of chromosomal DNA has been a long-standing goal for chemical biologists. Current strategies such as PNA, triplex-forming oligonucleotides, and polyamides are subject to target choice limitations and/or necessitate non-physiological conditions, leaving a need for alternative approaches. Toward this end, we have recently introduced double-stranded oligonucleotide probes that are energetically activated for DNA recognition through modification with +1 interstrand zippers of intercalator-functionalized nucleotide monomers. Here, probes with different chemistries and architectures - varying in the position, number, and distance between the intercalator zippers - are studied with respect to hybridization energetics and DNA-targeting properties. Experiments with model DNA targets demonstrate that optimized probes enable efficient (C50 < 1 μM), fast (t50 < 3h), kinetically stable (> 24h), and single nucleotide specific recognition of DNA targets at physiologically relevant ionic strengths. Optimized probes were used in non-denaturing fluorescence in situ hybridization experiments for detection of gender-specific mixed-sequence chromosomal DNA target regions. These probes present themselves as a promising strategy for recognition of chromosomal DNA, which will enable development of new tools for applications in molecular biology, genomic engineering and nanotechnology.
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Affiliation(s)
- Dale C. Guenther
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
| | - Grace H. Anderson
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
- Department of Biological Sciences , Montana Tech of the University of Montana , 1300 W Park St , Butte , MT 59701-8997 , USA
| | - Saswata Karmakar
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
| | - Brooke A. Anderson
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
| | | | - Wei Guo
- MoFA , PO Box 930187, 419 Venture Ct. , Verona , WI 53593 , USA
| | | | - Patrick J. Hrdlicka
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
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75
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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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76
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Anderson BA, Karmakar S, Hrdlicka PJ. Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes. Molecules 2015; 20:13780-93. [PMID: 26230684 PMCID: PMC6332310 DOI: 10.3390/molecules200813780] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 12/23/2022] Open
Abstract
Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA) continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-N-(pyren-1-yl)methyl-2'-N-methyl-2'-aminouridine and 2'-O-(pyren-1-yl)methyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders). The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
| | - Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
| | - Patrick J Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
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77
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Vilaivan T. Pyrrolidinyl PNA with α/β-Dipeptide Backbone: From Development to Applications. Acc Chem Res 2015; 48:1645-56. [PMID: 26022340 DOI: 10.1021/acs.accounts.5b00080] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The specific pairing between two complementary nucleobases (A·T, C·G) according to the Watson-Crick rules is by no means unique to natural nucleic acids. During the past few decades a number of nucleic acid analogues or mimics have been developed, and peptide nucleic acid (PNA) is one of the most intriguing examples. In addition to forming hybrids with natural DNA/RNA as well as itself with high affinity and specificity, the uncharged peptide-like backbone of PNA confers several unique properties not observed in other classes of nucleic acid analogues. PNA is therefore suited to applications currently performed by conventional oligonucleotides/analogues and others potentially beyond this. In addition, PNA is also interesting in its own right as a new class of oligonucleotide mimics. Unlimited opportunities exist to modify the PNA structure, stimulating the search for new systems with improved properties or additional functionality not present in the original PNA, driving future research and applications of these in nanotechnology and beyond. Although many structural variations of PNA exist, significant improvements to date have been limited to a few constrained derivatives of the privileged N-2-aminoethylglycine PNA scaffold. In this Account, we summarize our contributions in this field: the development of a new family of conformationally constrained pyrrolidinyl PNA having a nonchimeric α/β-dipeptide backbone derived from nucleobase-modified proline