1
|
Wang Q, Rao GS, Marsic T, Aman R, Mahfouz M. Fusion of FokI and catalytically inactive prokaryotic Argonautes enables site-specific programmable DNA cleavage. J Biol Chem 2024; 300:107720. [PMID: 39214308 PMCID: PMC11421335 DOI: 10.1016/j.jbc.2024.107720] [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: 04/26/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Site-specific nucleases are crucial for genome engineering applications in medicine and agriculture. The ideal site-specific nucleases are easily reprogrammable, highly specific in target site recognition, and robust in nuclease activities. Prokaryotic Argonaute (pAgo) proteins have received much attention as biotechnological tools due to their ability to recognize specific target sequences without a protospacer adjacent motif, but their lack of intrinsic dsDNA unwinding activity limits their utility in key applications such as gene editing. Recently, we developed a pAgo-based system for site-specific DNA cleavage at physiological temperatures independently of the DNA form, using peptide nucleic acids (PNAs) to facilitate unwinding dsDNA targets. Here, we fused catalytically dead pAgos with the nuclease domain of the restriction endonuclease FokI and named this modified platform PNA-assisted FokI-(d)pAgo (PNFP) editors. In the PNFP system, catalytically inactive pAgo recognizes and binds to a specific target DNA sequence based on a programmable guide DNA sequence; upon binding to the target site, the FokI domains dimerize and introduce precise dsDNA breaks. We explored key parameters of the PNFP system including the requirements of PNA and guide DNAs, the specificity of PNA and guide DNA on target cleavage, the optimal concentration of different components, reaction time for invasion and cleavage, and ideal temperature and reaction buffer, to ensure efficient DNA editing in vitro. The results demonstrated robust site-specific target cleavage by PNFP system at optimal conditions in vitro. We envision that the PNFP system will provide higher editing efficiency and specificity with fewer off-target effects in vivo.
Collapse
Affiliation(s)
- Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Saudi Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Saudi Arabia.
| |
Collapse
|
2
|
Ylagan M, Xu Q, Kowalski J. TTSBBC: triplex target site biomarkers and barcodes in cancer. Nucleic Acids Res 2024; 52:W547-W555. [PMID: 38661214 PMCID: PMC11223863 DOI: 10.1093/nar/gkae312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.
Collapse
Affiliation(s)
- Maya Ylagan
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX78712, USA
| | - Qi Xu
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX78712, USA
| | - Jeanne Kowalski
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX78712, USA
| |
Collapse
|
3
|
Prieto Otoya TD, McQuaid KT, Hennessy J, Menounou G, Gibney A, Paterson NG, Cardin DJ, Kellett A, Cardin CJ. Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ-[Ru(phen) 2 phi] 2. Angew Chem Int Ed Engl 2024; 63:e202318863. [PMID: 38271265 DOI: 10.1002/anie.202318863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ-[Ru(phen)2 phi]2+ , where phi=9,10-phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2 . The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ-enantiomer and show a high affinity for TA/TA steps and, more generally, TA-rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence.
Collapse
Affiliation(s)
| | - Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Joseph Hennessy
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Georgia Menounou
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Alex Gibney
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Neil G Paterson
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - David J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Andrew Kellett
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| |
Collapse
|
4
|
Garavís M, Edwards PJB, Serrano-Chacón I, Doluca O, Filichev V, González C. Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex. Nucleic Acids Res 2024; 52:2686-2697. [PMID: 38281138 PMCID: PMC10954471 DOI: 10.1093/nar/gkae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/21/2023] [Accepted: 01/06/2024] [Indexed: 01/30/2024] Open
Abstract
We present here the high-resolution structure of an antiparallel DNA triplex in which a monomer of para-twisted intercalating nucleic acid (para-TINA: (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol) is covalently inserted as a bulge in the third strand of the triplex. TINA is a potent modulator of the hybridization properties of DNA sequences with extremely useful properties when conjugated in G-rich oligonucleotides. The insertion of para-TINA between two guanines of the triplex imparts a high thermal stabilization (ΔTM = 9ºC) to the structure and enhances the quality of NMR spectra by increasing the chemical shift dispersion of proton signals near the TINA location. The structural determination reveals that TINA intercalates between two consecutive triads, causing only local distortions in the structure. The two aromatic moieties of TINA are nearly coplanar, with the phenyl ring intercalating between the flanking guanine bases in the sequence, and the pyrene moiety situated between the Watson-Crick base pair of the two first strands. The precise position of TINA within the triplex structure reveals key TINA-DNA interactions, which explains the high stabilization observed and will aid in the design of new and more efficient binders to DNA.
Collapse
Affiliation(s)
- Miguel Garavís
- Instituto de Química Física ‘Blas Cabrera’, (IQF-CSIC), Madrid 28006, Spain
| | - Patrick J B Edwards
- School of Natural Sciences, Massey University, Palmerston North 4412, New Zealand
| | | | - Osman Doluca
- School of Natural Sciences, Massey University, Palmerston North 4412, New Zealand
| | | | - Carlos González
- Instituto de Química Física ‘Blas Cabrera’, (IQF-CSIC), Madrid 28006, Spain
| |
Collapse
|
5
|
Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
Collapse
Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
| |
Collapse
|
6
|
Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.
Collapse
Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| |
Collapse
|
7
|
Dobrovolná M, Brázda V, Warner EF, Bidula S. Inverted repeats in the monkeypox virus genome are hot spots for mutation. J Med Virol 2023; 95:e28322. [PMID: 36400742 PMCID: PMC10100261 DOI: 10.1002/jmv.28322] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
The current monkeypox virus (MPXV) strain differs from the strain arising in 2018 by 50+ single nucleotide polymorphisms (SNPs) and is mutating much faster than expected. The cytidine deaminase apolipoprotein B messenger RNA editing enzyme, catalytic subunit B (APOBEC3) was hypothesized to be driving this increased mutation. APOBEC has recently been identified to preferentially mutate cruciform DNA secondary structures formed by inverted repeats (IRs). IRs were recently identified as hot spots for mutation in severe acute respiratory syndrome coronavirus 2, and we aimed to identify whether IRs were also hot spots for mutation within MPXV genomes. We found that MPXV genomes were replete with IR sequences. Of the 50+ SNPs identified in the 2022 outbreak strain, 63.9% of these were found to have arisen within IR regions in the 2018 reference strain (MT903344.1). Notably, IR sequences found in the 2018 reference strain were significantly lost over time, with an average of 32.5% of these sequences being conserved in the 2022 MPXV genomes. This evidence was highly indicative that mutations were arising within IRs. This data provides further support to the hypothesis that APOBEC may be driving MPXV mutation and highlights the necessity for greater surveillance of IRs of MPXV genomes to detect new mutations.
