1
|
Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair. Molecules 2020; 25:molecules25030735. [PMID: 32046275 PMCID: PMC7037966 DOI: 10.3390/molecules25030735] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022] Open
Abstract
Unusual nucleic acid structures are salient triggers of endogenous repair and can occur in sequence-specific contexts. Peptide nucleic acids (PNAs) rely on these principles to achieve non-enzymatic gene editing. By forming high-affinity heterotriplex structures within the genome, PNAs have been used to correct multiple human disease-relevant mutations with low off-target effects. Advances in molecular design, chemical modification, and delivery have enabled systemic in vivo application of PNAs resulting in detectable editing in preclinical mouse models. In a model of β-thalassemia, treated animals demonstrated clinically relevant protein restoration and disease phenotype amelioration, suggesting a potential for curative therapeutic application of PNAs to monogenic disorders. This review discusses the rationale and advances of PNA technologies and their application to gene editing with an emphasis on structural biochemistry and repair.
Collapse
|
2
|
Abstract
Antibacterial agents are a group of materials that selectively destroy bacteria by interfering with bacterial growth or survival. With the emergence of resistance phenomenon of bacterial pathogens to current antibiotics, new drugs are frequently entering into the market along with the existing drugs, and the alternative compounds with antibacterial functions are being explored. Due to the advantages of their inherent biochemical and biophysical properties including precise targeting ability, biocompatibility, biodegradability, long blood circulation time, and low cytotoxicity, biomolecules such as peptides, carbohydrates, and nucleic acids have huge potential for the antimicrobial application and have been extensively studied in recent years. In this review, antimicrobial therapeutic agents composed of three kinds of functional biological molecules were summarized. In addition, the research progress of antibacterial mechanism, chemical modification, and nanoparticle coupling of those biomolecules were also discussed.
Collapse
|
3
|
Li D, Peng P, Yang Z, Lv B. Formation of G-quadruplex structure in supercoiled DNA under molecularly crowded conditions. RSC Adv 2019; 9:26248-26251. [PMID: 35531037 PMCID: PMC9070399 DOI: 10.1039/c9ra06370f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 11/29/2022] Open
Abstract
G-quadruplex is a secondary structure of nucleic acids that plays crucial roles in many significant biological processes. Potential G-quadruplex-forming sequences exist widely in various regions of the genome such as telomeres and gene promoters. In spite of the fact that G-quadruplex can be readily assembled from a single-stranded segment of DNA, its formation from duplex DNA is very difficult under physiological conditions because Watson–Crick interactions in guanine rich segments need to be weakened first. It is demonstrated in our studies that intrastrand G-quadruplex generated from a perfectly matched guanine-rich duplex in a circular DNA as a result of significant quadruplex stabilization and duplex destabilization created by the combined actions of negative DNA supercoiling and molecular crowding conditions. It is demonstrated that G-quadruplex generated from G-rich duplex in a circular DNA as a result of quadruplex stabilization and duplex destabilization created by the combined actions of negative DNA supercoiling and molecular crowding condition.![]()
Collapse
Affiliation(s)
- Dawei Li
- The Southern Modern Forestry Collaborative Innovation Center
- College of Biology and the Environment
- Nanjing Forestry University
- Nanjing
- China
| | - Peiwen Peng
- The Southern Modern Forestry Collaborative Innovation Center
- College of Biology and the Environment
- Nanjing Forestry University
- Nanjing
- China
| | - Zhaoqi Yang
- School of Pharmaceutical Sciences
- Jiangnan University
- Wuxi
- China
| | - Bei Lv
- Jiangsu Key Laboratory for Biofunctional Molecules
- College of Life Science and Chemistry
- Jiangsu Second Normal University
- Nanjing
- China
| |
Collapse
|
4
|
Sawada S, Takao T, Kato N, Kaihatsu K. Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA. Molecules 2017; 22:molecules22111840. [PMID: 29077023 PMCID: PMC6150319 DOI: 10.3390/molecules22111840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/18/2017] [Accepted: 10/21/2017] [Indexed: 11/18/2022] Open
Abstract
DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA) offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures. Here, we synthesized a series of TC-PNAs that can possess different lengths of azobenzene-containing linkers and studied their binding behaviours to homopurine single-stranded DNA. Introduction of azobenzene at the N-terminus amine of PNA increased the thermal stability of PNA-DNA duplexes. Further extension of the homopyrimidine PNA strand at the N-terminus of PNA-AZO further increased the binding stability of the PNA/DNA/PNA triplex to the target homopurine sequence; however, it induced TC-PNA/DNA/TC-PNA complex formation. Among these TC-PNAs, 9W5H-C4-AZO consisting of nine Watson-Crick bases and five Hoogsteen bases tethered with a beta-alanine conjugated azobenzene linker gave a stable 1:1 TC-PNA/ssDNA complex and exhibited good mismatch recognition. Our design for TC-PNA-AZO can be utilized for detecting homopurine sequences in various genes.
