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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Kumpina I, Loubidi M, Rozners E. Comparison of 2-Aminopyridine and 4-Thiopseudisocytosine PNA Nucleobases for Hoogsteen Recognition of Guanosine in RNA. ACS OMEGA 2024; 9:7249-7254. [PMID: 38371848 PMCID: PMC10870399 DOI: 10.1021/acsomega.3c09775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of folded biologically relevant RNA. Chemical modifications are actively being developed to achieve high affinity and sequence specificity under physiological conditions. In this study, we compared two modified PNA nucleobases, 2-aminopyridine (M) and 4-thiopseudisocytosine (L), as alternatives to protonated cytosine (unfavorable under physiological conditions), to form more stable triplets than C+·G-C. Both nucleobases formed M+·G-C and L·G-C triplets of similar stability; however, the L-modified PNAs showed somewhat reduced sequence specificity. In conclusion, M and L represent two alternative solutions to the problem of cytosine protonation in triple-helical recognition of RNA. In M, the pKa is increased to favor partial protonation, which improves solubility and cellular uptake of M-modified PNAs. In L, the sulfur substitution enhances favorable hydrophobic interactions, which may have advantages in avoiding off-target effects that may be caused by cationic modifications. However, our results showed that substituting Ms with Ls did not restore the sequence specificity of a PNA containing cationic groups.
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Affiliation(s)
- Ilze Kumpina
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mohammed Loubidi
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
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3
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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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4
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Ryan C, Rahman MM, Kumar V, Rozners E. Triplex-Forming Peptide Nucleic Acid Controls Dynamic Conformations of RNA Bulges. J Am Chem Soc 2023; 145:10497-10504. [PMID: 37155726 PMCID: PMC10198159 DOI: 10.1021/jacs.2c12488] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Indexed: 05/10/2023]
Abstract
RNA folding is driven by the formation of double-helical segments interspaced by loops of unpaired nucleotides. Among the latter, bulges formed by one or several unpaired nucleotides are one of the most common structural motifs that play an important role in stabilizing RNA-RNA, RNA-protein, and RNA-small molecule interactions. Single-nucleotide bulges can fold in alternative structures where the unpaired nucleobase is either looped-out (flexible) in a solvent or stacked-in (intercalated) between the base pairs. In the present study, we discovered that triplex-forming peptide nucleic acids (PNAs) had unusually high affinity for single-purine-nucleotide bulges in double-helical RNA. Depending on the PNA's sequence, the triplex formation shifted the equilibrium between looped-out and stacked-in conformations. The ability to control the dynamic equilibria of RNA's structure will be an important tool for studying structure-function relationships in RNA biology and may have potential in novel therapeutic approaches targeting disease-related RNAs.
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Affiliation(s)
- Christopher
A. Ryan
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Md Motiar Rahman
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Vipin Kumar
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
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5
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Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:polym15040858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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
- Correspondence:
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6
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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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7
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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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8
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Brodyagin N, Kataoka Y, Kumpina I, McGee DW, Rozners E. Cellular uptake of 2-aminopyridine-modified peptide nucleic acids conjugated with cell-penetrating peptides. Biopolymers 2021; 113:e23484. [PMID: 34914092 DOI: 10.1002/bip.23484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 01/31/2023]
Abstract
Cell-penetrating peptides (CPPs) have been extensively used to deliver peptide nucleic acid (PNA) in cells. We have previously found that replacement of cytosine in triplex-forming PNAs with 2-aminopyridine (M) not only enhanced RNA binding, but also improved cellular uptake of PNAs. In this study, we used confocal fluorescence microscopy to evaluate the ability of CPPs to further improve cellular uptake of M-modified PNAs. We found that PNAs conjugated with Tat and octa-arginine peptides were effectively taken up in MCF7 cells when supplied in cell media at 1 μM. Remarkably, M-modified PNA without any CPP conjugation also showed strong uptake when the concentration was increased to 5 μM. Majority of PNA conjugates remained localized in distinct cytoplasmic vesicles, as judged by dot-like fluorescence patterns. However, M-modified PNAs conjugated with Tat, octa-arginine, and even a simple tri-lysine peptide also showed dispersed fluorescence in cytoplasm and were taken up in nuclei where they localized in larger vesicles, most likely nucleoli. Endosomolytic peptides or chemicals (chloroquine and CaCl2 ) did not release the conjugates from cytosolic vesicles, which suggested that the PNAs were not entrapped in endosomes. We hypothesize that M-modified PNAs escape endosomes and accumulate in cellular compartments rich in RNA, such as nucleoli, stress granules, and P-bodies.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Yuka Kataoka