Collapse
Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Emily F Warner
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Stefan Bidula
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
8
|
Kaushik Tiwari M, Colon-Rios DA, Tumu HCR, Liu Y, Quijano E, Krysztofiak A, Chan C, Song E, Braddock DT, Suh HW, Saltzman WM, Rogers FA. Direct targeting of amplified gene loci for proapoptotic anticancer therapy. Nat Biotechnol 2022; 40:325-334. [PMID: 34711990 PMCID: PMC8930417 DOI: 10.1038/s41587-021-01057-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
Gene amplification drives oncogenesis in a broad spectrum of cancers. A number of drugs have been developed to inhibit the protein products of amplified driver genes, but their clinical efficacy is often hampered by drug resistance. Here, we introduce a therapeutic strategy for targeting cancer-associated gene amplifications by activating the DNA damage response with triplex-forming oligonucleotides (TFOs), which drive the induction of apoptosis in tumors, whereas cells without amplifications process lower levels of DNA damage. Focusing on cancers driven by HER2 amplification, we find that TFOs targeting HER2 induce copy number-dependent DNA double-strand breaks (DSBs) and activate p53-independent apoptosis in HER2-positive cancer cells and human tumor xenografts via a mechanism that is independent of HER2 cellular function. This strategy has demonstrated in vivo efficacy comparable to that of current precision medicines and provided a feasible alternative to combat drug resistance in HER2-positive breast and ovarian cancer models. These findings offer a general strategy for targeting tumors with amplified genomic loci.
Collapse
Affiliation(s)
- Meetu Kaushik Tiwari
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Daniel A Colon-Rios
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Hemanta C Rao Tumu
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Yanfeng Liu
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Elias Quijano
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
| | - Adam Krysztofiak
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Cynthia Chan
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
| | | | - Hee-Won Suh
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
- Department of Chemical & Environmental Engineering, Yale University, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Faye A Rogers
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
9
|
Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands. Biomolecules 2022; 12:biom12030374. [PMID: 35327566 PMCID: PMC8945811 DOI: 10.3390/biom12030374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles—group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study’s main aim is to detect benzothiazole-based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds (1 and 6) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound (5) from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound 1 significantly inhibited RNase H. Compound 6 could differentiate between B- (binding of 6 dimers inside minor groove) and A-type (intercalation) helices by an induced CD signal, while both 5 and 6 selectively stabilized ATT triplex in regard to AT duplex. Compound 3 induced strong condensation-like changes in CD spectra of AT-rich DNA sequences.
Collapse
|
10
|
Kaufmann B, Willinger O, Kikuchi N, Navon N, Kermas L, Goldberg S, Amit R. An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro. ACS Synth Biol 2021; 10:1808-1820. [PMID: 34374529 DOI: 10.1021/acssynbio.1c00122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present Triplex-seq, a deep-sequencing method that systematically maps the interaction space between an oligo library of ssDNA triplex-forming oligos (TFOs) and a particular dsDNA triplex target site (TTS). We demonstrate the method using a randomized oligo library comprising 67 million variants, with five TTSs that differ in guanine (G) content, at two different buffer conditions, denoted pH 5 and pH 7. Our results show that G-rich triplexes form at both pH 5 and pH 7, with the pH 5 set being more stable, indicating that there is a subset of TFOs that form triplexes only at pH 5. In addition, using information analysis, we identify triplex-forming motifs (TFMs), which correspond to minimal functional TFO sequences. We demonstrate, in single-variant verification experiments, that TFOs with these TFMs indeed form a triplex with G-rich TTSs, and that a single mutation in the TFM motif can alleviate binding. Our results show that deep-sequencing platforms can substantially expand our understanding of triplex binding rules and aid in refining the DNA triplex code.
Collapse
Affiliation(s)
- Beate Kaufmann
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Or Willinger
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Nanami Kikuchi
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Noa Navon
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Lisa Kermas
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
11
|
Perera JDR, Carufe KEW, Glazer PM. Peptide nucleic acids and their role in gene regulation and editing. Biopolymers 2021; 112:e23460. [PMID: 34129732 DOI: 10.1002/bip.23460] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022]
Abstract
The unique properties of peptide nucleic acid (PNA) makes it a desirable candidate to be used in therapeutic and biotechnological interventions. It has been broadly utilized for numerous applications, with a major focus in regulation of gene expression, and more recently in gene editing. While the classic PNA design has mainly been employed to date, chemical modifications of the PNA backbone and nucleobases provide an avenue to advance the technology further. This review aims to discuss the recent developments in PNA based gene manipulation techniques and the use of novel chemical modifications to improve the current state of PNA mediated gene targeting.
Collapse
Affiliation(s)
- J Dinithi R Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
12
|
Lauria T, Slator C, McKee V, Müller M, Stazzoni S, Crisp AL, Carell T, Kellett A. A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors. Chemistry 2020; 26:16782-16792. [PMID: 32706904 DOI: 10.1002/chem.202002860] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/23/2020] [Indexed: 12/21/2022]
Abstract
Nucleic acid click chemistry was used to prepare a family of chemically modified triplex forming oligonucleotides (TFOs) for application as a new gene-targeted technology. Azide-bearing phenanthrene ligands-designed to promote triplex stability and copper binding-were 'clicked' to alkyne-modified parallel TFOs. Using this approach, a library of TFO hybrids was prepared and shown to effectively target purine-rich genetic elements in vitro. Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant. Therefore, the TFO and 'clicked' ligands work synergistically to provide sequence-selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex. To extend the boundaries of this hybrid system further, a click chemistry-based di-copper binding ligand was developed to accommodate designer ancillary ligands such as DPQ and DPPZ. When this ligand was inserted into a TFO, a dramatic improvement in targeted oxidative cleavage is afforded.