Collapse
Affiliation(s)
- Shinjiro Sawada
- Department of Organic Fine Chemicals, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Toshifumi Takao
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Nobuo Kato
- Department of Organic Fine Chemicals, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kunihiro Kaihatsu
- Department of Organic Fine Chemicals, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| |
Collapse
|
5
|
Morin TJ, Shropshire T, Liu X, Briggs K, Huynh C, Tabard-Cossa V, Wang H, Dunbar WB. Nanopore-Based Target Sequence Detection. PLoS One 2016; 11:e0154426. [PMID: 27149679 PMCID: PMC4858282 DOI: 10.1371/journal.pone.0154426] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/13/2016] [Indexed: 01/10/2023] Open
Abstract
The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented.
Collapse
Affiliation(s)
- Trevor J. Morin
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
| | | | - Xu Liu
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ontario, Canada
| | - Cindy Huynh
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
| | | | - Hongyun Wang
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
- Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - William B. Dunbar
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
- Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- * E-mail:
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Reza F, Glazer PM. Therapeutic genome mutagenesis using synthetic donor DNA and triplex-forming molecules. Methods Mol Biol 2015; 1239:39-73. [PMID: 25408401 PMCID: PMC6608751 DOI: 10.1007/978-1-4939-1862-1_4] [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] [Indexed: 06/04/2023]
Abstract
Genome mutagenesis can be achieved in a variety of ways, though a select few are suitable for therapeutic settings. Among them, the harnessing of intracellular homologous recombination affords the safety and efficacy profile suitable for such settings. Recombinagenic donor DNA and mutagenic triplex-forming molecules co-opt this natural recombination phenomenon to enable the specific, heritable editing and targeting of the genome. Editing the genome is achieved by designing the sequence-specific recombinagenic donor DNA to have base mismatches, insertions, and deletions that will be incorporated into the genome when it is used as a template for recombination. Targeting the genome is similarly achieved by designing the sequence-specific mutagenic triplex-forming molecules to further recruit the recombination machinery thereby upregulating its activity with the recombinagenic donor DNA. This combination of extracellularly introduced, designed synthetic molecules and intercellularly ubiquitous, evolved natural machinery enables the mutagenesis of chromosomes and engineering of whole genomes with great fidelity while limiting nonspecific interactions. Herein, we demonstrate the harnessing of recombinagenic donor DNA and mutagenic triplex-forming molecular technology for potential therapeutic applications. These demonstrations involve, among others, utilizing this technology to correct genes so that they become physiologically functional, to induce dormant yet functional genes in place of non-functional counterparts, to place induced genes under regulatory elements, and to disrupt genes to abrogate a cellular vulnerability. Ancillary demonstrations of the design and synthesis of this recombinagenic and mutagenic molecular technology as well as their delivery and assayed interaction with duplex DNA reveal a potent technological platform for engineering specific changes into the living genome.
Collapse
Affiliation(s)
- Faisal Reza
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, 06520-8040, USA
| | | |
Collapse
|
8
|
Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles. Nat Protoc 2014; 9:2206-23. [PMID: 25144271 DOI: 10.1038/nprot.2014.152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This protocol describes how to monitor individual naturally supercoiled circular DNA plasmids bound via peptide nucleic acid (PNA) handles between a bead and a surface. The protocol was developed for single-molecule investigation of the dynamics of supercoiled DNA, and it allows the investigation of both the dynamics of the molecule itself and of its interactions with a regulatory protein. Two bis-PNA clamps designed to bind with extremely high affinity to predetermined homopurine sequence sites in supercoiled DNA are prepared: one conjugated with digoxigenin for attachment to an anti-digoxigenin-coated glass cover slide, and one conjugated with biotin for attachment to a submicron-sized streptavidin-coated polystyrene bead. Plasmids are constructed, purified and incubated with the PNA handles. The dynamics of the construct is analyzed by tracking the tethered bead using video microscopy: less supercoiling results in more movement, and more supercoiling results in less movement. In contrast to other single-molecule methodologies, the current methodology allows for studying DNA in its naturally supercoiled state with constant linking number and constant writhe. The protocol has potential for use in studying the influence of supercoils on the dynamics of DNA and its associated proteins, e.g., topoisomerase. The procedure takes ~4 weeks.