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Ilze Kumpina
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
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9
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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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10
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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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11
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Endoh T, Brodyagin N, Hnedzko D, Sugimoto N, Rozners E. Triple-Helical Binding of Peptide Nucleic Acid Inhibits Maturation of Endogenous MicroRNA-197. ACS Chem Biol 2021; 16:1147-1151. [PMID: 34114795 DOI: 10.1021/acschembio.1c00133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Sequence specific recognition and functional inhibition of biomedically relevant double-helical RNAs is highly desirable but remains a formidable problem. The present study demonstrates that electroporation of a triplex-forming peptide nucleic acid (PNA), modified with 2-aminopyridine (M) nucleobases, inhibited maturation of endogenous microRNA-197 in SH-SY5Y cells, while having little effect on maturation of microRNA-155 or -27a. In vitro RNA binding and Dicer inhibition assays suggested that the observed biological activity was most likely due to a sequence-specific PNA-RNA triplex formation that inhibited the activity of endonucleases responsible for microRNA maturation. The present study is the first example of modulation of activity of endogenous noncoding RNA using M-modified triplex-forming PNA.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Dziyana Hnedzko
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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12
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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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13
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Ryan CA, Brodyagin N, Lok J, Rozners E. The 2-Aminopyridine Nucleobase Improves Triple-Helical Recognition of RNA and DNA When Used Instead of Pseudoisocytosine in Peptide Nucleic Acids. Biochemistry 2021; 60:1919-1925. [PMID: 34097400 DOI: 10.1021/acs.biochem.1c00275] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pseudoisocytosine (J), a neutral analogue of protonated cytosine, is currently the gold standard modified nucleobase in peptide nucleic acids (PNAs) for the formation of J·G-C triplets that are stable at physiological pH. This study shows that triple-helical recognition of RNA and DNA is significantly improved by using 2-aminopyridine (M) instead of J. The positively charged M forms 3-fold stronger M+·G-C triplets than J with uncompromised sequence selectivity. Replacement of six Js with Ms in a PNA 9-mer increased its binding affinity by ∼2 orders of magnitude. M-modified PNAs prefer binding double-stranded RNA over DNA and disfavor off-target binding to single-stranded nucleic acids. Taken together, the results show that M is a promising modified nucleobase that significantly improves triplex-forming PNAs and may provide breakthrough developments for therapeutic and biotechnology applications.
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Affiliation(s)
- Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Justin Lok
- 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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14
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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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15
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Topham CM, Smith JC. Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J Comput Aided Mol Des 2021; 35:355-369. [PMID: 33624202 DOI: 10.1007/s10822-021-00375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 24 Avenue Jacques Besse, 81500, Lavaur, France.
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
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16
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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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17
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Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA. Methods Mol Biol 2021; 2105:157-172. [PMID: 32088869 DOI: 10.1007/978-1-0716-0243-0_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the important roles noncoding RNAs play in gene expression, their sequence-specific recognition is important for both fundamental science and the pharmaceutical industry. However, most noncoding RNAs fold in complex helical structures that are challenging problems for molecular recognition. Herein, we describe a method for sequence-specific recognition of double-stranded RNA using peptide nucleic acids (PNAs) that form triple helices in the major grove of RNA under physiologically relevant conditions. We also outline methods for solid-phase conjugation of PNA with cell-penetrating peptides and fluorescent dyes. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.