Collapse
Affiliation(s)
- Teresa Lauria
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Samuele Stazzoni
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Antony L Crisp
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,CÚRAM, Centre for Research in Medical Devices, Dublin City University, Glasnevin, Dublin, 9, Ireland
| |
Collapse
|
13
|
Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
Collapse
Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| |
Collapse
|
14
|
Muangkaew P, Vilaivan T. Modulation of DNA and RNA by PNA. Bioorg Med Chem Lett 2020; 30:127064. [PMID: 32147357 DOI: 10.1016/j.bmcl.2020.127064] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.
Collapse
Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| |
Collapse
|
15
|
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
|
16
|
Mandke P, Vasquez KM. Interactions of high mobility group box protein 1 (HMGB1) with nucleic acids: Implications in DNA repair and immune responses. DNA Repair (Amst) 2019; 83:102701. [PMID: 31563843 DOI: 10.1016/j.dnarep.2019.102701] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/10/2023]
Abstract
High mobility group box protein 1 (HMGB1) is a highly versatile, abundant, and ubiquitously expressed, non-histone chromosomal protein, which belongs to the HMGB family of proteins. These proteins form an integral part of the architectural protein repertoire to support chromatin structure in the nucleus. In the nucleus, the role of HMGB1 is attributed to its ability to bind to undamaged DNA, damaged DNA, and alternative (i.e. non-B) DNA structures with high affinity and subsequently induce bending of the DNA substrates. Due to its binding to DNA, HMGB1 has been implicated in critical biological processes, such as DNA transcription, replication, repair, and recombination. In addition to its intracellular functions, HMGB1 can also be released in the extracellular space where it elicits immunological responses. HMGB1 associates with many different molecules, including DNA, RNA, proteins, and lipopolysaccharides to modulate a variety of processes in both DNA metabolism and in innate immunity. In this review, we will focus on the implications of the interactions of HMGB1 with nucleic acids in DNA repair and immune responses. We report on the roles of HMGB1 in nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR) and DNA double-strand break repair (DSBR). We also report on its roles in immune responses via its potential effects on antigen receptor diversity generation [V(D)J recombination] and interactions with foreign and self-nucleic acids. HMGB1 expression is altered in a variety of cancers and immunological disorders. However, due to the diversity and complexity of the biological processes influenced by HMGB1 (and its family members), a detailed understanding of the intracellular and extracellular roles of HMGB1 in DNA damage repair and immune responses is warranted to ensure the development of effective HMGB1-related therapies.
Collapse
Affiliation(s)
- Pooja Mandke
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA.
| |
Collapse
|
17
|
Li N, Wang J, Ma K, Liang L, Mi L, Huang W, Ma X, Wang Z, Zheng W, Xu L, Chen JH, Yu Z. The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics. Nucleic Acids Res 2019; 47:e86. [PMID: 31114915 PMCID: PMC6735771 DOI: 10.1093/nar/gkz464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 05/06/2019] [Accepted: 05/15/2019] [Indexed: 11/21/2022] Open
Abstract
A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3' overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson-Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.
Collapse
Affiliation(s)
- Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Junli Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Kangkang Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lipei Mi
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Xiaofeng Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Wei Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Linyan Xu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| |
Collapse
|
18
|
Osman AMA, Pedersen EB. Conjugation of N-(3-(9-Ethynyl-6 H-indolo[2,3- b]quinoxalin-6-yl)propyl)-2,2,2-trifluoroacetamide Intercalator to a Triplex Forming Oligonucleotide, a Three-Way Junction, and a G-Quadruplex. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Amany M. A. Osman
- Nucleic Acid Center; Department of Physics; Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
- Chemistry Department; Faculty of Science; Menoufia University; Shebin El-Koam Egypt
| | - Erik B. Pedersen
- Nucleic Acid Center; Department of Physics; Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
| |
Collapse
|
19
|
Mojžíšek M. Triplex Forming Oligonucleotides – Tool for Gene Targeting. ACTA MEDICA (HRADEC KRÁLOVÉ) 2019. [DOI: 10.14712/18059694.2018.82] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This review deals with the antigene strategy whereby an oligonucleotide binds to the major or minor groove of double helical DNA where it forms a local triple helix. Preoccupation of this article is triplex-forming oligonucleotides (TFO). These are short, synthetic single-stranded DNAs that recognize polypurine:polypyrimidine regions in double stranded DNA in a sequence-specific manner and form triplex. Therefore, the mechanisms for DNA recognition by triple helix formation are discussed, together with main characteristics of TFO and also major obstacles that remain to be overcome are highlighted. TFOs can selectively inhibit gene expression at the transcriptional level or repair genetic defect by direct genome modification in human cells. These qualities makes TFO potentially powerful therapeutic tool for gene repair and/or expression regulation.
Collapse
|
20
|
Abstract
Peptide nucleic acids (PNAs) can bind duplex DNA in a sequence-targeted manner, forming a triplex structure capable of inducing DNA repair and producing specific genome modifications. Since the first description of PNA-mediated gene editing in cell free extracts, PNAs have been used to successfully correct human disease-causing mutations in cell culture and in vivo in preclinical mouse models. Gene correction via PNAs has resulted in clinically-relevant functional protein restoration and disease improvement, with low off-target genome effects, indicating a strong therapeutic potential for PNAs in the treatment or cure of genetic disorders. This review discusses the progress that has been made in developing PNAs as an effective, targeted agent for gene editing, with an emphasis on recent in vivo, nanoparticle-based strategies.
Collapse
|
21
|
Zhang ZL, Wu YY, Xi K, Sang JP, Tan ZJ. Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex. Biophys J 2017; 113:517-528. [PMID: 28793207 DOI: 10.1016/j.bpj.2017.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.