and cyclic β-amino acids. The conformational constraints dictated by the pyrrolidine ring and the β-amino acid are essential requirements determining the binding efficiency, as the structure and stereochemistry of the PNA backbone significantly affect its ability to interact with DNA, RNA, and in self-pairing. The modular nature of the dipeptide backbone simplifies the synthesis and allows for rapid structural optimization. Pyrrolidinyl PNA having a (2'R,4'R)-proline/(1S,2S)-2-aminocyclopentanecarboxylic backbone (acpcPNA) binds to DNA with outstanding affinity and sequence specificity. It also binds to RNA in a highly sequence-specific fashion, albeit with lower affinity than to DNA. Additional characteristics include exclusive antiparallel/parallel selectivity and a low tendency for self-hybridization. Modification of the nucleobase or backbone allowing site-specific incorporation of labels and other functions to acpcPNA via click and other conjugation chemistries is possible, generating functional PNAs that are suitable for various applications. DNA sensing and biological applications of acpcPNA have been demonstrated, but these are still in their infancy and the full potential of pyrrolidinyl PNA is yet to be realized. With properties competitive with, and in some aspects superior to, the best PNA technology available to date, pyrrolidinyl PNA offers great promise as a platform system for future elaboration for the fabrication of new functional materials, nanodevices, and next-generation analytical tools.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research
Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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78
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Manna A, Rapireddy S, Sureshkumar G, Ly DH. Synthesis of optically pure γPNA monomers: a comparative study. Tetrahedron 2015; 71:3507-3514. [PMID: 30792557 PMCID: PMC6379906 DOI: 10.1016/j.tet.2015.03.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We report a systematic study examining two synthetic routes, reductive amination and Mitsunobu coupling, for preparation of chiral γ-peptide nucleic acid (γPNA) monomers and oligomers. We found that the reductive amination route is prone to epimerization, even under mild experimental conditions. The extent of epimerization could be minimized by utilizing a bulky protecting group such as PhFl; however, it is difficult to remove in the subsequent oligomer synthesis stage. On the other hand, we found that the Mitsunobu route produced optically superior products using standard carbamate protecting groups.
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Affiliation(s)
- Arunava Manna
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Gopalsamy Sureshkumar
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
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79
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Anderson BA, Onley JJ, Hrdlicka PJ. Recognition of Double-Stranded DNA Using Energetically Activated Duplexes Modified with N2'-Pyrene-, Perylene-, or Coronene-Functionalized 2'-N-Methyl-2'-amino-DNA Monomers. J Org Chem 2015; 80:5395-406. [PMID: 25984765 DOI: 10.1021/acs.joc.5b00742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Invader probes have been proposed as alternatives to polyamides, triplex-forming oligonucleotides, and peptide nucleic acids for recognition of chromosomal DNA targets. These double-stranded probes are activated for DNA recognition by +1 interstrand zippers of pyrene-functionalized nucleotides. This particular motif forces the intercalating pyrene moieties into the same region, resulting in perturbation and destabilization of the probe duplex. In contrast, the two probe strands display very high affinity toward complementary DNA. The energy difference between the probe duplexes and recognition complexes provides the driving force for DNA recognition. In the present study, we explore the properties of Invader probes based on larger intercalators, i.e., perylene and coronene, expecting that the larger π-surface area will result in additional destabilization of the probe duplex and further stabilization of probe-target duplexes, in effect increasing the thermodynamic driving force for DNA recognition. Toward this end, we developed protocols for 2'-N-methyl-2'-amino-2'-deoxyuridine phosphoramidites that are functionalized at the N2'-position with pyrene, perylene, or coronene moieties and incorporated these monomers into oligodeoxyribonucleotides (ONs). The resulting ONs and Invader probes are characterized by thermal denaturation experiments, analysis of thermodynamic parameters, absorption and fluorescence spectroscopy, and DNA recognition experiments. Invader probes based on large intercalators efficiently recognize model targets.