Collapse
|
9
|
Schleifman EB, Glazer PM. Peptide nucleic acid-mediated recombination for targeted genomic repair and modification. Methods Mol Biol 2014; 1050:207-22. [PMID: 24297362 DOI: 10.1007/978-1-62703-553-8_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to directly manipulate the human genome to correct a disease-related mutation, introduce a sequence change that would lead to site-specific gene knockout, or increase gene expression is a very powerful tool with tremendous clinical value. Triplex formation by synthetic DNA-binding molecules such as peptide nucleic acids (PNAs) has been studied for over 20 years and much of the work in the last 10 years has shown its great promise in its use to direct site-specific gene modification for the use in gene therapy. In this chapter, detailed protocols are described for the design and use of triplex-forming PNAs to bind and mediate gene modification at specific chromosomal targets. Target site identification, PNA and donor oligonucleotide design, in vitro characterization of binding, optimization with reporter systems, as well as various methods to assess gene modification and isolate modified cells are described.
Collapse
Affiliation(s)
- Erica B Schleifman
- Department of Genetics, Yale University School of Medicine, New Haven, USA
| | | |
Collapse
|
10
|
Aiba Y, Yasuda K, Komiyama M. Site-selective Scission of Double-stranded DNA by Combining a Triplex-forming bis-PNA and Ce(IV)/EDTA. CHEM LETT 2013. [DOI: 10.1246/cl.130650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yuichiro Aiba
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba
- Research Center for Advanced Science and Technology, The University of Tokyo
| | - Kohei Yasuda
- Research Center for Advanced Science and Technology, The University of Tokyo
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba
- Research Center for Advanced Science and Technology, The University of Tokyo
| |
Collapse
|
11
|
Yamazaki T, Aiba Y, Yasuda K, Sakai Y, Yamanaka Y, Kuzuya A, Ohya Y, Komiyama M. Clear-cut observation of PNA invasion using nanomechanical DNA origami devices. Chem Commun (Camb) 2013; 48:11361-3. [PMID: 23073563 DOI: 10.1039/c2cc36358e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Invasive binding event of PNA into DNA duplex was clearly observed both by atomic force microscope (AFM) imaging and electrophoretic mobility shift assay (EMSA) with the aid of nanomechanical DNA origami devices as 'single-molecule' visual probes, showing their potential as universal platform for the analysis of PNA invasion.
Collapse
Affiliation(s)
- Takahiro Yamazaki
- RCAST, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Singer A, Rapireddy S, Ly DH, Meller A. Electronic barcoding of a viral gene at the single-molecule level. NANO LETTERS 2012; 12:1722-8. [PMID: 22352964 PMCID: PMC3572535 DOI: 10.1021/nl300372a] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A new single-molecule approach for rapid and purely electronic discrimination among similar genes is presented. Combining solid-state nanopores and γ-modified synthetic peptide nucleic acid probes, we accurately barcode genes by counting the number of probes attached to each gene and measuring their relative spacing. We illustrate our method by sensing individual genes from two highly similar human immunodeficiency virus subtypes, demonstrating feasibility of a novel, single-molecule diagnostic platform for rapid pathogen classification.
Collapse
Affiliation(s)
- Alon Singer
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
| | - Srinivas Rapireddy
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
- Corresponding author.
| |
Collapse
|
13
|
Temperature-assisted cyclic hybridization (TACH): an improved method for supercoiled DNA hybridization. Mol Biotechnol 2010; 45:171-9. [PMID: 20238183 DOI: 10.1007/s12033-010-9261-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Accurate hybridization is dependent on the ratio between sequence-specific and unspecific binding. Dissociation of unspecifically bound, while maintaining specifically hybridized, nucleic acids are key steps to obtain a well-defined complex. We have developed a new method, temperature-assisted, cyclic hybridization (TACH), which increases cognate binding at the expense of unspecific hybridization. The method was used for optimizing binding of peptide nucleic acid (PNA) to supercoiled plasmids and has several advantages over previous methods: (1) it reduces the required amount of bis-PNA by three- to fourfold; (2) it results in less unspecific binding; (3) it extends cooperative hybridization, from 3 bp to 5 bp between two adjacent binding sites; and (4) it decreases the aggregation of bis-PNA. This method might be extended to other forms of hybridizations including the use of additional nucleic acids analogs, such as locked nucleic acid (LNA) and, also, to other areas where PNAs are used such as fluorescence in situ hybridization (FISH), microarrays, or in vivo plasmid delivery.