Collapse
Affiliation(s)
- Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; College of Physical Science and Technology, Yangzhou University, Yangzhou, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Jian-Ping Sang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
| |
Collapse
|
22
|
Yamayoshi A, Miyoshi D, Zouzumi YK, Matsuyama Y, Ariyoshi J, Shimada N, Murakami A, Wada T, Maruyama A. Selective and Robust Stabilization of Triplex DNA Structures Using Cationic Comb-type Copolymers. J Phys Chem B 2017; 121:4015-4022. [DOI: 10.1021/acs.jpcb.7b01926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Asako Yamayoshi
- The
Hakubi Center for Advanced Research, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daisuke Miyoshi
- Faculty
of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yu-ki Zouzumi
- Faculty
of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yohei Matsuyama
- Department
of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Jumpei Ariyoshi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Department
of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Naohiko Shimada
- Department
of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57
Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Akira Murakami
- Department
of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Takehiko Wada
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1,
Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Atsushi Maruyama
- Department
of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57
Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| |
Collapse
|
23
|
Analysis of RP2 and RPGR Mutations in Five X-Linked Chinese Families with Retinitis Pigmentosa. Sci Rep 2017; 7:44465. [PMID: 28294154 PMCID: PMC5353642 DOI: 10.1038/srep44465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/08/2017] [Indexed: 11/08/2022] Open
Abstract
Mutations in RP2 and RPGR genes are responsible for the X-linked retinitis pigmentosa (XLRP). In this study, we analyzed the RP2 and RPGR gene mutations in five Han Chinese families with XLRP. An approximately 17Kb large deletion including the exon 4 and exon 5 of RP2 gene was found in an XLRP family. In addition, four frameshift mutations including three novel mutations of c.1059 + 1 G > T, c.2002dupC and c.2236_2237del CT, as well as a previously reported mutation of c.2899delG were detected in the RPGR gene in the other four families. Our study further expands the mutation spectrum of RP2 and RPGR, and will be helpful for further study molecular pathogenesis of XLRP.
Collapse
|
24
|
Economopoulou P, Psyrri A. Organ-specific gene modulation: Principles and applications in cancer research. Cancer Lett 2017; 387:18-24. [PMID: 27224891 DOI: 10.1016/j.canlet.2016.05.015] [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: 02/26/2016] [Revised: 04/22/2016] [Accepted: 05/15/2016] [Indexed: 11/19/2022]
Abstract
Microarray and next generation sequencing has led to the exploration of correlated gene patterns and their shared functions. Gene modulators are proteins that alter the activity of transcription factors and influence the expression of their target genes. It is assumed that modulators are dependent on transcription factors. Several algorithms have been developed for the detection of gene modulators. On the other hand, it is becoming increasingly evident that modulators play a crucial role in carcinogenesis by interfering with fundamental biologic processes. Therapeutic gene modulation that is based on artificial modification of endogenous gene functions by designer molecules is an exciting new field of investigation.
Collapse
Affiliation(s)
- Panagiota Economopoulou
- Department of Internal Medicine, Section of Medical Oncology, Attikon University Hospital, National Kapodistrian University of Athens, School of Medicine, Athens, Greece.
| | - Amanda Psyrri
- Department of Internal Medicine, Section of Medical Oncology, Attikon University Hospital, National Kapodistrian University of Athens, School of Medicine, Athens, Greece
| |
Collapse
|
25
|
Bergquist H, Rocha CSJ, Álvarez-Asencio R, Nguyen CH, Rutland MW, Smith CIE, Good L, Nielsen PE, Zain R. Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)n Repeats by PNA or LNA Targeting. PLoS One 2016; 11:e0165788. [PMID: 27846236 PMCID: PMC5112992 DOI: 10.1371/journal.pone.0165788] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/07/2016] [Indexed: 01/08/2023] Open
Abstract
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression.
Collapse
Affiliation(s)
- Helen Bergquist
- Department of Medical Biochemistry and Microbiology, Microbiology-Immunology, Uppsala University, Uppsala, Sweden
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Cristina S. J. Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Rubén Álvarez-Asencio
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Stockholm, Sweden
| | - Chi-Hung Nguyen
- Laboratoire de Pharmacochimie, Institut Curie, PSL Research University, UMR 9187 – U 1196 CNRS-Institut Curie, INSERM, Centre Universitaire, Orsay, France
| | - Mark. W. Rutland
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Stockholm, Sweden
| | - C. I. Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Liam Good
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, United Kingdom
| | - Peter E. Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
26
|
Mukherjee A, Vasquez KM. Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks. J Vis Exp 2016. [PMID: 27911399 DOI: 10.3791/54678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic. While ICL-forming agents show preferences for certain base sequences (e.g., 5'-TA-3' is the preferred crosslinking site for psoralen), they largely induce DNA damage in an indiscriminate fashion. However, by covalently coupling the ICL-inducing agent to a triplex-forming oligonucleotide (TFO), which binds to DNA in a sequence-specific manner, targeted DNA damage can be achieved. Here, we use a TFO covalently conjugated on the 5' end to a 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) psoralen to generate a site-specific ICL on a mutation-reporter plasmid to use as a tool to study the architectural modification, processing, and repair of complex DNA lesions by HMGB1 in human cells. We describe experimental techniques to prepare TFO-directed ICLs on reporter plasmids, and to interrogate the association of HMGB1 with the TFO-directed ICLs in a cellular context using chromatin immunoprecipitation assays. In addition, we describe DNA supercoiling assays to assess specific architectural modification of the damaged DNA by measuring the amount of superhelical turns introduced on the psoralen-crosslinked plasmid by HMGB1. These techniques can be used to study the roles of other proteins involved in the processing and repair of TFO-directed ICLs or other targeted DNA damage in any cell line of interest.