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Affiliation(s)
- Brooke A Anderson
- †Department of Chemistry, University of Idaho, Moscow, Idaho 83844, United States
| | - Jared J Onley
- †Department of Chemistry, University of Idaho, Moscow, Idaho 83844, United States.,‡Department of Chemistry, Whitworth University, Spokane, Washington 99251, United States
| | - Patrick J Hrdlicka
- †Department of Chemistry, University of Idaho, Moscow, Idaho 83844, United States
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80
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Barluenga S, Winssinger N. PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions. Acc Chem Res 2015; 48:1319-31. [PMID: 25947113 DOI: 10.1021/acs.accounts.5b00109] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The programmability of oligonucleotide hybridization offers an attractive platform for the design of assemblies with emergent properties or functions. Developments in DNA nanotechnologies have transformed our thinking about the applications of nucleic acids. Progress from designed assemblies to functional outputs will continue to benefit from functionalities added to the nucleic acids that can participate in reactions or interactions beyond hybridization. In that respect, peptide nucleic acids (PNAs) are interesting because they combine the hybridization properties of DNA with the modularity of peptides. In fact, PNAs form more stable duplexes with DNA or RNA than the corresponding natural homoduplexes. The high stability achieved with shorter oligomers (an 8-mer is sufficient for a stable duplex at room temperature) typically results in very high sequence fidelity in the hybridization with negligible impact of the ionic strength of the buffer due to the lack of electrostatic repulsion between the duplex strands. The simple peptidic backbone of PNA has been shown to be tolerant of modifications with substitutions that further enhance the duplex stability while providing opportunities for functionalization. Moreover, the metabolic stability of PNAs facilitates their integration into systems that interface with biology. Over the past decade, there has been a growing interest in using PNAs as biosupramolecular tags to program assemblies and reactions. A series of robust templated reactions have been developed with functionalized PNA. These reactions can be used to translate DNA templates into functional polymers of unprecedented complexity, fluorescent outputs, or bioactive small molecules. Furthermore, cellular nucleic acids (mRNA or miRNA) have been harnessed to promote assemblies and reactions in live cells. The tolerance of PNA synthesis also lends itself to the encoding of small molecules that can be further assembled on the basis of their nucleic acid sequences. It is now well-established that hybridization-based assemblies displaying two or more ligands can interact synergistically with a target biomolecule. These assemblies have now been shown to be functional in vivo. Similarly, PNA-tagged macromolecules have been used to prepare bioactive assemblies and three-dimensional nanostructures. Several technologies based on DNA-templated synthesis of sequence-defined polymers or DNA-templated display of ligands have been shown to be compatible with reiterative cycles of selection/amplification starting with large libraries of DNA templates, bringing the power of in vitro evolution to synthetic molecules and offering the possibility of exploring uncharted molecular diversity space with unprecedented scope and speed.
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Affiliation(s)
- Sofia Barluenga
- Department of Organic Chemistry,
NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
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81
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Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 2015; 66:297-307. [DOI: 10.1016/j.bios.2014.11.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/28/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
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82
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Abstract
Triplex-forming oligonucleotides (TFOs) are capable of coordinating genome modification in a targeted, site-specific manner, causing mutagenesis or even coordinating homologous recombination events. Here, we describe the use of TFOs such as peptide nucleic acids for targeted genome modification. We discuss this method and its applications and describe protocols for TFO design, delivery, and evaluation of activity in vitro and in vivo.
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83
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Aiba Y, Honda Y, Komiyama M. Promotion of double-duplex invasion of peptide nucleic acids through conjugation with nuclear localization signal peptide. Chemistry 2015; 21:4021-6. [PMID: 25640012 DOI: 10.1002/chem.201406085] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/10/2022]
Abstract
Pseudo-complementary peptide nucleic acid (pcPNA), as one of the most widely used synthetic DNA analogues, invades double-stranded DNA according to Watson-Crick rules to form invasion complexes. This unique mode of DNA recognition induces structural changes at the invasion site and can be used for a range of applications. In this paper, pcPNA is conjugated with a nuclear localization signal (NLS) peptide, and its invading activity is notably promoted both thermodynamically and kinetically. Thus, the double-duplex invasion complex is formed promptly at low pcPNA concentrations under high salt conditions, where the invasion otherwise never occurs. Furthermore, NLS-modified pcPNA is successfully employed for site-selective DNA scission, and the targeted DNA is selectively cleaved under conditions that are not conducive for DNA cutters using unmodified pcPNAs. This strategy of pcPNA modification is expected to be advantageous and promising for a range of in vitro and in vivo applications.
