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Fracchioni G, Vailati S, Grazioli M, Pirota V. Structural Unfolding of G-Quadruplexes: From Small Molecules to Antisense Strategies. Molecules 2024; 29:3488. [PMID: 39124893 PMCID: PMC11314335 DOI: 10.3390/molecules29153488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid secondary structures that have gathered significant interest in medicinal chemistry over the past two decades due to their unique structural features and potential roles in a variety of biological processes and disorders. Traditionally, research efforts have focused on stabilizing G4s, while in recent years, the attention has progressively shifted to G4 destabilization, unveiling new therapeutic perspectives. This review provides an in-depth overview of recent advances in the development of small molecules, starting with the controversial role of TMPyP4. Moreover, we described effective metal complexes in addition to G4-disrupting small molecules as well as good G4 stabilizing ligands that can destabilize G4s in response to external stimuli. Finally, we presented antisense strategies as a promising approach for destabilizing G4s, with a particular focus on 2'-OMe antisense oligonucleotide, peptide nucleic acid, and locked nucleic acid. Overall, this review emphasizes the importance of understanding G4 dynamics as well as ongoing efforts to develop selective G4-unfolding strategies that can modulate their biological function and therapeutic potential.
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Affiliation(s)
- Giorgia Fracchioni
- Department of Chemistry, University of Pavia, via Taramelli 10, 27100 Pavia, Italy; (G.F.); (S.V.); (M.G.)
- G4-INTERACT Group, Universal Scientific Education and Research Network (USERN), 27100 Pavia, Italy
| | - Sabrina Vailati
- Department of Chemistry, University of Pavia, via Taramelli 10, 27100 Pavia, Italy; (G.F.); (S.V.); (M.G.)
- PhD National Program in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Marta Grazioli
- Department of Chemistry, University of Pavia, via Taramelli 10, 27100 Pavia, Italy; (G.F.); (S.V.); (M.G.)
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, via Taramelli 10, 27100 Pavia, Italy; (G.F.); (S.V.); (M.G.)
- G4-INTERACT Group, Universal Scientific Education and Research Network (USERN), 27100 Pavia, Italy
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2
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Mazzini S, Borgonovo G, Princiotto S, Artali R, Musso L, Aviñó A, Eritja R, Gargallo R, Dallavalle S. Quadruplex-duplex junction in LTR-III: A molecular insight into the complexes with BMH-21, namitecan and doxorubicin. PLoS One 2024; 19:e0306239. [PMID: 39046961 PMCID: PMC11268700 DOI: 10.1371/journal.pone.0306239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Quadruplex-Duplex (Q-D) junctions are unique structural motifs garnering increasing interest as drug targets, due to their frequent occurrence in genomic sequences. The viral HIV LTR-III sequence was chosen as a Q-D junction model to study the affinity of the selected compounds BMH-21, namitecan (ST-1968), and doxorubicin (DOXO), all containing a planar polycyclic aromatic moiety, linked to either one short aminoalkyl or an aminoglycosyl group. A multidisciplinary approach that combines NMR spectroscopy, molecular modelling, circular dichroism (CD) and fluorescence spectroscopy was employed. The studied ligands induced moderate but clear stabilization to the Q-D junction by interacting with the interfacial tetrad. DOXO was found to be the best Q-D junction binder. Interestingly, the removal of the aminoglycosyl group significantly changed the pattern of the interactions, indicating that highly polar substituents have a stronger affinity with the exposed regions of the Q-D junction, particularly at the level of the interfacial tetrad.
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Affiliation(s)
- Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Roberto Artali
- Scientia Advice di Roberto Artali, Cesano Maderno (MB), Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), ISCIII, Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), ISCIII, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
- National Institute of Fundamental Studies, Kandy, Sri Lanka
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3
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Ding B, Hong XY, Yin H, Xu JY, Zhang XY, Zhou Q, Shen Y. Detection and Separation of DNA and Silver Nanoparticles Using a Solid-State Nanopore. ACS OMEGA 2023; 8:17682-17688. [PMID: 37251189 PMCID: PMC10210173 DOI: 10.1021/acsomega.3c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023]
Abstract
Nanopore sensors, a new generation of single-molecule sensors, are increasingly used to detect and analyze various analytes and have great potential for rapid gene sequencing. However, there are still some problems in the preparation of small diameter nanopores, such as imprecise pore size and porous defects, while the detection accuracy of large-diameter nanopores is relatively low. Therefore, how to achieve more precise detection of large diameter nanopore sensors is an urgent problem to be studied. Here, SiN nanopore sensors were used to detect DNA molecules and silver nanoparticles (NPs) separately and in combination. The experimental results show that large-size solid-state nanopore sensors can identify and discriminate between DNA molecules, NPs, and NP-bound DNA molecules clearly according to resistive pulses. In addition, the detection mechanism of using NPs to assist in identifying target DNA molecules in this study is different from previous reports. We find that silver NPs can simultaneously bind to multiple probes and target DNA molecules and generate a larger blocking current than free DNA molecules when passing through the nanopore. In conclusion, our research indicates that large-sized nanopores can distinguish the translocation events, thereby identifying the presence of the target DNA molecules in the sample. This nanopore-sensing platform can produce rapid and accurate nucleic acid detection. Its application in medical diagnosis, gene therapy, virus identification, and many other fields is highly significant.