Collapse
Affiliation(s)
- Anirban Mukherjee
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin;
| |
Collapse
|
27
|
Saleh AF, Fellows MD, Ying L, Gooderham NJ, Priestley CC. The Lack of Mutagenic Potential of a Guanine-Rich Triplex Forming Oligonucleotide in Physiological Conditions. Toxicol Sci 2016; 155:101-111. [PMID: 27660205 DOI: 10.1093/toxsci/kfw179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Triplex forming oligonucleotides (TFOs) bind in the major groove of DNA duplex in a sequence-specific manner imparted by Hoogsteen hydrogen bonds. There have been several reports demonstrating the ability of guanine-rich TFOs to induce targeted mutagenesis on an exogenous plasmid or an endogenous chromosomal locus. In particular, a 30mer guanine-rich triplex forming oligonucleotide, AG30, optimally designed to target the supFG1 reporter gene was reported to be mutagenic in the absence of DNA reactive agents in cultured cells and in vivo Here, we investigated the mutagenic potential of AG30 using the supFG1 shuttle vector forward mutation assay under physiological conditions. We also assessed the triplex binding potential of AG30 alongside cytotoxic and mutagenic assessment. In a cell free condition, AG30 was able to bind its polypurine target site in the supFG1 gene in the absence of potassium chloride and also aligned with a 5-fold increase in the mutant frequency when AG30 was pre-incubated with the supFG1 plasmid in the absence of potassium prior to transfection into COS-7 cells. However, when we analyzed triplex formation of AG30 and the supFG1 target duplex at physiological potassium levels, triplex formation was inhibited due to the formation of competing secondary structures. Subsequent assessment of mutant frequency under physiological conditions, by pre-transfecting COS-7 cells with the supFG1 plasmid prior to AG30 treatment led to a very small increase (1.4-fold) in the mutant frequency. Transfection of cells with even higher concentrations of AG30 did result in an elevated mutagenic response but this was also seen with a scrambled sequence, and was therefore considered unlikely to be biologically relevant as an associated increase in cytotoxicity was also apparent. Our findings also provide further assurance on the low potential of triplex-mediated mutation as a consequence of unintentional genomic DNA binding by therapeutic antisense oligonucleotides.
Collapse
Affiliation(s)
- Amer F Saleh
- Genetic Toxicology, Drug Safety and Metabolism, AstraZeneca, Macclesfield, Cheshire, United Kingdom
| | - Mick D Fellows
- Genetic Toxicology, Drug Safety and Metabolism, AstraZeneca, Macclesfield, Cheshire, United Kingdom
| | - Liming Ying
- Molecular medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Catherine C Priestley
- Genetic Toxicology, Drug Safety and Metabolism, AstraZeneca, Macclesfield, Cheshire, United Kingdom;
| |
Collapse
|
28
|
Janas MM, Jiang Y, Duncan RG, Hayes AN, Liu J, Kasperkovitz PV, Placke ME, Barros SA. Exposure to siRNA-GalNAc Conjugates in Systems of the Standard Test Battery for Genotoxicity. Nucleic Acid Ther 2016; 26:363-371. [PMID: 27387336 DOI: 10.1089/nat.2016.0622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Registration of pharmaceuticals requires an assessment of their genotoxic potential using in vitro and in vivo tests outlined in the International Conference on Harmonisation (ICH) guidance S2(R1). We have evaluated numerous siRNA-N-acetylgalactosamine (GalNAc) conjugates containing phosphorothioate linkages and various combinations of 2'-fluoro and 2'-O-methyl ribose modifications of multiple nucleotides in the ICH battery of assays, all of which have uniformly yielded negative results. To verify these negative genotoxicity results, in this study we confirm test article exposure using toolkit small interfering RNAs (siRNAs) representative of those in the clinic. In the Ames test, the highest uptake of the siRNA-GalNAc conjugates occurred at 1 h postdose in all bacterial strains independent of siRNA sequence or chemistry (up to ∼14,000 siRNA molecules per cell), followed by metabolic degradation of the parent siRNA at 6, 24, and 48 h postdose. siRNA-GalNAc conjugates were internalized by bacteria as assessed by protection from the addition of nucleases to the culture media following uptake and by the requirement of cell lysis for detection of the siRNA. In the in vitro chromosome aberration assay, uptake was observed in Chinese hamster ovary cells (up to ∼5,500 siRNA molecules per cell at 21 h postdose) and in CD3+ human peripheral blood lymphocytes (up to ∼500 siRNA molecules per cell at 21 h postdose). In the in vivo micronucleus assay in rat bone marrow, exposure to parent siRNA was 100-350 μg of antisense strand per gram of protein at 24 and 48 h postlimit dose of 2 g/kg. Loss of terminal nucleotides was detected in bone marrow by mass spectrometry, indicating exposure to monomer metabolites as well. Negative genotoxicity results were also confirmed in an in vitro double-strand DNA break assay in HeLa and HepG2 cells where exposure was maximized using transfection reagents. Thus negative genotoxicity assay results for siRNA-GalNAc conjugates were valid and not the result of poor or no intracellular exposure.
Collapse
Affiliation(s)
- Maja M Janas
- Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts
| | | | | | - Ju Liu
- Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts
| | | | | | - Scott A Barros
- Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts
| |
Collapse
|
29
|
Fellows MD. Targeting safety in the clinic for precise genome editing using CRISPR: a genotoxicologist's perspective. Per Med 2016; 13:279-282. [PMID: 29749810 DOI: 10.2217/pme-2016-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Mick D Fellows
- AstraZeneca Innovative Medicines & Early Development Darwin Building 310, Milton Science Park, Cambridge, CB4 OWG, UK
| |
Collapse
|
30
|
Kaushik Tiwari M, Adaku N, Peart N, Rogers FA. Triplex structures induce DNA double strand breaks via replication fork collapse in NER deficient cells. Nucleic Acids Res 2016; 44:7742-54. [PMID: 27298253 PMCID: PMC5027492 DOI: 10.1093/nar/gkw515] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
Structural alterations in DNA can serve as natural impediments to replication fork stability and progression, resulting in DNA damage and genomic instability. Naturally occurring polypurine mirror repeat sequences in the human genome can create endogenous triplex structures evoking a robust DNA damage response. Failures to recognize or adequately process these genomic lesions can result in loss of genomic integrity. Nucleotide excision repair (NER) proteins have been found to play a prominent role in the recognition and repair of triplex structures. We demonstrate using triplex-forming oligonucleotides that chromosomal triplexes perturb DNA replication fork progression, eventually resulting in fork collapse and the induction of double strand breaks (DSBs). We find that cells deficient in the NER damage recognition proteins, XPA and XPC, accumulate more DSBs in response to chromosomal triplex formation than NER-proficient cells. Furthermore, we demonstrate that XPC-deficient cells are particularly prone to replication-associated DSBs in the presence of triplexes. In the absence of XPA or XPC, deleterious consequences of triplex-induced genomic instability may be averted by activating apoptosis via dual phosphorylation of the H2AX protein. Our results reveal that damage recognition by XPC and XPA is critical to maintaining replication fork integrity and preventing replication fork collapse in the presence of triplex structures.