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Affiliation(s)
- Yuichiro Aiba
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577 (Japan); Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Present address: Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041 (USA)
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84
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Artificial Nucleic Acid Probes and Their Applications in Clinical Microbiology. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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85
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Komiyama M. Chemical modifications of artificial restriction DNA cutter (ARCUT) to promote its in vivo and in vitro applications. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1112457. [PMID: 26744220 PMCID: PMC5329899 DOI: 10.1080/1949095x.2015.1112457] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 05/10/2023]
Abstract
Recently, completely chemistry-based tools for site-selective scission of DNA (ARCUT) have been prepared by combining 2 strands of pseudo-complementary PNA (pcPNA: site-selective activator) and a Ce(IV)-EDTA complex (molecular scissors). Its site-specificity is sufficient to cut the whole human genome at one predetermined site. In this first-generation ARCUT, however, there still remain several problems to be solved for wider applications. This review presents recent approaches to solve these problems. They are divided into (i) covalent modification of pcPNA with other functional groups and (ii) new strategies using conventional PNA, in place of pcPNA, as site-selective activator. Among various chemical modifications, conjugation with positively-charged nuclear localization signal peptide is especially effective. Furthermore, unimolecular activators, a single strand of which successfully activates the target site in DNA for site-selective scission, have been also developed. As the result of these modifications, the site-selective scission by Ce(IV)-EDTA was achieved promptly even under high salt conditions which are otherwise unfavourable for double-duplex invasion. Furthermore, it has been shown that "molecular crowding effect," which characterizes the inside of living cells, enormously promotes the invasion, and thus the invasion seems to proceed effectively and spontaneously in the cells. Strong potential of pcPNA for further applications in vivo and in vitro has been confirmed.
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Affiliation(s)
- Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance; University of Tsukuba; Tsukuba, Ibaraki, Japan
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86
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Moccia M, Adamo MFA, Saviano M. Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1107176. [PMID: 26752710 PMCID: PMC5329900 DOI: 10.1080/1949095x.2015.1107176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022]
Abstract
PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed.
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Affiliation(s)
- Maria Moccia
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
| | - Mauro F A Adamo
- Centre for Synthesis and Chemical Biology (CSCB); Department of Pharmaceutical & Medicinal Chemistry; Royal College of Surgeons in Ireland; Dublin, Ireland
| | - Michele Saviano
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
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87
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Olsen AG, Dahl O, Petersen AB, Nielsen J, Nielsen PE. A novel pseudo-complementary PNA G-C base pair. ARTIFICIAL DNA, PNA & XNA 2014; 2:33-37. [PMID: 21686250 DOI: 10.4161/adna.2.1.15554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/18/2011] [Accepted: 03/22/2011] [Indexed: 01/02/2023]
Abstract
Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting of the unnatural nucleobases n6-methoxy-2,6-diaminopurine (previously described in a DNA context) and N4-benzoylcytosine is now presented for design of pseudo-complementary PNA oligomers (pcPNAs).
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Affiliation(s)
- Anne G Olsen
- Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; University of Copenhagen; Copenhagen, Denmark
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88
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Kuhn H, Sahu B, Rapireddy S, Ly DH, Frank-Kamenetskii MD. Sequence specificity at targeting double-stranded DNA with a γ-PNA oligomer modified with guanidinium G-clamp nucleobases. ARTIFICIAL DNA, PNA & XNA 2014; 1:45-53. [PMID: 21687526 DOI: 10.4161/adna.1.1.12444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 05/19/2010] [Accepted: 05/24/2010] [Indexed: 11/19/2022]
Abstract
γ-PNA, a new class of peptide nucleic acids, promises to overcome previous sequence limitations of double-stranded DNA (dsDNA) targeting with PNA. To check the potential of γ-PNA, we have synthesized a biotinylated, pentadecameric γ-PNA of mixed sequence carrying three guanidinium G-clamp nucleobases. We have found that strand invasion reactions of the γ-PNA oligomer to its fully complementary target within dsDNA occurs with significantly higher binding rates than to targets containing single mismatches. Association of the PNA oligomer to mismatched targets does not go to completion but instead reaches a stationary level at or below 60%, even at conditions of very low ionic strength. Initial binding rates to both matched and mismatched targets experience a steep decrease with increasing salt concentration. We demonstrate that a linear DNA target fragment with the correct target sequence can be purified from DNA mixtures containing mismatched target or unrelated genomic DNA by affinity capture with streptavidin-coated magnetic beads. Similarly, supercoiled plasmid DNA is obtained with high purity from an initial sample mixture that included a linear DNA fragment with the fully complementary sequence. Based on the results obtained in this study we believe that γ-PNA has a great potential for specific targeting of chosen duplex DNA sites in a sequence-unrestricted fashion.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology; Department of Biomedical Engineering; Boston University; Boston, MA USA
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89
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Karmakar S, Madsen AS, Guenther DC, Gibbons BC, Hrdlicka PJ. Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers. Org Biomol Chem 2014; 12:7758-73. [PMID: 25144705 PMCID: PMC4167914 DOI: 10.1039/c4ob01183j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and--more recently--engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2'-alkylated uridine monomers X-Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔT(m)/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID 83844, USA.