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Affiliation(s)
- Bo Ding
- Department
of Obstetrics and Gynecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Xin-Yi Hong
- Department
of Obstetrics and Gynecology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Han Yin
- Department
of Obstetrics and Gynecology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Jing-Yun Xu
- Department
of Obstetrics and Gynecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Xiao-Yu Zhang
- Department
of Obstetrics and Gynecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Qing Zhou
- Department
of Obstetrics and Gynecology, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yang Shen
- Department
of Obstetrics and Gynecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
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4
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Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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5
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Díaz-Casado L, Serrano-Chacón I, Montalvillo-Jiménez L, Corzana F, Bastida A, Santana AG, González C, Asensio JL. De Novo Design of Selective Quadruplex-Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot-Spot. Chemistry 2021; 27:6204-6212. [PMID: 33368678 DOI: 10.1002/chem.202005026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Indexed: 01/03/2023]
Abstract
Targeting the interface between DNA quadruplex and duplex regions by small molecules holds significant promise in both therapeutics and nanotechnology. Herein, a new pharmacophore is reported, which selectively binds with high affinity to quadruplex-duplex junctions, while presenting a poorer affinity for G-quadruplex or duplex DNA alone. Ligands complying with the reported pharmacophore exhibit a significant affinity and selectivity for quadruplex-duplex junctions, including the one observed in the HIV-1 LTR-III sequence. The structure of the complex between a quadruplex-duplex junction with a ligand of this family has been determined by NMR methods. According to these data, the remarkable selectivity of this structural motif for quadruplex-duplex junctions is achieved through an unprecedented interaction mode so far unexploited in medicinal and biological chemistry: the insertion of a benzylic ammonium moiety into the centre of the partially exposed G-tetrad at the interface with the duplex. Further decoration of the described scaffolds with additional fragments opens up the road to the development of selective ligands for G-quadruplex-forming regions of the genome.
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Affiliation(s)
- Laura Díaz-Casado
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Israel Serrano-Chacón
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Laura Montalvillo-Jiménez
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Madre de Dios, 53., 26006, Logroño, Spain
| | - Agatha Bastida
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
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6
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Abstract
The growing interest in G-quadruplex (G4) structure and function is motivating intense efforts to develop G4-binding ligands. This chapter describes the design and testing of peptide nucleic acid (PNA) oligomers, which can bind to G4 DNA or RNA in two distinct ways, leading to formation of heteroduplexes or heteroquadruplexes. Guidelines for designing G4-targeting PNAs and step-by-step protocols for characterizing their binding through biophysical or biochemical methods are provided.
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7
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Park Y, Kim KT, Kim BH. G-Quadruplex formation using fluorescent oligonucleotides as a detection method for discriminating AGG trinucleotide repeats. Chem Commun (Camb) 2018; 52:12757-12760. [PMID: 27722273 DOI: 10.1039/c6cc06566j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have developed a simple and sensitive system for detecting AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes using a fluorescent oligonucleotide. The fluorescence signal increased rapidly and dramatically by 44.7-fold with respect to the low background signal in the presence of RNA agg repeats and by 35.0-fold in the presence of DNA AGG repeats.
