1
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Lee ETT, Sato Y, Ujuagu AF, Nishizawa S. Forced intercalation-induced light-up peptides as fluorogenic indicators for the HIV-1 TAR RNA-ligand assay. Analyst 2024. [PMID: 38860915 DOI: 10.1039/d4an00530a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Fluorescence indicators capable of binding to human immunodeficiency virus-1 (HIV-1) trans-activation responsive (TAR) RNA are powerful tools for the exploratory studies of the identification of anti-HIV drug candidates. This work presents a new design strategy for fluorogenic indicators with a transactivator of transcription (Tat)-derived peptide based on the forced intercalation of thiazole orange (TO) dyes (FIT). The developed 9-mer FIT peptide (RKKRR-TO-RRR: named FiLuP) features the TO unit integrated onto a Dap (2,3-diaminopropionic acid) residue in the middle of the Tat peptide sequence; the Q (glutamic acid) residue in the Tat peptide (RKKRR-Q-RRR) is replaced with TO as if it were an amino acid surrogate. This facilitates a significant light-up response (450-fold at λem = 541 nm, Φfree = 0.0057, and Φbound = 0.61) upon binding to TAR RNA. The response of FiLuP is highly selective to TAR RNA over other non-cognate RNAs, and FiLuP maintains strong binding affinity (Kd = 1.0 ± 0.6 nM). Significantly, in contrast to previously developed Tat peptide-based FRET probes, FiLuP is able to discriminate between "competitive" and "noncompetitive" inhibitors when used in the fluorescence indicator displacement (FID) assay. The FID assay under stringent screening conditions is also possible, enabling super-strong competitive binders toward TAR RNA to be sieved out.
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Affiliation(s)
- En Ting Tabitha Lee
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Akunna F Ujuagu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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2
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Katkevics M, MacKay JA, Rozners E. Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs. Chem Commun (Camb) 2024; 60:1999-2008. [PMID: 38259187 PMCID: PMC10922694 DOI: 10.1039/d3cc05409h] [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] [Indexed: 01/24/2024]
Abstract
Over the last three decades, our view of RNA has changed from a simple intermediate supporting protein synthesis to a major regulator of biological processes. In the expanding area of RNA research, peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of complex RNAs. As discussed in this feature article, the key advantages of PNAs are high sequence specificity and affinity for RNA (>10 fold higher than for DNA) that are difficult to achieve with small molecule ligands. Emerging studies demonstrate that triple-helical binding of PNAs can modulate biological function and control dynamic conformational equilibria of complex folded RNAs. These results suggest that PNA has a unique potential as a research tool and therapeutic compound targeting RNA. The remaining problems hampering advances in these directions are limitations of sequences that can be recognized by Hoogsteen triplexes (typically purine rich tracts), poor cellular uptake and bioavailability of PNA, and potential off-target effects in biological systems. Recent exciting studies are discussed that illustrate how synthetic nucleic acid chemistry provides innovative solutions for these problems.
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Affiliation(s)
- Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
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3
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Singh G, Monga V. Peptide Nucleic Acids: Recent Developments in the Synthesis and Backbone Modifications. Bioorg Chem 2023; 141:106860. [PMID: 37748328 DOI: 10.1016/j.bioorg.2023.106860] [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: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
Nucleic acid represents the ideal drug candidate for protein targets that are hard to target or against which drug development is not easy. Peptide nucleic acids (PNAs) are synthesized by attaching modified peptide backbones generally derived from repetitive N-2-aminoethyl glycine units in place of the regular phosphodiester backbone and represent synthetic impersonator of nucleic acids that offers an exciting research field due to their fascinating spectrum of biotechnological, diagnostic and potential therapeutic applications. The semi-rigid peptide nucleic acid backbone serves as a nearly-perfect template for attaching complimentary base pairs on DNA or RNA in a sequence-dependent manner as described by Watson-Crick models. PNAs and their analogues are endowed with exceptionally high affinity and specificity for receptor sites, essentially due to their polyamide backbone's uncharged and flexible nature. The present review compiled various strategies to modify the polypeptide backbone for improving the target selectivity and stability of the PNAs in the body. The investigated biological activities carried out on PNAs have also been summarized in the present review.
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Affiliation(s)
- Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, VPO-Ghudda, Bathinda 151401, Punjab, India.