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90
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Solé A, Villalobos X, Ciudad CJ, Noé V. Repair of single-point mutations by polypurine reverse Hoogsteen hairpins. Hum Gene Ther Methods 2014; 25:288-302. [PMID: 25222154 DOI: 10.1089/hgtb.2014.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Polypurine reverse Hoogsteen hairpins (PPRHs) are formed by two intramolecularly bound antiparallel homopurine domains linked by a five-thymidine loop. One of the homopurine strands binds with antiparallel orientation by Watson-Crick bonds to the polypyrimidine target sequence, forming a triplex. We had previously reported the ability of PPRHs to effectively bind dsDNA displacing the fourth strand away from the newly formed triplex. The main goal of this work was to explore the possibility of repairing a point mutation in mammalian cells using PPRHs as tools. These repair-PPRHs contain different combinations of extended sequences of DNA with the corrected nucleotide to repair the point mutation. As a model we used the dihydrofolate reductase gene. On the one hand, we demonstrate in vitro that PPRHs bind specifically to their polypyrimidine target sequence, opening the two strands of the dsDNA, and allowing the binding of a given repair oligonucleotide to the displaced strand of the DNA. Subsequently, we show at a cellular level (Chinese ovary hamster cells) that repair-PPRHs are able to correct a single-point mutation in a dihydrofolate reductase minigene bearing a nonsense mutation, both in an extrachromosomal location and when the mutated plasmid was stably transfected into the cells. Finally, this methodology was successfully applied to repair a single-point mutation at the endogenous locus, using the DA5 cell line with a deleted nucleotide in exon six of the dhfr gene.
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Affiliation(s)
- Anna Solé
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , E08028 Barcelona, Spain
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91
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Pham HH, Murphy CT, Sureshkumar G, Ly DH, Opresko PL, Armitage BA. Cooperative hybridization of γPNA miniprobes to a repeating sequence motif and application to telomere analysis. Org Biomol Chem 2014; 12:7345-7354. [PMID: 25115693 PMCID: PMC4162129 DOI: 10.1039/c4ob00953c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
GammaPNA oligomers having one or two repeats of the sequence AATCCC were designed to hybridize to DNA having one or more repeats of the complementary TTAGGG sequence found in the human telomere. UV melting curves and surface plasmon resonance experiments demonstrate high affinity and cooperativity for hybridization of these miniprobes to DNA having multiple complementary repeats. Fluorescence spectroscopy for Cy3-labeled miniprobes demonstrate increases in fluorescence intensity for assembling multiple short probes on a DNA target compared with fewer longer probes. The fluorescent γPNA miniprobes were then used to stain telomeres in metaphase chromosomes derived from U2OS cells possessing heterogeneous long telomeres and Jurkat cells harboring homogenous short telomeres. The miniprobes yielded comparable fluorescence intensity to a commercially available PNA 18mer probe in U2OS cells, but significantly brighter fluorescence was observed for telomeres in Jurkat cells. These results suggest that γPNA miniprobes can be effective telomere-staining reagents with applications toward analysis of critically short telomeres, which have been implicated in a range of human diseases.