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18
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Kumar V, Brodyagin N, Rozners E. Triplex-Forming Peptide Nucleic Acids with Extended Backbones. Chembiochem 2020; 21:3410-3416. [PMID: 32697857 PMCID: PMC7783598 DOI: 10.1002/cbic.202000432] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/20/2020] [Indexed: 01/15/2023]
Abstract
Peptide nucleic acid (PNA) forms a triple helix with double-stranded RNA (dsRNA) stabilized by a hydrogen-bonding zipper formed by PNA's backbone amides (N-H) interacting with RNA phosphate oxygens. This hydrogen-bonding pattern is enabled by the matching ∼5.7 Å spacing (typical for A-form dsRNA) between PNA's backbone amides and RNA phosphate oxygens. We hypothesized that extending the PNA's backbone by one -CH2 - group might bring the distance between PNA amide groups closer to 7 Å, which is favourable for hydrogen bonding to the B-form dsDNA phosphate oxygens. Extension of the PNA backbone was expected to selectively stabilize PNA-DNA triplexes compared to PNA-RNA. To test this hypothesis, we synthesized triplex-forming PNAs that had the pseudopeptide backbones extended by an additional -CH2 - group in three different positions. Isothermal titration calorimetry measurements of the binding affinity of these extended PNA analogues for the matched dsDNA and dsRNA showed that, contrary to our structural reasoning, extending the PNA backbone at any position had a strong negative effect on triplex stability. Our results suggest that PNAs might have an inherent preference for A-form-like conformations when binding double-stranded nucleic acids. It appears that the original six-atom-long PNA backbone is an almost perfect fit for binding to A-form nucleic acids.
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Affiliation(s)
- Vipin Kumar
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
| | - Nikita Brodyagin
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
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19
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Ryan C, Rozners E. Impact of Chirality and Position of Lysine Conjugation in Triplex-Forming Peptide Nucleic Acids. ACS OMEGA 2020; 5:28722-28729. [PMID: 33195925 PMCID: PMC7659144 DOI: 10.1021/acsomega.0c04021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Conjugation with cationic lysine residues improves the biophysical and biological properties of peptide nucleic acids (PNAs). A single lysine is routinely used to improve the solubility and prevent aggregation of the neutral and hydrophobic amide backbone of PNA. Literature precedents include the attachment of lysine at either the N- or the C-terminus. Moreover, conjugation with short lysine peptides (four to eight residues) improves the cellular uptake of PNA akin to more complex cell-penetrating peptides. Herein, we report a systematic study of the effect of lysine location (N- vs C-terminus) and chirality (d- vs l-) on triple-helical binding of PNA to double-stranded RNA and DNA (dsRNA and dsDNA). The results confirmed our earlier findings that conjugation with lysine significantly increased the stability of PNA-dsRNA and PNA-dsDNA triplexes and that PNA affinity for dsRNA was about an order of magnitude higher than for the same sequence of dsDNA. In contrast, conjugation of PNA with noncharged amino acids decreased the affinity of PNA. Surprisingly, neither the location nor the chirality of lysine had significant impact on PNA affinity for either dsRNA or dsDNA. The results are consistent with the lack of chiral preorganization of single-stranded PNAs, even after conjugation with four d- or l-amino acids. Instead, the positive charge of lysine appears to be the main driving force behind the increased affinity.