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4
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Talbott JM, Tessier BR, Harding EE, Walby GD, Hess KJ, Baskevics V, Katkevics M, Rozners E, MacKay JA. Improved Triplex-Forming Isoorotamide PNA Nucleobases for A-U Recognition of RNA Duplexes. Chemistry 2023; 29:e202302390. [PMID: 37647091 DOI: 10.1002/chem.202302390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA2 triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.
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Affiliation(s)
- John M Talbott
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Brandon R Tessier
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
| | - Emily E Harding
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Grant D Walby
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Kyle J Hess
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | | | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
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5
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Mikame Y, Yamayoshi A. Recent Advancements in Development and Therapeutic Applications of Genome-Targeting Triplex-Forming Oligonucleotides and Peptide Nucleic Acids. Pharmaceutics 2023; 15:2515. [PMID: 37896275 PMCID: PMC10609763 DOI: 10.3390/pharmaceutics15102515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Recent developments in artificial nucleic acid and drug delivery systems present possibilities for the symbiotic engineering of therapeutic oligonucleotides, such as antisense oligonucleotides (ASOs) and small interfering ribonucleic acids (siRNAs). Employing these technologies, triplex-forming oligonucleotides (TFOs) or peptide nucleic acids (PNAs) can be applied to the development of symbiotic genome-targeting tools as well as a new class of oligonucleotide drugs, which offer conceptual advantages over antisense as the antigene target generally comprises two gene copies per cell rather than multiple copies of mRNA that are being continually transcribed. Further, genome editing by TFOs or PNAs induces permanent changes in the pathological genes, thus facilitating the complete cure of diseases. Nuclease-based gene-editing tools, such as zinc fingers, CRISPR-Cas9, and TALENs, are being explored for therapeutic applications, although their potential off-target, cytotoxic, and/or immunogenic effects may hinder their in vivo applications. Therefore, this review is aimed at describing the ongoing progress in TFO and PNA technologies, which can be symbiotic genome-targeting tools that will cause a near-future paradigm shift in drug development.
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Affiliation(s)
- Yu Mikame
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
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6
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Alavijeh NS, Serrano A, Peters MS, Wölper C, Schrader T. Design and Synthesis of Artificial Nucleobases for Sequence-Selective DNA Recognition within the Major Groove. Chem Asian J 2023; 18:e202300637. [PMID: 37616375 DOI: 10.1002/asia.202300637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/26/2023]
Abstract
We present the design and synthesis of artificial specific nucleobases, each one recognizing a single base pair within the major groove of duplex DNA. Computational calculations indicate that PNAs modified with these nucleobases enable the formation of highly stable triple helices with no sequence restrictions through multiple hydrogen bonding and π⋅⋅⋅π stacking interactions, without significantly widening the DNA double helix. New synthetic routes were developed to the structures of these fused heterocycles which have rarely been described in the literature. NMR titration experiments indicate specific hydrogen bonding at the Hoogsteen sites. The new building blocks allow the construction of four PNA monomers for each canonic base pair and their covalent connection to PNA oligomers. These can be designed complementary to any given DNA sequence. With high efficiency and relative simplicity of operation, the described methodologies and strategies hence form the basis for a new supramolecular ligand system targeting double-stranded DNA without strand invasion.
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Affiliation(s)
- Nahid S Alavijeh
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Alvaro Serrano
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Max S Peters
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Christoph Wölper
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
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7
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López-Tena M, Chen SK, Winssinger N. Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits. Bioconjug Chem 2023; 34:111-123. [PMID: 35856656 DOI: 10.1021/acs.bioconjchem.2c00292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.