Collapse
Affiliation(s)
- Meetu Kaushik Tiwari
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Nneoma Adaku
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Natoya Peart
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Faye A Rogers
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
31
|
Affiliation(s)
- Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Sevilla 41092, Spain; ,
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Sevilla 41092, Spain; ,
| |
Collapse
|
32
|
Bertucat G, Lavery R, Prévost C. A Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA, via Triple-Helical Intermediates. J Biomol Struct Dyn 2016; 17 Suppl 1:147-53. [PMID: 22607418 DOI: 10.1080/07391102.2000.10506615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract A central function of RecA protein during homologous recombination is to promote sequence recognition and strand exchange between a stretched and unwound single-stranded DNA, to which it is complexed, and a duplex DNA. By studying the properties of DNA under the conditions of deformation imposed by RecA, we propose a model for recognition and strand exchange at the atomic level, via unusual triple-helical intermediates. In this model, association takes place within a stretched and unwound triple helix of a new type, where the invading single strand occupies the minor groove of the duplex in a parallel orientation. Our calculations indicate that strand exchange within this structure is exothermic and results in a triple helix where the third strand interacts in the major groove, the so-called R-DNA triple helix. Preliminary calculations suggest that sequence homology recognition within the triplex of association is partial and that it is completed during strand exchange and product formation.
Collapse
Affiliation(s)
- G Bertucat
- a Laboratoire de Biochimie Théorique, CNRS UPR 9080 , Institut de Biologie Physico-Chimique , 13, rue Pierre et Marie Curie , 75005 , Paris , France
| | | | | |
Collapse
|
33
|
Amirbekyan K, Duchemin N, Benedetti E, Joseph R, Colon A, Markarian SA, Bethge L, Vonhoff S, Klussmann S, Cossy J, Vasseur JJ, Arseniyadis S, Smietana M. Design, Synthesis, and Binding Affinity Evaluation of Hoechst 33258 Derivatives for the Development of Sequence-Specific DNA-Based Asymmetric Catalysts. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00495] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen Amirbekyan
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Nicolas Duchemin
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Erica Benedetti
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Rinah Joseph
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Aude Colon
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Shiraz A. Markarian
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Stephan Vonhoff
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Janine Cossy
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Jean-Jacques Vasseur
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
| | - Stellios Arseniyadis
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
- School
of Biological and Chemical Sciences, Queen Mary University of London, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
| |
Collapse
|
34
|
Berman CL, Barros SA, Galloway SM, Kasper P, Oleson FB, Priestley CC, Sweder KS, Schlosser MJ, Sobol Z. OSWG Recommendations for Genotoxicity Testing of Novel Oligonucleotide-Based Therapeutics. Nucleic Acid Ther 2016; 26:73-85. [PMID: 26978711 DOI: 10.1089/nat.2015.0534] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Oligonucleotide Safety Working Group subcommittee on genotoxicity testing considers therapeutic oligonucleotides (ONs) unlikely to be genotoxic based on their properties and on the negative results for ONs tested to date. Nonetheless, the subcommittee believes that genotoxicity testing of new ONs is warranted because modified monomers could be liberated from a metabolized ON and incorporated into DNA and could hypothetically cause chain termination, miscoding, and/or faulty replication or repair. The standard test battery as described in Option 1 of International Conference on Harmonisation S2(R1) is generally adequate to assess such potential. However, for the in vitro assay for gene mutations, mammalian cells are considered more relevant than bacteria for most ONs due to their known responsiveness to nucleosides and their greater potential for ON uptake; on the other hand, bacterial assays may be more appropriate for ONs containing non-ON components. Testing is not recommended for ONs with only naturally occurring chemistries or for ONs with chemistries for which there is documented lack of genotoxicity in systems with demonstrated cellular uptake. Testing is recommended for ONs that contain non-natural chemical modifications and use of the complete drug product (including linkers, conjugates, and liposomes) is suggested to provide the most clinically relevant assessment. Documentation of uptake into cells comparable to those used for genotoxicity testing is proposed because intracellular exposure cannot be assumed for these large molecules. ONs could also hypothetically cause mutations through triple helix formation with genomic DNA and no tests are available for detection of such sequence-specific mutations across the entire genome. However, because the potential for triplex formation by therapeutic ONs is extremely low, this potential can be assessed adequately by sequence analysis.
Collapse
Affiliation(s)
| | | | | | - Peter Kasper
- 4 Federal Institute for Drugs and Medical Devices (BfArM) , Bonn, Germany
| | | | | | - Kevin S Sweder
- 7 Forensic and National Security Sciences Institute, Syracuse University , Syracuse, New York
| | | | | |
Collapse
|
35
|
Sauer NJ, Mozoruk J, Miller RB, Warburg ZJ, Walker KA, Beetham PR, Schöpke CR, Gocal GFW. Oligonucleotide-directed mutagenesis for precision gene editing. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:496-502. [PMID: 26503400 PMCID: PMC5057361 DOI: 10.1111/pbi.12496] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 05/23/2023]
Abstract
Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed.
Collapse
|
36
|
Gupta A, Bahal R, Gupta M, Glazer PM, Saltzman WM. Nanotechnology for delivery of peptide nucleic acids (PNAs). J Control Release 2016; 240:302-311. [PMID: 26776051 DOI: 10.1016/j.jconrel.2016.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/10/2015] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Over the past three decades, peptide nucleic acids have been employed in numerous chemical and biological applications. Peptide nucleic acids possess enormous potential because of their superior biophysical properties, compared to other oligonucleotide chemistries. However, for therapeutic applications, intracellular delivery of peptide nucleic acids remains a challenge. In this review, we summarize the progress that has been made in delivering peptide nucleic acids to intracellular targets. In addition, we emphasize recent nanoparticle-based strategies for efficient delivery of conventional and chemically-modified peptides nucleic acids.
Collapse
Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Meera Gupta
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Chemical Engineering, Indian Institute of Technology-Delhi, New Delhi, India
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA; Department of Genetics, Yale University, New Haven, CT, USA.