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Affiliation(s)
- 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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20
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Kumpina I, Brodyagin N, MacKay JA, Kennedy SD, Katkevics M, Rozners E. Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids. J Org Chem 2019; 84:13276-13298. [PMID: 31538780 DOI: 10.1021/acs.joc.9b01133] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triple-helix formation, using Hoogsteen hydrogen bonding of triplex-forming oligonucleotides, represents an attractive method for sequence-specific recognition of double-stranded nucleic acids. However, practical applications using triple-helix-forming oligonucleotides and their analogues are limited to long homopurine sequences. The key problem for recognition of pyrimidines is that they present only one hydrogen-bond acceptor or donor group in the major groove. Herein, we report our first attempt to overcome this problem by using peptide nucleic acids (PNAs) modified with extended nucleobases that form three hydrogen bonds along the entire Hoogsteen edge of the Watson-Crick base pair. New nucleobase triples (five) were designed, and their hydrogen bonding feasibility was confirmed by ab initio calculations. PNA monomers carrying the modified nucleobases were synthesized and incorporated in short model PNA sequences. Isothermal titration calorimetry showed that these nucleobases had a modest binding affinity for their double-stranded RNA (dsRNA) targets. Finally, molecular modeling of the modified triples in PNA-dsRNA helix suggested that the modest binding affinity was caused by subtle structural deviations from ideal hydrogen-bonding arrangements or disrupted π-stacking of the extended nucleobase scaffolds.
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Affiliation(s)
- Ilze Kumpina
- Latvian Institute of Organic Synthesis , Aizkraukles 21 , Riga LV-1006 , Latvia
| | - Nikita Brodyagin
- Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States
| | - James A MacKay
- Department of Chemistry and Biochemistry , Elizabethtown College , Elizabethtown , Pennsylvania 17022 , United States
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics , University of Rochester School of Medicine and Dentistry , Rochester , New York 14642 , United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis , Aizkraukles 21 , Riga LV-1006 , Latvia
| | - Eriks Rozners
- Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States
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21
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Tähtinen V, Verhassel A, Tuomela J, Virta P. γ-(S)-Guanidinylmethyl-Modified Triplex-Forming Peptide Nucleic Acids Increase Hoogsteen-Face Affinity for a MicroRNA and Enhance Cellular Uptake. Chembiochem 2019; 20:3041-3051. [PMID: 31206960 DOI: 10.1002/cbic.201900393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 12/14/2022]
Abstract
γ-Modified (i.e., (S)-aminomethyl, (S)-acetamidomethyl, (R)-4-(hydroxymethyl)triazol-1-ylmethyl, and (S)-guanidinylmethyl) triplex-forming peptide nucleic acids (TFPNAs) were synthesized and the effect of the backbone modifications on the binding to a miR-215 model was studied. Among the modifications, an appropriate pattern of three γ-(S)-guanidinylmethyl modifications increased the affinity and Hoogsteen-face selectivity for the miR-215 model without ternary (PNA)2 /RNA complex formation. Moreover, the γ-(S)-guanidinylmethyl groups were observed to facilitate internalization of the TFPNAs into living PC-3 prostate cancer cells.
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Affiliation(s)
- Ville Tähtinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Alejandra Verhassel
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Institution of Biomedicine, Medisiina D, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Johanna Tuomela
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Institution of Biomedicine, Medisiina D, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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22
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Krishna MS, Wang Z, Zheng L, Bowry J, Ong AAL, Mu Y, Prabakaran M, Chen G. Incorporating G-C Pair-Recognizing Guanidinium into PNAs for Sequence and Structure Specific Recognition of dsRNAs over dsDNAs and ssRNAs. Biochemistry 2019; 58:3777-3788. [PMID: 31424191 DOI: 10.1021/acs.biochem.9b00608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recognition of RNAs under physiological conditions is important for the development of chemical probes and therapeutic ligands. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) are promising for the recognition of dsRNAs in a sequence and structure specific manner under near-physiological conditions. Guanidinium is often present in proteins and small molecules for the recognition of G bases in nucleic acids, in cell-penetrating carriers, and in bioactive drug molecules, which might be due to the fact that guanidinium is amphiphilic and has unique hydrogen bonding and stacking properties. We hypothesized that a simple guanidinium moiety can be directly incorporated into PNAs to facilitate enhanced molecular recognition of G-C pairs in dsRNAs and improved bioactivity. We grafted a guanidinium moiety directly into a PNA monomer (designated as R) using a two-carbon linker as guided by computational modeling studies. The synthetic scheme of the PNA R monomer is relatively simple compared to that of the previously reported L monomer. We incorporated the R residue into various dbPNAs for binding studies. dbPNAs incorporated with R residues are excellent in sequence specifically recognizing G-C pairs in dsRNAs over dsDNA and ssRNAs. We demonstrated that the R residue is compatible with unmodified T and C and previously developed modified L and Q residues in dbPNAs for targeting model dsRNAs, the influenza A viral panhandle duplex structure, and the HIV-1 frameshift site RNA hairpin. Furthermore, R residues enhance the cellular uptake of PNAs.