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Affiliation(s)
- Miguel López-Tena
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Si-Kai Chen
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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8
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Swenson C, Argueta-Gonzalez HS, Sterling SA, Robichaux R, Knutson SD, Heemstra JM. Forced Intercalation Peptide Nucleic Acid Probes for the Detection of an Adenosine-to-Inosine Modification. ACS OMEGA 2023; 8:238-248. [PMID: 36643573 PMCID: PMC9835161 DOI: 10.1021/acsomega.2c03568] [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] [Received: 06/07/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The deamination of adenosine to inosine is an important modification in nucleic acids that functionally recodes the identity of the nucleobase to a guanosine. Current methods to analyze and detect this single nucleotide change, such as sequencing and PCR, typically require time-consuming or costly procedures. Alternatively, fluorescent "turn-on" probes that result in signal enhancement in the presence of target are useful tools for real-time detection and monitoring of nucleic acid modification. Here we describe forced-intercalation PNA (FIT-PNA) probes that are designed to bind to inosine-containing nucleic acids and use thiazole orange (TO), 4-dimethylamino-naphthalimide (4DMN), and malachite green (MG) fluorogenic dyes to detect A-to-I editing events. We show that incorporation of the dye as a surrogate base negatively affects the duplex stability but does not abolish binding to targets. We then determined that the identity of the adjacent nucleobase and temperature affect the overall signal and fluorescence enhancement in the presence of inosine, achieving an 11-fold increase, with a limit of detection (LOD) of 30 pM. We determine that TO and 4DMN probes are viable candidates to enable selective inosine detection for biological applications.
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Affiliation(s)
- Colin
S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | - Sierra A. Sterling
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ryan Robichaux
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Steve D. Knutson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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9
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Shavrina OM, Onys`ko PP, Rassukana YV. Mono- and difluorination of methylene group in isomeric pyrimidinyl- and pyridinylacetates with N-fluorobenzenesulfonimide. J Fluor Chem 2022. [DOI: 10.1016/j.jfluchem.2022.110027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Ryan CA, Baskevics V, Katkevics M, Rozners E. 2-Guanidyl pyridine PNA nucleobase for triple-helical Hoogsteen recognition of cytosine in double-stranded RNA. Chem Commun (Camb) 2022; 58:7148-7151. [PMID: 35666682 DOI: 10.1039/d2cc02615e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In triplex-forming peptide nucleic acid, a novel 2-guanidyl pyridine nucleobase (V) enables recognition of up to two cytosine interruptions in polypurine tracts of dsRNA by engaging the entire Hoogsteen face of C-G base pair. Ab initio and molecular dynamics simulations provided insights into H-bonding interactions that stabilized V·C-G triplets. Our results provided insights for future design of improved nucleobases, which is an important step towards the ultimate goal of recognition of any sequence of dsRNA.
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Affiliation(s)
- Christopher A Ryan
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
| | | | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
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11
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Sato Y, Miura H, Tanabe T, Okeke CU, Kikuchi A, Nishizawa S. Fluorescence Sensing of the Panhandle Structure of the Influenza A Virus RNA Promoter by Thiazole Orange Base Surrogate-Carrying Peptide Nucleic Acid Conjugated with Small Molecule. Anal Chem 2022; 94:7814-7822. [PMID: 35604144 DOI: 10.1021/acs.analchem.1c05488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a new class of triplex-forming peptide nucleic acid (PNA)-based fluorogenic probes for sensing of the panhandle structure of the influenza A virus (IAV) RNA promoter region. Here, a small molecule (DPQ) capable of selectively binding to the internal loop structure was conjugated with triplex-forming forced intercalation of the thiazole orange (tFIT) probe with natural PNA nucleobases. The resulting conjugate, tFIT-DPQ, showed a significant light-up response (83-fold) upon strong (Kd = 107 nM) and structure-selective binding to the IAV RNA promoter region under physiological conditions (pH 7.0, 100 mM NaCl). We demonstrated the conjugation of these two units through the suitable spacer was key to show useful binding and fluorogenic signaling functions. tFIT-DPQ facilitated the sensitive and selective detection of IAV RNA based on its binding to the promoter region. Furthermore, we found that tFIT-DPQ could work as a sensitive indicator for screening of test compounds targeting the IAV RNA promoter region in the fluorescence indicator displacement assay.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiromasa Miura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Chioma Uche Okeke
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Akiko Kikuchi
- Department of Kampo and Integrative Medicine, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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12
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NISHIZAWA S, SATO T, LEE ETT, SAKAMOTO N, CHIBA T, TANABE T, YOSHINO Y, TAKAHASHI Y, SATO Y. Triplex-Forming Peptide Nucleic Acid Probes Having Cyanine Base Surrogates for Fluorogenic Sensing of Double-Stranded RNA. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seiichi NISHIZAWA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Takaya SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | | | - Naonari SAKAMOTO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Toshiki CHIBA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Takaaki TANABE
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yukina YOSHINO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yuki TAKAHASHI
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yusuke SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
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13
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Liang Y, Miao S, Mao J, Devari S, Gonzalez M, Bong D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry 2022; 28:e202103616. [PMID: 34693570 PMCID: PMC8758549 DOI: 10.1002/chem.202103616] [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: 10/06/2021] [Indexed: 01/12/2023]
Abstract
We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Jie Mao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Maricarmen Gonzalez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
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14
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Filho MS, Massi L, Millet A, Michel D, Moussa W, Ronco C, Benhida R. Energy-resolved mass spectrometry to investigate nucleobase triplexes – a study applied to triplex-forming artificial nucleobases. NEW J CHEM 2022. [DOI: 10.1039/d2nj00665k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper discloses the use of an energy-resolved mass spectrometric-based approach to assess the stabilities of base triplexes encompassing artificial nucleobases by using variable energy collision-induced dissociation.