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Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| | - Ki Tae Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
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8
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Oyaghire SN, Cherubim CJ, Telmer CA, Martinez JA, Bruchez MP, Armitage BA. RNA G-Quadruplex Invasion and Translation Inhibition by Antisense γ-Peptide Nucleic Acid Oligomers. Biochemistry 2016; 55:1977-88. [PMID: 26959335 DOI: 10.1021/acs.biochem.6b00055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the abilities of three complementary γ-peptide nucleic acid (γPNA) oligomers to invade an RNA G-quadruplex and potently inhibit translation of a luciferase reporter transcript containing the quadruplex-forming sequence (QFS) within its 5'-untranslated region. All three γPNA oligomers bind with low nanomolar affinities to an RNA oligonucleotide containing the QFS. However, while all probes inhibit translation with low to midnanomolar IC50 values, the γPNA designed to hybridize to the first two G-tracts of the QFS and adjacent 5'-overhanging nucleotides was 5-6 times more potent than probes directed to either the 3'-end or internal regions of the target at 37 °C. This position-dependent effect was eliminated after the probes and target were preincubated at an elevated temperature prior to translation, demonstrating that kinetic effects exert significant control over quadruplex invasion and translation inhibition. We also found that antisense γPNAs exhibited similarly potent effects against luciferase reporter transcripts bearing QFS motifs having G2, G3, or G4 tracts. Finally, our results indicate that γPNA oligomers exhibit selectivity and/or potency higher than those of other antisense molecules such as standard PNA and 2'-OMe RNA previously reported to target G-quadruplexes in RNA.
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Affiliation(s)
- Stanley N Oyaghire
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Collin J Cherubim
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Cheryl A Telmer
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Joe A Martinez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Marcel P Bruchez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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9
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Kormuth KA, Woolford JL, Armitage BA. Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes. Biochemistry 2016; 55:1749-57. [PMID: 26950608 DOI: 10.1021/acs.biochem.6b00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potential guanine (G) quadruplex-forming sequences (QFSs) found throughout the genomes and transcriptomes of organisms have emerged as biologically relevant structures. These G-quadruplexes represent novel opportunities for gene regulation at the DNA and RNA levels. Recently, the definition of functional QFSs has been expanding to include a variety of unconventional motifs, including relatively long loop sequences (i.e., >7 nucleotides) separating adjacent G-tracts. We have identified a QFS within the 25S rDNA gene from Saccharomyces cerevisae that features a long loop separating the two 3'-most G-tracts. An oligonucleotide based on this sequence, QFS3, folds into a stable G-quadruplex in vitro. We have studied the interaction between QFS3 and several loop mutants with a small, homologous (G-rich) peptide nucleic acid (PNA) oligomer that is designed to form a DNA/PNA heteroquadruplex. The PNA successfully invades the DNA quadruplex target to form a stable heteroquadruplex, but with surprisingly high PNA:DNA ratios based on surface plasmon resonance and mass spectrometric results. A model for high stoichiometry PNA-DNA heteroquadruplexes is proposed, and the implications for quadruplex targeting by G-rich PNA are discussed.
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Affiliation(s)
- Karen A Kormuth
- Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - John L Woolford
- Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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10
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Gupta P, Rastede EE, Appella DH. Multivalent LKγ-PNA oligomers bind to a human telomere DNA G-rich sequence to form quadruplexes. Bioorg Med Chem Lett 2015; 25:4757-4760. [PMID: 26259805 PMCID: PMC5603266 DOI: 10.1016/j.bmcl.2015.07.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 12/15/2022]
Abstract
We report G-quadruplex formation between peptide nucleic acids (PNAs) composed of (L)Kγ-PNA-G monomers and a known portion of human telomeric DNA that adopts three G3 tracts via intramolecular hydrogen bonding. The resulting complex is a bimolecular PNA-DNA heteroquadruplex. In this Letter, we show that introduction of a γ-modification and addition of a peptide ligand does not disrupt the heteroquadruplex. Although the unmodified PNA1 forms a quadruplex with itself, the γ-substituted PNAs (PNA2-PNA6) do not form G-quadruplexes on their own, at even high concentrations. The selectivity of these PNAs could influence the design of new quadruplex-targeting molecules or allow the quadruplex structure to be used as a scaffold for multivalent display of protein binding ligands.
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Affiliation(s)
- Pankaj Gupta
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA
| | | | - Daniel H Appella
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA.
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11
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Lee EK, Kim CW, Kawanami H, Kishimura A, Niidome T, Mori T, Katayama Y. Utilization of a PNA-peptide conjugate to induce a cancer protease-responsive RNAi effect. RSC Adv 2015. [DOI: 10.1039/c5ra17737e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We designed a new siRNA system which turns on RNAi responding to a cancer cell-specific protease by using a peptide nucleic acid (PNA)-peptide conjugate.
