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Oyaghire SN, Quijano E, Perera JDR, Mandl HK, Saltzman WM, Bahal R, Glazer PM. DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101635. [PMID: 37920723 PMCID: PMC10621889 DOI: 10.1016/j.xcrp.2023.101635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Peptide nucleic acids (PNAs) can target and stimulate recombination reactions in genomic DNA. We have reported that γPNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene-editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity than that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.
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Affiliation(s)
- Stanley N. Oyaghire
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- These authors contributed equally
| | - Elias Quijano
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- These authors contributed equally
| | - J. Dinithi R. Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hanna K. Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Department of Chemical & Environmental Engineering, Yale University, New Haven, CT 06511, USA
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Lead contact
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Abdelbaky AS, Prokhorov IA, Gnuskova EV, Esipova OV, Kirillova YG. Convenient and Efficient Syntheses of Peptide Nucleic Acid Purine Monomers. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666191014161442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Currently, peptide nucleic acids (PNAs) play an important role as therapeutic
agents, molecular tools for diagnosis and detection of genetic diseases as well as in biosensor
probes. This research aims to optimize the synthesis of aeg- and γ-(S)-Me PNA
monomers based on L-Ala, intended for oligomerization according to the Boc protocol.
The monomers were obtained through the condensation of the corresponding pseudopeptides
with carboxymethyl purine nucleic bases. During the work, the optimization of benzyloxycarbonyl-
N6-adenine-9-yl-acetic acid and benzyloxycarbonyl-N2-guanine-9-ylacetic
acid was carried out. The synthesis of benzyloxycarbonyl-N6-adenine-9-yl-acetic
acid was conducted in three stages based on adenine with an overall yield of 22%. At the
same time, the conditions for effective recrystallization of the mixture after alkylation of
benzyloxycarbonyl-N6-adenine with ethyl bromoacetic acid ether have been developed to isolate the desired
N9-regioisomer. Also, the optimization of a known method for producing benzyloxycarbonyl-N2-guanine-9-ylacetic
acid from 2-amino-6-chloropurine was carried out. The total yield of the five-stage scheme was 55%.
Condensation of aeg- and γ-(S)-Me pseudopeptides with benzyloxycarbonyl-N6-adenine-9-yl-acetic acid and
benzyloxycarbonyl-N2-guanine-9-yl-acetic acid was performed by the standard carbodiimide method,
DCC/HOBt in DMF followed by the removal of C-terminal methyl protective group by alkaline hydrolysis.
The structure of the new compounds obtained was confirmed by spectral analysis methods. This work provides
simple and optimized methods for obtaining protected carboxymethyl purine bases and increasing the efficiency
of the synthesis and synthesized purine PNA monomers in an acceptable yield.
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Affiliation(s)
- Ahmed S. Abdelbaky
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Ivan A. Prokhorov
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Elena V. Gnuskova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Olga V. Esipova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Yulia G. Kirillova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
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Abdelbaky AS, Prokhorov IA, Smirnov IP, Koroleva KM, Shvets VI, Kirillova YG. Synthesis of α-(R)-/γ-(S)-Dimethyl Substituted Peptide Nucleic Acid Submonomer Using Mitsunobu Reaction. LETT ORG CHEM 2019. [DOI: 10.2174/1570178616666190118155031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
One of the major challenges facing modern biochemical and biomedical technologies are
finding molecular tools for diagnosis and detection of genetic diseases. In this connection, several classes
of oligonucleotides have been developed that can recognize and bind to DNA and RNA with high
affinity and sequence selectivity and withstand enzymatic degradation by proteases and nucleases;
however, few can traverse the cell membrane on their own. One such promising class of nucleic acid
mimics developed in the last two decades which showed good results in vitro, are the peptide nucleic
acids (PNAs). New chiral α- and γ-peptide Nucleic Acid (PNA) submonomer with methyl substituents
in pseudopeptide backbone were synthesized via Mitsunobu reaction. The α-(R)-/γ-(S)-configuration of
the chiral centres will ensure the preorganization of the PNA oligomer into a right-handed helix. The
results obtained showed that Boc/Fmoc-submonomer compatible with Boc-protocol PNAs solid-phase
synthesis on an MBHA resin. We synthesized simple and efficient α-R-, γ-S-disubstituted PNA submonomer
based on L-Ala and D-Ala with the construction of the intermediate pseudopeptide moiety
by Mitsunobu reaction for subsequent use in the Boc-Protocol of solid phase PNA synthesis.
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Affiliation(s)
- Ahmed S. Abdelbaky
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Ivan A. Prokhorov
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Igor P. Smirnov
- Department of Biophysics, Federal Research and Clinical Center of Physical-Chemical Medicine, 119571 Moscow, Russian Federation
| | - Kristina M. Koroleva
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Vitaliy I. Shvets
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Yulia G. Kirillova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
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Manukyan AK. Structural characteristics of cyclopentane-modified peptide nucleic acids from molecular dynamics simulations. Struct Chem 2017. [DOI: 10.1007/s11224-017-0970-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kirillova Y, Boyarskaya N, Dezhenkov A, Tankevich M, Prokhorov I, Varizhuk A, Eremin S, Esipov D, Smirnov I, Pozmogova G. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs): Synthesis and DNA Binding. PLoS One 2015; 10:e0140468. [PMID: 26469337 PMCID: PMC4607454 DOI: 10.1371/journal.pone.0140468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022] Open
Abstract
New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA.
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Affiliation(s)
- Yuliya Kirillova
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- * E-mail:
| | - Nataliya Boyarskaya
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Andrey Dezhenkov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Mariya Tankevich
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Ivan Prokhorov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Anna Varizhuk
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Sergei Eremin
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Dmitry Esipov
- Department of Bioorganic Chemistry, Biology Faculty, Moscow State University, Moscow, Russia
| | - Igor Smirnov
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Galina Pozmogova
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
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Sacui I, Hsieh WC, Manna A, Sahu B, Ly DH. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly. J Am Chem Soc 2015; 137:8603-10. [PMID: 26079820 DOI: 10.1021/jacs.5b04566] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.
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Affiliation(s)
- Iulia Sacui
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Che Hsieh
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Arunava Manna
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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Regioselective alkylation of guanine derivatives in the synthesis of peptide nucleic acid monomers. Russ Chem Bull 2015. [DOI: 10.1007/s11172-015-0986-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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