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Affiliation(s)
- Mauro Safir Filho
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Lionel Massi
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Antoine Millet
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Dylan Michel
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Wafa Moussa
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Cyril Ronco
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Rachid Benhida
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
- Mohamed VI Polytechnic University, UM6P, 43150, Ben Guerir, Morocco
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15
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Zhan X, Deng L, Chen G. Mechanisms and applications of peptide nucleic acids selectively binding to double-stranded RNA. Biopolymers 2021; 113:e23476. [PMID: 34581432 DOI: 10.1002/bip.23476] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022]
Abstract
RNAs form secondary structures containing double-stranded base paired regions and single-stranded regions. Probing, detecting and modulating RNA structures and dynamics requires the development of molecular sensors that can differentiate the sequence and structure of RNAs present in viruses and cells, as well as in extracellular space. In this review, we summarize the recent progress on the development of chemically modified peptide nucleic acids (PNAs) for the selective recognition of double-stranded RNA (dsRNA) sequences over both single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) sequences. We also briefly discuss the applications of sequence-specific dsRNA-binding PNAs in sensing and stabilizing dsRNA structures and inhibiting dsRNA-protein interactions.
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Affiliation(s)
- Xuan Zhan
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Liping Deng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
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16
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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17
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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18
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Brodyagin N, Kumpina I, Applegate J, Katkevics M, Rozners E. Pyridazine Nucleobase in Triplex-Forming PNA Improves Recognition of Cytosine Interruptions of Polypurine Tracts in RNA. ACS Chem Biol 2021; 16:872-881. [PMID: 33881836 DOI: 10.1021/acschembio.1c00044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sequence specific recognition of regulatory noncoding RNAs would open new possibilities for fundamental science and medicine. However, molecular recognition of such complex double-stranded RNA (dsRNA) structures remains a formidable problem. Recently, we discovered that peptide nucleic acids (PNAs) form an unusually stable and sequence-specific triple helix with dsRNA. Triplex-forming PNAs could become universal tools for recognition of noncoding dsRNAs but are limited by the requirement of polypurine tracts in target RNAs as only purines form stable Hoogsteen hydrogen bonded base triplets. Herein, we systematically surveyed simple nitrogen heterocycles PN as modified nucleobases for recognition of cytosine in PN*C-G triplets. We found that a 3-pyridazinyl nucleobase formed significantly more stable PN*C-G triplets than other heterocycles including the pyrimidin-2-one previously used by us and others for recognition of cytosine interruptions in polypurine tracts of PNA-dsRNA triplexes. Our results improve triple helical recognition of dsRNA and provide insights for future development of new nucleobases to expand the sequence scope of noncoding dsRNAs that can be targeted by triplex-forming PNAs.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Ilze Kumpina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Justin Applegate
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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19
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Brodyagin N, Maryniak AL, Kumpina I, Talbott JM, Katkevics M, Rozners E, MacKay JA. Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A-U Base Pairs in Double-Stranded RNA. Chemistry 2021; 27:4332-4335. [PMID: 33439519 DOI: 10.1002/chem.202005401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/12/2021] [Indexed: 02/06/2023]
Abstract
Peptide nucleic acids (PNA) with extended isoorotamide containing nucleobases (Io ) were designed for binding A-U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments revealed improved affinity for A-U using the Io scaffold in PNA. PNAs having four sequential Io extended nucleobases maintained high binding affinity.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Aubrey L Maryniak
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
| | - Ilze Kumpina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - John M Talbott
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
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