Collapse
|
14
|
Application of peptide nucleic acid towards development of nanobiosensor arrays. Bioelectrochemistry 2010; 79:153-61. [PMID: 20356802 DOI: 10.1016/j.bioelechem.2010.02.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 01/20/2010] [Accepted: 02/23/2010] [Indexed: 11/20/2022]
Abstract
Peptide nucleic acid (PNA) is the modified DNA or DNA analogue with a neutral peptide backbone instead of a negatively charged sugar phosphate. PNA exhibits chemical stability, resistant to enzymatic degradation inside living cell, recognizing specific sequences of nucleic acid, formation of stable hybrid complexes like PNA/DNA/PNA triplex, strand invasion, extraordinary thermal stability and ionic strength, and unique hybridization relative to nucleic acids. These unique physicobiochemical properties of PNA enable a new mode of detection, which is a faster and more reliable analytical process and finds applications in the molecular diagnostics and pharmaceutical fields. Besides, a variety of unique characteristic features, PNAs replace DNA as a probe for biomolecular tool in the molecular genetic diagnostics, cytogenetics, and various pharmaceutical potentials as well as for the development of sensors/arrays/chips and many more investigation purposes. This review paper discusses the various current aspects related with PNAs, making a new hot device in the commercial applications like nanobiosensor arrays.
Collapse
|
15
|
Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M, Meller A. Nanopore based sequence specific detection of duplex DNA for genomic profiling. NANO LETTERS 2010; 10:738-42. [PMID: 20088590 PMCID: PMC2834191 DOI: 10.1021/nl100058y] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We demonstrate a purely electrical method for the single-molecule detection of specific DNA sequences, achieved by hybridizing double-stranded DNA (dsDNA) with peptide nucleic acid (PNA) probes and electrophoretically threading the DNA through sub-5 nm silicon nitride pores. Bis-PNAs were used as the tagging probes in order to achieve high affinity and sequence specificity. Sequence detection is performed by reading the ion current traces of individual translocating DNA molecules, which display a characteristic secondary blockade level, absent in untagged molecules. The potential for barcoding DNA is demonstrated through nanopore analysis of once-tagged and twice-tagged DNA at different locations on the same genomic fragment. Our high-throughput, long-read length method can be used to identify key sequences embedded in individual DNA molecules, without the need for amplification or fluorescent/radio labeling. This opens up a wide range of possibilities in human genomics as well as in pathogen detection for fighting infectious diseases.
Collapse
Affiliation(s)
- Alon Singer
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Meni Wanunu
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Will Morrison
- Department of Physics, Boston University, Boston, MA 02215
| | - Heiko Kuhn
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | | | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
- Department of Physics, Boston University, Boston, MA 02215
| |
Collapse
|
16
|
Abstract
Gene targeting with DNA-binding molecules such as triplex-forming oligonucleotides or peptide nucleic acids can be utilized to direct mutagenesis or induce recombination site-specifically. In this chapter, several detailed protocols are described for the design and use of triplex-forming molecules to bind and mediate gene modification at specific chromosomal targets. Target site identification, binding molecule design, as well as various methods to test binding and assess gene modification are described.
Collapse
|
17
|
Boutimah-Hamoudi F, Leforestier E, Sénamaud-Beaufort C, Nielsen PE, Giovannangeli C, Saison-Behmoaras TE. Cellular antisense activity of peptide nucleic acid (PNAs) targeted to HIV-1 polypurine tract (PPT) containing RNA. Nucleic Acids Res 2007; 35:3907-17. [PMID: 17537815 PMCID: PMC1919497 DOI: 10.1093/nar/gkm374] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
DNA and RNA oligomers that contain stretches of guanines can associate to form stable secondary structures including G-quadruplexes. Our study shows that the (UUAAAAGAAAAGGGGGGAU) RNA sequence, from the human immunodeficiency virus type 1 (HIV-1 polypurine tract or PPT sequence) forms in vitro a stable folded structure involving the G-run. We have investigated the ability of pyrimidine peptide nucleic acid (PNA) oligomers targeted to the PPT sequence to invade the folded RNA and exhibit biological activity at the translation level in vitro and in cells. We find that PNAs can form stable complexes even with the structured PPT RNA target at neutral pH. We show that T-rich PNAs, namely the tridecamer-I PNA (C4T4CT4) forms triplex structures whereas the C-rich tridecamer-II PNA (TC6T4CT) likely forms a duplex with the target RNA. Interestingly, we find that both C-rich and T-rich PNAs arrested in vitro translation elongation specifically at the PPT target site. Finally, we show that T-rich and C-rich tridecamer PNAs that have been identified as efficient and specific blockers of translation elongation in vitro, specifically inhibit translation in streptolysin-O permeabilized cells where the PPT target sequence has been introduced upstream the reporter luciferase gene.