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Affiliation(s)
- Ha H. Pham
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Connor T. Murphy
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Environmental and Occupational Health, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15219
| | - Gopalsamy Sureshkumar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Danith H. Ly
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Patricia L. Opresko
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Environmental and Occupational Health, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15219
| | - Bruce A. Armitage
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
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92
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Murphy CT, Gupta A, Armitage BA, Opresko PL. Hybridization of G-quadruplex-forming peptide nucleic acids to guanine-rich DNA templates inhibits DNA polymerase η extension. Biochemistry 2014; 53:5315-22. [PMID: 25068499 DOI: 10.1021/bi5006859] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The guanine quadruplex (G-quadruplex) is a highly stable secondary structure that forms in G-rich repeats of DNA, which can interfere with DNA processes, including DNA replication and transcription. We showed previously that short guanine-rich peptide nucleic acids (PNAs) can form highly stable hybrid quadruplexes with DNA. We hypothesized that such structures would provide a stronger block to polymerase extension on G-rich templates than a native DNA homoquadruplex because of the greater thermodynamic stability of the PNA-DNA hybrid structures. To test this, we analyzed the DNA primer extension activity of polymerase η, a translesion polymerase implicated in synthesis past G-quadruplex blocks, on DNA templates containing guanine repeats. We observed a PNA concentration-dependent decrease in the level of polymerase η extension to the end of the template and an increase in the level of polymerase η inhibition at the sequence prior to the G-rich repeats. In contrast, the addition of a complementary C-rich PNA that hybridizes to the G-rich repeats by Watson-Crick base pairing led to a decrease in the level of polymerase inhibition and an increase in the level of full-length extension products. The G-quadruplex-forming PNA exhibited inhibition (IC50=16.2±3.3 nM) of polymerase η DNA synthesis on the G-rich templates stronger than that of the established G-quadruplex-stabilizing ligand BRACO-19 (IC50=42.5±4.8 nM). Our results indicate that homologous PNA targeting of G-rich sequences creates stable PNA-DNA heteroquadruplexes that inhibit polymerase η extension more effectively than a DNA homoquadruplex. The implications of these results for the potential development of homologous PNAs as therapeutics for halting proliferating cancer cells are discussed.
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Affiliation(s)
- Connor T Murphy
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health , Pittsburgh, Pennsylvania 15219, United States
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93
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Jester SS, Famulok M. Mechanically interlocked DNA nanostructures for functional devices. Acc Chem Res 2014; 47:1700-9. [PMID: 24627986 DOI: 10.1021/ar400321h] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: Self-assembled functional DNA oligonucleotide based architectures represent highly promising candidates for the creation of nanoscale devices. The field of DNA nanotechnology has emerged to a high level of maturity and currently constitutes one of the most dynamic, creative, and exciting modern research areas. The transformation from structural DNA nanotechnology to functional DNA architectures is already taking place with tremendous pace. Particularly the advent of DNA origami technology has propelled DNA nanotechnology forward. DNA origami provided a versatile method for precisely aligning structural and functional DNA modules in two and three dimensions, thereby serving as a means for constructing scaffolds and chassis required for the precise orchestration of multiple functional DNA architectures. Key modules of these will contain interlocked nanomechanical components made of DNA. The mechanical interlocking allows for performing highly specific and controlled motion, by reducing the dimensionality of diffusion-controlled processes without restrictions in motional flexibility. Examples for nanoscale interlocked DNA architectures illustrate how elementary functional units of future nanomachines can be designed and realized, and show what role interlocked DNA architectures may play in this endeavor. Functional supramolecular systems, in general, and nanomachinery, in particular, self-organize into architectures that reflect different levels of complexity with respect to their function, their arrangement in the second and third dimension, their suitability for different purposes, and their functional interplay. Toward this goal, DNA nanotechnology and especially the DNA origami technology provide opportunities for nanomechanics, nanorobotics, and nanomachines. In this Account, we address approaches that apply to the construction of interlocked DNA nanostructures, drawing largely form our own contributions to interlocked architectures based on double-stranded (ds) circular geometries, and describe progress, opportunities, and challenges in rotaxanes and pseudorotaxanes made of dsDNA. Operating nanomechanical devices in a reliable and repetitive fashion requires methods for switching movable parts in DNA nanostructures from one state to another. An important issue is the orthogonality of switches that allow for operating different parts in parallel under spatiotemporal control. A variety of switching methods have been applied to switch individual components in interlocked DNA nanostructures like rotaxanes and catenanes. They are based on toehold, light, pseudocomplementary peptide nucleic acids (pcPNAs), and others. The key issues discussed here illustrate our perspective on the future prospects of interlocked DNA-based devices and the challenges that lay ahead.