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
| |
Collapse
|
37
|
Rogers FA, Lloyd JA, Tiwari MK. Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases. ARTIFICIAL DNA, PNA & XNA 2015; 5:e27792. [PMID: 25483840 DOI: 10.4161/adna.27792] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Triplex structures generated by sequence-specific triplex-forming oligonucleotides (TFOs) have proven to be promising tools for gene targeting strategies. In addition, triplex technology has been highly utilized to study the molecular mechanisms of DNA repair, recombination and mutagenesis. However, triplex formation utilizing guanine-rich oligonucleotides as third strands can be inhibited by potassium-induced self-association resulting in G-quadruplex formation. We report here that guanine-rich TFOs partially substituted with 8-aza-7-deaza-guanine (PPG) have improved target site binding in potassium compared with TFOs containing the natural guanine base. We designed PPG-substituted TFOs to bind to a polypurine sequence in the supFG1 reporter gene. The binding efficiency of PPG-substituted TFOs to the target sequence was analyzed using electrophoresis mobility gel shift assays. We have determined that in the presence of potassium, the non-substituted TFO, AG30 did not bind to its target sequence, however binding was observed with the PPG-substituted AG30 under conditions with up to 140 mM KCl. The PPG-TFOs were able to maintain their ability to induce genomic modifications as measured by an assay for gene-targeted mutagenesis. In addition, these compounds were capable of triplex-induced DNA double strand breaks, which resulted in activation of apoptosis.
Collapse
Affiliation(s)
- Faye A Rogers
- a Department of Therapeutic Radiology; Yale University School of Medicine; New Haven, CT USA
| | | | | |
Collapse
|
38
|
Abstract
Structure-prone DNA repeats are common components of genomic DNA in all kingdoms of life. In humans, these repeats are linked to genomic instabilities that result in various hereditary disorders, including many cancers. It has long been known that DNA repeats are not only highly polymorphic in length but can also cause chromosomal fragility and stimulate gross chromosomal rearrangements, i.e., deletions, duplications, inversions, translocations and more complex shuffles. More recently, it has become clear that inherently unstable DNA repeats dramatically elevate mutation rates in surrounding DNA segments and that these mutations can occur up to ten kilobases away from the repetitive tract, a phenomenon we call repeat-induced mutagenesis (RIM). This review describes experimental data that led to the discovery and characterization of RIM and discusses the molecular mechanisms that could account for this phenomenon.
Collapse
Affiliation(s)
- Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
| |
Collapse
|
39
|
Shen W, Liang XH, Sun H, Crooke ST. 2'-Fluoro-modified phosphorothioate oligonucleotide can cause rapid degradation of P54nrb and PSF. Nucleic Acids Res 2015; 43:4569-78. [PMID: 25855809 PMCID: PMC4482069 DOI: 10.1093/nar/gkv298] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/26/2015] [Indexed: 12/14/2022] Open
Abstract
Synthetic oligonucleotides are used to regulate gene expression through different mechanisms. Chemical modifications of the backbone of the nucleic acid and/or of the 2′ moiety of the ribose can increase nuclease stability and/or binding affinity of oligonucleotides to target molecules. Here we report that transfection of 2′-F-modified phosphorothioate oligonucleotides into cells can reduce the levels of P54nrb and PSF proteins through proteasome-mediated degradation. Such deleterious effects of 2′-F-modified oligonucleotides were observed in different cell types from different species, and were independent of oligonucleotide sequence, positions of the 2′-F-modified nucleotides in the oligonucleotides, method of delivery or mechanism of action of the oligonucleotides. Four 2′-F-modified nucleotides were sufficient to cause the protein reduction. P54nrb and PSF belong to Drosophila behavior/human splicing (DBHS) family. The third member of the family, PSPC1, was also reduced by the 2′-F-modified oligonucleotides. Preferential association of 2′-F-modified oligonucleotides with P54nrb was observed, which is partially responsible for the protein reduction. Consistent with the role of DBHS proteins in double-strand DNA break (DSB) repair, elevated DSBs were observed in cells treated with 2′-F-modified oligonucleotides, which contributed to severe impairment in cell proliferation. These results suggest that oligonucleotides with 2′-F modifications can cause non-specific loss of cellular protein(s).
Collapse
Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
40
|
Abstract
Triplex-forming oligonucleotides (TFOs) are capable of coordinating genome modification in a targeted, site-specific manner, causing mutagenesis or even coordinating homologous recombination events. Here, we describe the use of TFOs such as peptide nucleic acids for targeted genome modification. We discuss this method and its applications and describe protocols for TFO design, delivery, and evaluation of activity in vitro and in vivo.
Collapse
|
41
|
Kosbar TR, Sofan MA, Waly MA, Pedersen EB. Anti-parallel triplexes: Synthesis of 8-aza-7-deazaadenine nucleosides with a 3-aminopropynyl side-chain and its corresponding LNA analog. Bioorg Med Chem 2015; 23:2458-69. [PMID: 25868748 DOI: 10.1016/j.bmc.2015.03.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/13/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
Abstract
The phosphoramidites of DNA monomers of 7-(3-aminopropyn-1-yl)-8-aza-7-deazaadenine (Y) and 7-(3-aminopropyn-1-yl)-8-aza-7-deazaadenine LNA (Z) are synthesized, and the thermal stability at pH 7.2 and 8.2 of anti-parallel triplexes modified with these two monomers is determined. When, the anti-parallel TFO strand was modified with Y with one or two insertions at the end of the TFO strand, the thermal stability was increased 1.2°C and 3°C at pH 7.2, respectively, whereas one insertion in the middle of the TFO strand decreased the thermal stability 1.4°C compared to the wild type oligonucleotide. In order to be sure that the 3-aminopropyn-1-yl chain was contributing to the stability of the triplex, the nucleobase X without the aminopropynyl group was inserted in the same positions. In all cases the thermal stability was lower than the corresponding oligonucleotides carrying the 3-aminopropyn-1-yl chain, especially at the end of the TFO strand. On the other hand, the thermal stability of the anti-parallel triplex was dramatically decreased when the TFO strand was modified with the LNA monomer analog Z in the middle of the TFO strand (ΔTm=-9.1°C). Also the thermal stability decreased about 6.1°C when the TFO strand was modified with Z and the Watson-Crick strand with adenine-LNA (A(L)). The molecular modeling results showed that, in case of nucleobases Y and Z a hydrogen bond (1.69 and 1.72Ǻ, respectively) was formed between the protonated 3-aminopropyn-1-yl chain and one of the phosphate groups in Watson-Crick strand. Also, it was shown that the nucleobase Y made a good stacking and binding with the other nucleobases in the TFO and Watson-Crick duplex, respectively. In contrast, the nucleobase Z with LNA moiety was forced to twist out of plane of Watson-Crick base pair which is weakening the stacking interactions with the TFO nucleobases and the binding with the duplex part.