Collapse
Affiliation(s)
- Fatima Boutimah-Hamoudi
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France, MNHN, USM503, Département de « Régulations, développement et diversité moléculaire », Laboratoire des Régulations et dynamique des génomes, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France and Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
| | - Erwan Leforestier
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France, MNHN, USM503, Département de « Régulations, développement et diversité moléculaire », Laboratoire des Régulations et dynamique des génomes, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France and Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
| | - Catherine Sénamaud-Beaufort
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France, MNHN, USM503, Département de « Régulations, développement et diversité moléculaire », Laboratoire des Régulations et dynamique des génomes, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France and Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
| | - Peter E. Nielsen
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France, MNHN, USM503, Département de « Régulations, développement et diversité moléculaire », Laboratoire des Régulations et dynamique des génomes, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France and Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
| | - Carine Giovannangeli
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France, MNHN, USM503, Département de « Régulations, développement et diversité moléculaire », Laboratoire des Régulations et dynamique des génomes, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France and Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
| | - Tula Ester Saison-Behmoaras
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F-75231, France, MNHN, USM503, Département de « Régulations, développement et diversité moléculaire », Laboratoire des Régulations et dynamique des génomes, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France, CNRS, UMR5153, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 5, F-75231, France and Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark
- *To whom correspondence should be addressed. +33 1 40 79 36 86+33 1 40 79 37 05
| |
Collapse
|
18
|
Smolina IV, Kuhn H, Lee C, Frank-Kamenetskii MD. Fluorescence-based detection of short DNA sequences under non-denaturing conditions. Bioorg Med Chem 2007; 16:84-93. [PMID: 17512202 DOI: 10.1016/j.bmc.2007.04.063] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 02/26/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
The ability of peptide nucleic acid (PNA) to open up duplex DNA in a highly sequence-specific manner makes it possible to detect short DNA sequences on the background of or within genomic DNA under non-denaturing conditions. To do so, chosen marker sites in double-stranded DNA are locally opened by a pair of PNA openers, thus transforming one strand within the target region (20-30 bp) into the single-stranded form. Onto this accessible DNA sequence a circular oligonucleotide probe is assembled, which serves as a template for rolling circle amplification (RCA). Both homogeneous and heterogeneous assay formats are investigated, as are different formats for fluorescence-based amplicon detection. Our recent data with immobilized analytes suggest that marker sequences in plasmid and bacterial chromosomal DNA can be successfully detected.
Collapse
Affiliation(s)
- Irina V Smolina
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, MA 02215, USA
| | | | | | | |
Collapse
|
19
|
Bentin T, Hansen GI, Nielsen PE. Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes. Nucleic Acids Res 2006; 34:5790-9. [PMID: 17053099 PMCID: PMC1635314 DOI: 10.1093/nar/gkl736] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Sequence-selective recognition of double-stranded (ds) DNA by homopyrimidine peptide nucleic acid (PNA) oligomers can occur by major groove triplex binding or by helix invasion via triplex P-loop formation. We have compared the binding of a decamer, a dodecamer and a pentadecamer thymine–cytosine homopyrimidine PNA oligomer to a sequence complementary homopurine target in duplex DNA using gel-shift and chemical probing analyses. We find that all three PNAs form stable triplex invasion complexes, and also conventional triplexes with the dsDNA target. Triplexes form with much faster kinetics than invasion complexes and prevail at lower PNA concentrations and at shorter incubation times. Furthermore, increasing the ionic strength strongly favour triplex formation over invasion as the latter is severely inhibited by cations. Whereas a single triplex invasion complex is formed with the decameric PNA, two structurally different target-specific invasion complexes were characterized for the dodecameric PNA and more than five for the pentadecameric PNA. Finally, it is shown that isolated triplex complexes can be converted to specific invasion complexes without dissociation of the Hoogsteen base-paired triplex PNA. These result demonstrate a clear example of a ‘triplex first’ mechanism for PNA helix invasion.
Collapse
Affiliation(s)
| | | | - Peter E. Nielsen
- To whom correspondence should be addressed. Tel: +45 35327762/61; Fax: +45 35396042;
| |
Collapse
|
20
|
Kim KH, Nielsen PE, Glazer PM. Site-specific gene modification by PNAs conjugated to psoralen. Biochemistry 2006; 45:314-23. [PMID: 16388608 DOI: 10.1021/bi051379a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding molecules, including triplex-forming oligonucleotides (TFOs) and peptide nucleic acids (PNAs), can be utilized to introduce site-specific mutations or to promote recombination at selected genomic sites. To further evaluate the utility of PNAs for site-specific gene modification, we tested dimeric bis-PNAs conjugated to psoralen. These PNAs are designed to form a triplex-invasion complex within the supF reporter gene in an episomal shuttle vector and to direct site-specific photoadduct formation by the conjugated psoralen. The psoralen-bis-PNA conjugate was found to direct photoadduct formation to the intended 5'-TpA base step next to the PNA-binding site, and the photoadduct formation efficiency displayed both concentration and UVA irradiation dependence. The effect of PNA-targeted photoadducts in a mammalian system was tested by SV40-based shuttle vector assay. After in vitro binding, we found that photoadducts directed by PNAs conjugated to psoralen-induced mutations at frequencies in the range of 0.46%, 6.5-fold above the background. In a protocol for intracellular gene targeting in the episomal shuttle vector, the psoralen-PNA-induced mutation frequency was 0.13%, 3.5-fold higher than the background. Most of the induced mutations were deletions and single-base-pair substitutions at or adjacent to the targeted PNA-binding and photoadduct-formation sites. When the results are taken together, they demonstrate the ability of bis-PNAs conjugated with psoralen to mediate site-specific gene modification, and they further support the development of PNAs as tools for gene-targeting applications.