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Affiliation(s)
- Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhenzhang Wang
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604
| | - Liangzhen Zheng
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Jogesh Bowry
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,Department of Chemistry , University of Southampton , Southampton SO17 1BJ , U.K
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yuguang Mu
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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23
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Ong AAL, Toh DFK, Krishna MS, Patil KM, Okamura K, Chen G. Incorporating 2-Thiouracil into Short Double-Stranded RNA-Binding Peptide Nucleic Acids for Enhanced Recognition of A-U Pairs and for Targeting a MicroRNA Hairpin Precursor. Biochemistry 2019; 58:3444-3453. [PMID: 31318532 DOI: 10.1021/acs.biochem.9b00521] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemically modified short peptide nucleic acids (PNAs) recognize RNA duplexes under near physiological conditions by major-groove PNA·RNA-RNA triplex formation and show great promise for the development of RNA-targeting probes and therapeutics. Thymine (T) and uracil (U) are often incorporated into PNAs to recognize A-U pairs through major-groove T·A-U and U·A-U base triple formation. Incorporation of a modified nucleobase, 2-thiouracil (s2U), into triplex-forming oligonucleotides stabilizes both DNA and RNA triplexes. Thiolation of uracil causes a decrease in the dehydration energy penalty for triplex formation as well as a decrease in the pKa of the N3 atom, which may result in improved hydrogen bonding in addition to enhanced base stacking interactions, similar to the previously reported thiolation effect of pseudoisocytosine (J to L substitution). Here, we incorporated s2U into short PNAs, followed by binding studies of a series of s2U-modified PNAs. We demonstrated by nondenaturing polyacrylamide gel electrophoresis and thermal melting experiments that s2U and L incorporated into dsRNA-binding PNAs (dbPNAs) enhance the recognition of A-U and G-C pairs, respectively, in RNA duplexes in a position-independent manner, with no appreciable binding to the DNA duplex. Combining s2U and L modifications in dbPNAs facilitates enhanced recognition of dsRNAs and maintains selective binding to dsRNAs over ssRNAs. We further demonstrated through a cell-free assay the application of the s2U- and L-modified dbPNAs (8-mer, with a molecular mass of ∼2.3 kDa) in the inhibition of the pre-microRNA-198 maturation in a substrate-specific manner. Thus, s2U-modified dbPNAs may be generally useful for the enhanced and selective recognition of RNA duplexes and for the regulation of RNA functions.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Katsutomo Okamura
- Division of Biological Sciences , Nara Institute of Science and Technology , 8916-5 Takayama , Ikoma , Nara 630-0192 , Japan
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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24
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RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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25
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Xia X, Zhou Z, DeSantis C, Rossi JJ, Bong D. Triplex Hybridization of siRNA with Bifacial Glycopolymer Nucleic Acid Enables Hepatocyte-Targeted Silencing. ACS Chem Biol 2019; 14:1310-1318. [PMID: 31141333 PMCID: PMC7001860 DOI: 10.1021/acschembio.9b00273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Herein, we describe a versatile non-covalent strategy for packaging nucleic acid cargo with targeting modalities, based on triplex hybridization of oligo-uridylate RNA with bifacial polymer nucleic acid (bPoNA). Polyacrylate