Collapse
Affiliation(s)
- Tamer R Kosbar
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
| | - Mamdouh A Sofan
- Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
| | - Mohamed A Waly
- Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
42
|
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
|
43
|
Solé A, Villalobos X, Ciudad CJ, Noé V. Repair of single-point mutations by polypurine reverse Hoogsteen hairpins. Hum Gene Ther Methods 2014; 25:288-302. [PMID: 25222154 DOI: 10.1089/hgtb.2014.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Polypurine reverse Hoogsteen hairpins (PPRHs) are formed by two intramolecularly bound antiparallel homopurine domains linked by a five-thymidine loop. One of the homopurine strands binds with antiparallel orientation by Watson-Crick bonds to the polypyrimidine target sequence, forming a triplex. We had previously reported the ability of PPRHs to effectively bind dsDNA displacing the fourth strand away from the newly formed triplex. The main goal of this work was to explore the possibility of repairing a point mutation in mammalian cells using PPRHs as tools. These repair-PPRHs contain different combinations of extended sequences of DNA with the corrected nucleotide to repair the point mutation. As a model we used the dihydrofolate reductase gene. On the one hand, we demonstrate in vitro that PPRHs bind specifically to their polypyrimidine target sequence, opening the two strands of the dsDNA, and allowing the binding of a given repair oligonucleotide to the displaced strand of the DNA. Subsequently, we show at a cellular level (Chinese ovary hamster cells) that repair-PPRHs are able to correct a single-point mutation in a dihydrofolate reductase minigene bearing a nonsense mutation, both in an extrachromosomal location and when the mutated plasmid was stably transfected into the cells. Finally, this methodology was successfully applied to repair a single-point mutation at the endogenous locus, using the DA5 cell line with a deleted nucleotide in exon six of the dhfr gene.
Collapse
Affiliation(s)
- Anna Solé
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , E08028 Barcelona, Spain
| | | | | | | |
Collapse
|
44
|
Alam R, Thazhathveetil AK, Li H, Seidman MM. Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction. Methods Mol Biol 2014; 1114:103-13. [PMID: 24557899 DOI: 10.1007/978-1-62703-761-7_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Strategies for site-specific modulation of genomic sequences in mammalian cells require two components. One must be capable of recognizing and activating a specific target sequence in vivo, driving that site into an exploitable repair pathway. Information is transferred to the site via participation in the pathway by the second component, a donor nucleic acid, resulting in a permanent change in the target sequence. We have developed biologically active triple helix forming oligonucleotides (TFOs) as site-specific gene targeting reagents. These TFOs, linked to DNA reactive compounds (such as a cross-linking agent), activate pathways that can engage informational donors. We have used the combination of a psoralen-TFO and single strand oligonucleotide donors to generate novel cell lines with directed sequence changes at the target site. Here we describe the synthesis and purification of bioactive psoralen-linked TFOs, their co-introduction into mammalian cells with donor nucleic acids, and the identification of cells with sequence conversion of the target site. We have emphasized details in the synthesis and purification of the oligonucleotides that are essential for preparation of reagents with optimal activity.
Collapse
|
45
|
Esguerra M, Nilsson L, Villa A. Triple helical DNA in a duplex context and base pair opening. Nucleic Acids Res 2014; 42:11329-38. [PMID: 25228466 PMCID: PMC4191418 DOI: 10.1093/nar/gku848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region.
Collapse
Affiliation(s)
- Mauricio Esguerra
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| |
Collapse
|
46
|
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
|
47
|
Abstract
Repetitive genomic sequences can adopt a number of alternative DNA structures that differ from the canonical B-form duplex (i.e. non-B DNA). These non-B DNA-forming sequences have been shown to have many important biological functions related to DNA metabolic processes; for example, they may have regulatory roles in DNA transcription and replication. In addition to these regulatory functions, non-B DNA can stimulate genetic instability in the presence or absence of DNA damage, via replication-dependent and/or replication-independent pathways. This review focuses on the interactions of non-B DNA conformations with DNA repair proteins and how these interactions impact genetic instability.
Collapse
Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
| |
Collapse
|
48
|
Abstract
Genome targeting and editing in vitro and in vivo can be achieved through an interplay of exogenously introduced molecules and the induction of endogenous recombination machinery. The former includes a repertoire of sequence-specific binding molecules for targeted induction and appropriation of this machinery, such as by triplex-forming oligonucleotides (TFOs) or triplex-forming peptide nucleic acids (PNAs) and recombinagenic donor DNA, respectively. This versatile targeting and editing via recombination approach facilitates high-fidelity and low-off-target genome mutagenesis, repair, expression, and regulation. Herein, we describe the current state-of-the-art in triplex-mediated genome targeting and editing with a perspective towards potential translational and therapeutic applications. We detail several materials and methods for the design, delivery, and use of triplex-forming and recombinagenic molecules for mediating and introducing specific, heritable, and safe genomic modifications. Furthermore we denote some guidelines for endogenous genome targeting and editing site identification and techniques to test targeting and editing efficiency.
Collapse
Affiliation(s)
- Faisal Reza
- Departments of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | | |
Collapse
|
49
|
Therapeutic applications of anti-sense mechanisms for the treatment of cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
50
|
Belotserkovskii BP, Mirkin SM, Hanawalt PC. DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev 2013; 113:8620-37. [PMID: 23972098 DOI: 10.1021/cr400078y] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|