Collapse
Affiliation(s)
- Ki-Hyun Kim
- Department of Therapeutic Radiology, Yale University School of Medicine, Post Office Box 208040, New Haven, Connecticut 06520-8040, USA
| | | | | |
Collapse
|
21
|
Ziemba AJ, Zhilina ZV, Krotova-Khan Y, Stankova L, Ebbinghaus SW. Targeting and regulation of the HER-2/neu oncogene promoter with bis-peptide nucleic acids. Oligonucleotides 2005; 15:36-50. [PMID: 15788899 DOI: 10.1089/oli.2005.15.36] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antigene oligonucleotides have the potential to regulate gene expression through site-specific DNA binding. However, in vivo applications have been hindered by inefficient cellular uptake, degradation, and strand displacement. Peptide nucleic acids (PNAs) address several of these problems, as they are resistant to degradation and bind DNA with high affinity. We designed two cationic pyrimidine bis-PNAs (cpy-PNAs) to target the polypurine tract of the HER-2/neu promoter and compared them to an unmodified phosphodiester triplex-forming oligonucleotide (TFO1) and a TFO-nitrogen mustard conjugate (TFO2). PNA1 contains a + 2 charge and bound two adjacent 9-bp target sequences with high affinity and specificity, but only at low pH. PNA2 contains a +5 charge and bound one 11-bp target with high affinity up to pH 7.4, but with lower specificity. The PNA:DNA:PNA triplex formed by these cpy-bis-PNAs presented a stable barrier to DNA polymerase extension. The cpy-bis-PNAs and the TFO-alkylator conjugate prevented HER-2/neu transcription in a reporter gene assay (TFO2 = PNA1 > PNA2 >> TFO1). Both PNAs and TFOs were effective at binding the target sequence in naked genomic DNA, but only the TFO-alkylator (TFO2) and the more cationic PNA (PNA2) were detected at the endogenous HER-2/neu promoter in permeabilized cells. This work demonstrates the potential for preventing HER-2/neu gene expression with cpy-bis-PNAs in tumor cells.
Collapse
|
22
|
|
23
|
Krupnik OV, Fadeeva NV, Kvitko NP, Shepelev VA, Nielsen PE, Lazurkin YS. Stability and transformations of bis-PNA/DNA triplex structural isomers. J Biomol Struct Dyn 2004; 21:503-12. [PMID: 14692795 DOI: 10.1080/07391102.2004.10506944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Structurally isomeric complexes formed between homopyrimidine bis-PNAs (T(2)JT(2)JT(4)-linker-T(4)CT(2)CT(2)) and single- and double-stranded DNA targets were investigated. These complexes are triplexes designated S1, S2 and S3 in order of increased mobility by polyacrylamide gel electrophoresis. It is shown that the S3 isomer is formed only on double-stranded DNA and possesses highest stability. Isomers S2 and S1 are formed upon binding of bis-PNA to double-stranded as well as to single-stranded DNA. It was found that the stability of the isomer S1 increases dramatically in the presence of excess single-stranded oligonucleotide complementary to the bis-PNA. The structure of the stabilized S1 isomer is proposed to consist of two bis-PNA/DNA triplexes. The relationship between the yield of the isomer S1 formed on single-stranded DNA and the bis-PNA concentration was investigated and a kinetic model of the formation of S1 is presented.
Collapse
Affiliation(s)
- Olga V Krupnik
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia.