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Affiliation(s)
- Stefan-S. Jester
- Kekulé-Institut für Organische Chemie und Biochemie and ‡LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und BiochemieUniversität Bonn, Gerhard-Domagk-Straße. 1, 53121 Bonn, Germany
| | - Michael Famulok
- Kekulé-Institut für Organische Chemie und Biochemie and ‡LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und BiochemieUniversität Bonn, Gerhard-Domagk-Straße. 1, 53121 Bonn, Germany
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94
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Aiba Y, Hamano Y, Kameshima W, Araki Y, Wada T, Accetta A, Sforza S, Corradini R, Marchelli R, Komiyama M. PNA-NLS conjugates as single-molecular activators of target sites in double-stranded DNA for site-selective scission. Org Biomol Chem 2014; 11:5233-8. [PMID: 23820872 DOI: 10.1039/c3ob40947c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Artificial DNA cutters have been developed by us in our previous studies by combining two strands of pseudo-complementary peptide nucleic acid (pcPNA) with Ce(IV)-EDTA-promoted hydrolysis. The pcPNAs have two modified nucleobases (2,6-diaminopurine and 2-thiouracil) instead of conventional A and T, and can invade double-stranded DNA to activate the target site for the scission. This system has been applied to site-selective scissions of plasmid, λ-phage, E. coli genomic DNA, and human genomic DNA. Here, we have reported a still simpler and more convenient DNA cutter obtained by conjugating peptide nucleic acid (PNA) with a nuclear localization signal (NLS) peptide. This new DNA cutter requires only one PNA strand (instead of two) bearing conventional (non-pseudo-complementary) nucleobases. This PNA-NLS conjugate effectively activated the target site in double-stranded DNA and induced site-selective scission by Ce(IV)-EDTA. The complex formation between the conjugate and DNA was concretely evidenced by spectroscopic results based on time-resolved fluorescence. The target scission site of this new system was straightforwardly determined by the Watson-Crick base pairing rule, and mismatched sequences were clearly discriminated. Importantly, even highly GC-rich regions, which are difficult to be targeted by a previous strategy using pcPNA, were successfully targeted. All these features of the present DNA cutter make it promising for various future applications.
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Affiliation(s)
- Yuichiro Aiba
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577, Japan
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95
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Devi G, Yuan Z, Lu Y, Zhao Y, Chen G. Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes. Nucleic Acids Res 2014; 42:4008-18. [PMID: 24423869 PMCID: PMC3973316 DOI: 10.1093/nar/gkt1367] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Peptide nucleic acids (PNAs) have been developed for applications in biotechnology and therapeutics. There is great potential in the development of chemically modified PNAs or other triplex-forming ligands that selectively bind to RNA duplexes, but not single-stranded regions, at near-physiological conditions. Here, we report on a convenient synthesis route to a modified PNA monomer, thio-pseudoisocytosine (L), and binding studies of PNAs incorporating the monomer L. Thermal melting and gel electrophoresis studies reveal that L-incorporated 8-mer PNAs have superior affinity and specificity in recognizing the duplex region of a model RNA hairpin to form a pyrimidine motif major-groove RNA2–PNA triplex, without appreciable binding to single-stranded regions to form an RNA–PNA duplex or, via strand invasion, forming an RNA–PNA2 triplex at near-physiological buffer condition. In addition, an L-incorporated 8-mer PNA shows essentially no binding to single-stranded or double-stranded DNA. Furthermore, an L-modified 6-mer PNA, but not pseudoisocytosine (J) modified or unmodified PNA, binds to the HIV-1 programmed −1 ribosomal frameshift stimulatory RNA hairpin at near-physiological buffer conditions. The stabilization of an RNA2–PNA triplex by L modification is facilitated by enhanced van der Waals contacts, base stacking, hydrogen bonding and reduced dehydration energy. The destabilization of RNA–PNA and DNA–PNA duplexes by L modification is due to the steric clash and loss of two hydrogen bonds in a Watson–Crick-like G–L pair. An RNA2–PNA triplex is significantly more stable than a DNA2–PNA triplex, probably because the RNA duplex major groove provides geometry compatibility and favorable backbone–backbone interactions with PNA. Thus, L-modified triplex-forming PNAs may be utilized for sequence-specifically targeting duplex regions in RNAs for biological and therapeutic applications.
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Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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96
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Ito K, Komiyama M. Site-selective scission of human genome using PNA-based artificial restriction DNA cutter. Methods Mol Biol 2014; 1050:111-120. [PMID: 24297354 DOI: 10.1007/978-1-62703-553-8_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Site-selective scission of genomes is quite important for future biotechnology. However, naturally occurring restriction enzymes cut these huge DNAs at too many sites and cannot be used for this purpose. Recently, we have developed a completely chemistry-based artificial restriction DNA cutter (ARCUT) by combining a pair of pseudo-complementary PNA (pcPNA) strands (sequence recognition moiety) and Ce(IV)/EDTA complex (molecular scissors). The scission site of ARCUT and its scission specificity can be freely modulated in terms of the sequences and lengths of the pcPNA strands so that even huge genomes can be selectively cut at only one predetermined site. In this chapter, the method of site-selective scission of human genomic DNA using ARCUT is described in detail.