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Affiliation(s)
- Eun Kyung Lee
- Graduate School of Systems Life Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Chan Woo Kim
- Department of Applied Chemistry
- Faculty of Engineering
- Kyushu University
- Fukuoka
- Japan
| | - Hiroyuki Kawanami
- Graduate School of Systems Life Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Akihiro Kishimura
- Graduate School of Systems Life Sciences
- Kyushu University
- Fukuoka
- Japan
- Department of Applied Chemistry
| | - Takuro Niidome
- Department of Applied Chemistry
- Faculty of Engineering
- Kyushu University
- Fukuoka
- Japan
| | - Takeshi Mori
- Graduate School of Systems Life Sciences
- Kyushu University
- Fukuoka
- Japan
- Department of Applied Chemistry
| | - Yoshiki Katayama
- Graduate School of Systems Life Sciences
- Kyushu University
- Fukuoka
- Japan
- Department of Applied Chemistry
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12
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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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13
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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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14
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Armitage BA. Analysis of PNA hybridization by surface plasmon resonance. Methods Mol Biol 2014; 1050:159-65. [PMID: 24297358 DOI: 10.1007/978-1-62703-553-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reactions templated by a specific nucleic acid sequence have emerged as an attractive strategy for nucleic acid sensing. The Staudinger reaction using an azide-quenched fluorophore and a phosphine is particularly well suited by virtue of its bioorthogonality and biocompatibility. The reaction is promoted by a complementary nucleic acid that aligns the phosphine with the azide-quenched fluorophore. Cellular RNAs can catalyze the Staudinger reaction, and signal amplification can be achieved through multiple turnover of the template. Peptide nucleic acids (PNAs) provide a convenient platform for the preparation of specific probes as they combine desirable hybridization properties, robust synthesis, ease of fluorophore conjugation, and high biochemical stability. Herein, we describe protocols for fast fluorescent detection of miRNAs in human cells with PNA-based probes via reductive unquenching of bis-azidorhodamine by trialkylphosphine.
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Affiliation(s)
- Bruce A Armitage
- Department of Chemistry, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, USA
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Formation and characterization of PNA-containing heteroquadruplexes. Methods Mol Biol 2014; 1050:73-82. [PMID: 24297351 DOI: 10.1007/978-1-62703-553-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The guanine quadruplex is a secondary structure formed by DNA and RNA that has been implicated in regulation of gene expression and maintenance of genome stability. Guanine-rich PNA oligomers can invade DNA or RNA quadruplex targets to form heteroquadruplex structures. Affinities in the low nanomolar range are routinely observed, making PNAs among the tightest binding of all quadruplex-targeted agents. Although inherently more promiscuous than heteroduplex formation based on Watson-Crick pairing, selectivity of heteroquadruplex formation can be improved through rational design of the sequence and backbone structure of the PNA. This chapter presents design rules and methods for characterizing PNA-DNA/RNA heteroquadruplexes.
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Gupta A, Lee LL, Roy S, Tanious FA, Wilson WD, Ly DH, Armitage BA. Strand invasion of DNA quadruplexes by PNA: comparison of homologous and complementary hybridization. Chembiochem 2013; 14:1476-84. [PMID: 23868291 PMCID: PMC3856695 DOI: 10.1002/cbic.201300263] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Indexed: 12/18/2022]
Abstract
Molecular recognition of DNA quadruplex structures is envisioned to be a strategy for regulating gene expression at the transcriptional level and for in situ analysis of telomere structure and function. The recognition of DNA quadruplexes by peptide nucleic acid (PNA) oligomers is presented here, with a focus on comparing complementary, heteroduplex-forming and homologous, heteroquadruplex-forming PNAs. Surface plasmon resonance and optical spectroscopy experiments demonstrated that the efficacy of a recognition mode depended strongly on the target. Homologous PNA readily invades a quadruplex derived from the promoter regulatory region found upstream of the MYC proto-oncogene to form a heteroquadruplex at high potassium concentration mimicking the intracellular environment, whereas complementary PNA exhibits virtually no hybridization. In contrast, complementary PNA is superior to the homologous in hybridizing to a quadruplex modeled on the human telomere sequence. The results are discussed in terms of the different structural morphologies of the quadruplex targets and the implications for in vivo recognition of quadruplexes by PNAs.
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Affiliation(s)
- Anisha Gupta
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Ling-Ling Lee
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Subhadeep Roy
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Farial A. Tanious
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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