| | | | | | | | | | | |
Collapse
|
24
|
Liu B, Han Y, Ferdous A, Corey DR, Kodadek T. Transcription activation by a PNA-peptide chimera in a mammalian cell extract. ACTA ACUST UNITED AC 2004; 10:909-16. [PMID: 14583257 DOI: 10.1016/j.chembiol.2003.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Bo Liu
- Center for Biomedical Inventions, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | | | | | | | | |
Collapse
|
25
|
Kuhn H, Cherny DI, Demidov VV, Frank-Kamenetskii MD. Inducing and modulating anisotropic DNA bends by pseudocomplementary peptide nucleic acids. Proc Natl Acad Sci U S A 2004; 101:7548-53. [PMID: 15136738 PMCID: PMC419643 DOI: 10.1073/pnas.0308756101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA bending is significant for various DNA functions in the cell. Here, we demonstrate that pseudocomplementary peptide nucleic acids (pcPNAs) represent a class of versatile, sequence-specific DNA-bending agents. The occurrence of anisotropic DNA bends induced by pcPNAs is shown by gel electrophoretic phasing analysis. The magnitude of DNA bending is determined by circular permutation assay and by electron microscopy, with good agreement of calculated mean values between both methods. Binding of a pair of 10-meric pcPNAs to its target DNA sequence results in moderate DNA bending with a mean value of 40-45 degrees, while binding of one self-pc 8-mer PNA to target DNA yields a somewhat larger average value of the induced DNA bend. Both bends are found to be in phase when the pcPNA target sites are separated by distances of half-integer numbers of helical turns of regular duplex DNA, resulting in an enhanced DNA bend with an average value in the range of 80-90 degrees. The occurrence of such a sharp bend within the DNA double helix is confirmed and exploited through efficient formation of 170-bp-long DNA minicircles by means of dimerization of two bent DNA fragments. The pcPNAs offer two main advantages over previously designed classes of nonnatural DNA-bending agents: they have very mild sequence limitations while targeting duplex DNA and they can easily be designed for a chosen target sequence, because their binding obeys the principle of complementarity. We conclude that pcPNAs are promising tools for inducing bends in DNA at virtually any chosen site.
Collapse
Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
| | | | | | | |
Collapse
|
26
|
Kaihatsu K, Shah RH, Zhao X, Corey DR. Extending recognition by peptide nucleic acids (PNAs): binding to duplex DNA and inhibition of transcription by tail-clamp PNA-peptide conjugates. Biochemistry 2004; 42:13996-4003. [PMID: 14636068 DOI: 10.1021/bi035194k] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide nucleic acids (PNAs) are a powerful tool for recognition of double-stranded DNA. Strand invasion is most efficient when pyrimidine PNAs are linked to form a bisPNA in which one strand binds by Watson-Crick base pairing while the other binds by Hoogsteen base pairing to the newly formed PNA-DNA duplex. Within many genes, however, polypyrimidine target sequences may not be located in optimal positions relative to transcription factor binding sites, and this deficiency may complicate attempts to identify potent antigene PNAs. To increase the versatility of strand invasion by PNAs, we have synthesized bisPNAs and bisPNA-peptide conjugates containing a mixed base extension of the Watson-Crick polypyrimidine strand. We find that these tail-clamp PNAs (TC-PNAs) bind duplex DNA and inhibit transcription. DNA recognition occurs with single-stranded or TC-bisPNAs and requires attachment of positively charged amino acids. Association rate constants, k(a), for binding to DNA by TC-PNAs are as high as 35000 M(-1) s(-1) and are usually only a fewfold lower than for analogous PNAs that lack mixed base extensions. The ability to bind duplex DNA is not always necessary for inhibition of transcription, possibly because PNAs can bind to accessible DNA within the transcription bubble created by RNA polymerase. These results, together with similar findings independently obtained by Nielsen and colleagues [Bentin, T., Larsen, H. J., and Nielsen, P. E. (2003) Biochemistry 42, 13987-13995], expand the range of sequences within duplex DNA that are accessible to PNAs and suggest that TC-PNA-peptide conjugates are good candidates for further testing as antigene agents.
Collapse
Affiliation(s)
- Kunihiro Kaihatsu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9041, USA
| | | | | | | |
Collapse
|
27
|
Vaysse L, Harbottle R, Bigger B, Bergau A, Tolmachov O, Coutelle C. Development of a Self-assembling Nuclear Targeting Vector System Based on the Tetracycline Repressor Protein. J Biol Chem 2004; 279:5555-64. [PMID: 14607832 DOI: 10.1074/jbc.m311894200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ultimate destination for most gene therapy vectors is the nucleus and nuclear import of potentially therapeutic DNA is one of the major barriers for nonviral vectors. We have developed a novel approach of attaching a nuclear localization sequence (NLS) peptide to DNA in a non-essential position, by generating a fusion between the tetracycline repressor protein TetR and the SV40-derived NLS peptide. The high affinity and specificity of TetR for the short DNA sequence tetO was used in these studies to bind the NLS to DNA as demonstrated by the reduced electrophoretic mobility of the TetR.tetO-DNA complexes. The protein TetR-NLS, but not control protein TetR, specifically enhances gene expression from lipofected tetO-containing DNA between 4- and 16-fold. The specific enhancement is observed in a variety of cell types, including primary and growth-arrested cells. Intracellular trafficking studies demonstrate an increased accumulation of fluorescence labeled DNA in the nucleus after TetR-NLS binding. In comparison, binding studies using the similar fusion of peptide nucleic acid (PNA) with NLS peptide, demonstrate specific binding of PNA to plasmid DNA. However, although we observed a 2-8.5-fold increase in plasmid-mediated luciferase activity with bis-PNA-NLS, control bis-PNA without an NLS sequence gave a similar increase, suggesting that the effect may not be because of a specific bis-PNA-NLS-mediated enhancement of nuclear transfer of the plasmid. Overall, we found TetRNLS-enhanced plasmid-mediated transgene expression at a similar level to that by bis-PNA-NLS or bis-PNA alone but specific to nuclear uptake and significantly more reliable and reproducible.