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Affiliation(s)
- Kenichiro Ito
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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97
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Tanaka M, Shigi N, Sumaoka J, Komiyama M. Thiazole orange-conjugated peptide nucleic acid for fluorescent detection of specific DNA sequences and site-selective photodamage. RSC Adv 2014. [DOI: 10.1039/c4ra13780a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugates of thiazole orange (TO) with a pseudo-complementary peptide nucleic acid (pcPNA) functioned as (i) fluorescent detector of specific DNA and (ii) site-selective photodamage inducer through generation of 1O2.
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Affiliation(s)
- Makiko Tanaka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
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98
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Morihiro K, Kodama T, Mori S, Obika S. Photoinduced changes in hydrogen bonding patterns of 8-thiopurine nucleobase analogues in a DNA strand. Org Biomol Chem 2014; 12:2468-73. [DOI: 10.1039/c3ob42427h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoinduced changes in hydrogen bonding patterns have a strong effect on base recognition by nucleobase analogues.
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Affiliation(s)
- Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Suita, Japan
- National Institute of Biomedical Innovation (NIBIO)
- Ibaraki, Japan
| | - Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences
- Nagoya University
- Nagoya, Japan
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Suita, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Suita, Japan
- National Institute of Biomedical Innovation (NIBIO)
- Ibaraki, Japan
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99
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Karmakar S, Guenther DC, Hrdlicka PJ. Recognition of mixed-sequence DNA duplexes: design guidelines for invaders based on 2'-O-(pyren-1-yl)methyl-RNA monomers. J Org Chem 2013; 78:12040-8. [PMID: 24195730 PMCID: PMC3903098 DOI: 10.1021/jo402085v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The development of agents that recognize mixed-sequence double-stranded DNA (dsDNA) is desirable because of their potential as tools for detection, regulation, and modification of genes. Despite progress with triplex-forming oligonucleotides, peptide nucleic acids, polyamides, and other approaches, recognition of mixed-sequence dsDNA targets remains challenging. Our laboratory studies Invaders as an alternative approach toward this end. These double-stranded oligonucleotide probes are activated for recognition of mixed-sequence dsDNA through modification with +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl-RNA monomers and have recently been shown to recognize linear dsDNA, DNA hairpins, and chromosomal DNA. In the present work, we systematically studied the influence that the nucleobase moieties of the 2'-O-(pyren-1-yl)methyl-RNA monomers have on the recognition efficiency of Invader duplexes. Results from thermal denaturation, binding energy, and recognition experiments using Invader duplexes with different +1 interstrand zippers of the four canonical 2'-O-(pyren-1-yl)methyl-RNA A/C/G/U monomers show that incorporation of these motifs is a general strategy for activation of probes for recognition of dsDNA. Probe duplexes with interstrand zippers comprising C and/or U monomers result in the most efficient recognition of dsDNA. The insight gained from this study will drive the design of efficient Invaders for applications in molecular biology, nucleic acid diagnostics, and biotechnology.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho , 875 Perimeter Drive, MS 2343, Moscow, Idaho 83844-2343, United States
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100
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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of peptide nucleic acid with a pyrrole/imidazole polyamide to specifically recognize and cleave DNA. Angew Chem Int Ed Engl 2013; 52:13681-4. [PMID: 24155125 DOI: 10.1002/anie.201305489] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/03/2013] [Indexed: 11/06/2022]
Abstract
Cut loose: A pseudocomplementary peptide nucleic acid was tethered to a pyrrole/imidazole hairpin polyamide, and was used to selectively target a specific DNA sequence. Binding even occurs under high salt conditions. Furthermore, the conjugate facilitated sequence-specific scission of long dsDNA. This simple approach promises to resolve the technical difficulties in targeting DNA sequences with PNA.
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Affiliation(s)
- Wataru Kameshima
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 (Japan)
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