bPoNA was prepared and side chain-functionalized with N-acetylgalactosamine (GalNAc), which is known to enable delivery to hepatocytes and liver via binding to the asialoglycoprotein receptor (ASGPR). Polymer binding resulted in successful delivery of both native and synthetically modified siRNAs to HepG2 cells in culture, yielding in low nanomolar IC50 silencing of the endogenous ApoB target, in line with observations of expected Dicer processing of the polymer-siRNA targeting complex. Indeed, in vitro Dicer treatment of the polymer complex indicated that triplex hybridization does not impede RNA processing and release from the polymer. The complex itself elicited a quiescent immunostimulation profile relative to free RNA in a cytokine screen, setting the stage for a preliminary in vivo study in a high-calorie-diet mouse model. Gratifyingly, we observed significant ApoB silencing in a preliminary animal study, validating bPoNA as an in vivo carrier platform for systemic siRNA delivery. Thus, this new siRNA carrier platform exhibits generally useful function and is accessible through scalable synthesis. In addition to its utility as a carrier, the triplex-hybridizing synthetic platform could be useful for optimization screens of siRNA sequences using the identical polymer carriers, thus alleviating the need for covalent ligand modification of each RNA substrate.
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Affiliation(s)
- Xin Xia
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Zhun Zhou
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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26
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Wang F, Sun Y, Liu X, Li Y, Tan L. Third-strand stabilizing effects of the RNA poly(U)·poly(A)*poly(U) triplex by a ruthenium(II) polypyridine complex and its hexaarginine peptide conjugate. Int J Biol Macromol 2019; 135:1134-1141. [PMID: 31176864 DOI: 10.1016/j.ijbiomac.2019.06.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/28/2019] [Accepted: 06/04/2019] [Indexed: 01/14/2023]
Abstract
In this work, a Ru(II) complex [Ru(bpy)2(pip-CO2H)]2+ (Ru1) and its hexaarginine peptide conjugate [Ru(bpy)2(pic-Arg6)]8+ (Ru2) have been synthesized and characterized. The binding of Ru1 and Ru2 with poly(U)•poly(A)*poly(U) triplex has been studied. Results suggest that Ru1 binds in the surface of the minor groove while Ru2 binds to the minor groove of the triplex. Consequently, the triplex stabilization is barely affected by Ru1, while with Ru2 the triplex stabilizing effect is so strong that that dissociation of the triplex shows an overlapping of both melting processes with the melting temperature increased to a maximum of 56.1 °C at the CRu2/CUAU ratio of 0.05, where ΔTm1 and ΔTm2 are 19.6 and 10.1 °C, respectively. Furthermore, the effect of Ru2 stabilizing the third strand at such a low binding ratio of 0.05 is more marked than what obsereved for flavone luteolin and [Ru(bpy)2(mdpz)]2+, which are so far the strongest triplex stabilizers in the reported organic small molecules and metal complexes, respectively. Considering the structure natures of Ru2, conceivably except for electrostatic interaction, the forces stabilizing the triplex should also involve hydrophobic interaction and hydrogen bingding. To our knowledge, this work represents a first example of improving the triplex stabilization by a metallopeptide.
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Affiliation(s)
- Fangfang Wang
- College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Yanmei Sun
- College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, PR China
| | - Yi Li
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, PR China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, PR China; Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan 411105, PR China.