Collapse
Affiliation(s)
- Laurence Vaysse
- Gene Therapy Research Group, Division of Biomedical Science, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| | | | | | | | | | | |
Collapse
|
28
|
Zhao X, Kaihatsu K, Corey DR. Inhibition of transcription by bisPNA-peptide conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:535-46. [PMID: 14565228 DOI: 10.1081/ncn-120021953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Homopyrimidine bisPNAs have been reported to arrest transcription elongation by invading double-stranded DNA and forming a stable (PNA)2/DNA complex. We previously reported that attachment of a designed cationic peptide to the bisPNA enhances the efficiency of strand invasion. Here we investigate whether conjugation to cationic peptides can also improve inhibition of transcription. We observe that a conjugate between a bisPNA and a peptide containing eight lysines is a superior agent for inhibition of transcription, but that inhibition of transcription is reduced as pH and the concentration of magnesium are increased. Our studies provide useful characterization of bisPNAs as agents for inhibiting transcription.
Collapse
Affiliation(s)
- Xin Zhao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041, USA
| | | | | |
Collapse
|
29
|
Kaihatsu K, Braasch DA, Cansizoglu A, Corey DR. Enhanced strand invasion by peptide nucleic acid-peptide conjugates. Biochemistry 2002; 41:11118-25. [PMID: 12220176 DOI: 10.1021/bi0263659] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient and selective recognition of DNA by proteins is due to sequence-specific interactions with a target site and nonselective electrostatic interactions that promote the target's rapid location. If synthetic molecules could mimic these functions, they would render a wide range of chromosome sequences accessible to rationally designed probes. Here we describe conjugates between bispeptide nucleic acids (bisPNAs) designed to specifically recognize duplex DNA and peptides that have been designed to promote rapid sequence recognition. Peptide design was based on the surface of staphylococcal nuclease, a cationic DNA binding protein with low sequence selectivity. We observe that attachment of the designed peptide increases rates of strand invasion by 100-fold relative to unmodified bisPNA. The peptide can contain D-amino acids, increasing the likelihood that it will be stable in cell extract and inside cells. Binding of the conjugate containing the D-amino acid peptide occurred over a broad range of experimental conditions and was sensitive to a single mismatch. Strand invasion was efficient at neutral to basic pH, a wide range of temperatures (0-65 degrees C), and in the presence of up to 7 mM Mg(2+) and 100 mM Na(+) or K(+). Our data suggest that attachment of peptides that mimic cationic protein surfaces to PNAs can afford conjugates that mimic the rapid and selective binding that characterizes native DNA binding proteins. Rapid strand invasion over a wide range of experimental conditions should further expand the utility of strand invasion by PNAs.
Collapse
Affiliation(s)
- Kunihiro Kaihatsu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9041, USA
| | | | | | | |
Collapse
|
30
|
Abstract
DNA nanostructures are ordered oligonucleotide arrangements that have applications for DNA computers, crystallography, diagnostics and material sciences. Peptide nucleic acid (PNA) is a DNA/RNA mimic that offers many advantages for hybridization, but its potential for application in the field of DNA nanotechnology has yet to be thoroughly examined. We report the synthesis and characterization of tethered PNA molecules (bisPNAs) designed to assemble two individual DNA molecules through Watson-Crick base pairing. The spacer regions linking the PNAs were varied in length and contained amino acids with different electrostatic properties. We observed that bisPNAs effectively assembled oligonucleotides that were either the exact length of the PNA or that contained overhanging regions that projected outwards. In contrast, DNA assembly was much less efficient if the oligonucleotides contained overhanging regions that projected inwards. Surprisingly, the length of the spacer region between the PNA sequences did not greatly affect the efficiency of DNA assembly. Reasons for inefficient assembly of inward projecting DNA oligonucleotides include non-sequence-specific intramolecular interactions between the overhanging region of the bisPNA and steric conflicts that complicate simultaneous binding of two inward projecting strands. These results suggest that bisPNA molecules can be used for self-assembling DNA nanostructures provided that the arrangement of the hybridizing DNA oligonucleotides does not interfere with simultaneous hybridization to the bisPNA molecule.
Collapse
Affiliation(s)
- Christopher J Nulf
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-9041, USA
| | | |
Collapse
|