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27
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Kotikam V, Kennedy SD, MacKay JA, Rozners E. Synthetic, Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids. Chemistry 2019; 25:4367-4372. [PMID: 30746843 DOI: 10.1002/chem.201806293] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 12/21/2022]
Abstract
The development of new RNA-binding ligands is attracting increasing interest in fundamental science and the pharmaceutical industry. The goal of this study was to improve the RNA binding properties of triplex-forming peptide nucleic acids (PNAs) by further increasing the pKa of 2-aminopyridine (M). Protonation of M was the key for enabling triplex formation at physiological pH in earlier studies. Substitution on M by an electron-donating 4-methoxy substituent resulted in slight destabilization of the PNA-dsRNA triplex, contrary to the expected stabilization due to more favorable protonation. To explain this unexpected result, the first NMR structural studies were performed on an M-modified PNA-dsRNA triplex which, combined with computational modeling identified unfavorable steric and electrostatic repulsion between the 4-methoxy group of M and the oxygen of the carbonyl group connecting the adjacent nucleobase to PNA backbone. The structural studies also provided insights into hydrogen-bonding interactions that might be responsible for the high affinity and unusual RNA-binding preference of PNAs.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, 14642, USA
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
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28
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Abstract
While <2% of DNA encodes for functional proteins, >70% is transcribed into RNA. Although the function of most RNA transcripts is unknown, such non-coding RNAs are attractive targets for molecular recognition because of the potentially important roles they play in regulation of gene expression and development of disease. In this chapter, we describe peptide nucleic acids (PNAs) that form sequence-specific triple helices with double-stranded RNA (dsRNA). We provide protocols for sequence design and biophysical characterization of PNAs and discuss first examples where such PNAs have been used for functional modulation of dsRNA. The triplex-forming PNAs represent a new approach for RNA recognition that may find future applications in fundamental science, biotechnology and medicine.
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Tanabe T, Sato T, Sato Y, Nishizawa S. Design of a fluorogenic PNA probe capable of simultaneous recognition of 3'-overhang and double-stranded sequences of small interfering RNAs. RSC Adv 2018; 8:42095-42099. [PMID: 35558768 PMCID: PMC9092112 DOI: 10.1039/c8ra08759h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/09/2018] [Indexed: 11/21/2022] Open
Abstract
We developed a new fluorescent peptide nucleic acid (PNA) probe, COT probe, capable of simultaneous recognition of 3'-overhang and double stranded sequences of target small interfering RNA (siRNA).
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Affiliation(s)
- Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
| | - Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
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30
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Chiba T, Sato T, Sato Y, Nishizawa S. Red-emissive triplex-forming PNA probes carrying cyanine base surrogates for fluorescence sensing of double-stranded RNA. Org Biomol Chem 2018; 15:7765-7769. [PMID: 28905972 DOI: 10.1039/c7ob02077e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Red-emissive fluorescent probes have been developed by integration of quinoline blue or thiazole red as the base surrogate into triplex-forming PNAs, allowing selective sensing of a sequence of double-stranded RNA.
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Affiliation(s)
- Toshiki Chiba
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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31
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Kim KT, Chang D, Winssinger N. Double-Stranded RNA-Specific Templated Reaction with Triplex Forming PNA. Helv Chim Acta 2018. [DOI: 10.1002/hlca.201700295] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology; Faculty of Science; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology; Faculty of Science; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology; Faculty of Science; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
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32
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Novosjolova I, Kennedy SD, Rozners E. 2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies. Chembiochem 2017; 18:2165-2170. [PMID: 28858428 PMCID: PMC5920655 DOI: 10.1002/cbic.201700400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 12/21/2022]
Abstract
The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required.
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Affiliation(s)
- Irina Novosjolova
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
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33
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Toh DFK, Patil KM, Chen G. Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids. J Vis Exp 2017:56221. [PMID: 28994801 PMCID: PMC5752312 DOI: 10.3791/56221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNAs are emerging as important biomarkers and therapeutic targets. Thus, there is great potential in developing chemical probes and therapeutic ligands for the recognition of RNA sequence and structure. Chemically modified Peptide Nucleic Acid (PNA) oligomers have been recently developed that can recognize RNA duplexes in a sequence-specific manner. PNAs are chemically stable with a neutral peptide-like backbone. PNAs can be synthesized relatively easily by the manual Boc-chemistry solid-phase peptide synthesis method. PNAs are purified by reverse-phase HPLC, followed by molecular weight characterization by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Non-denaturing polyacrylamide gel electrophoresis (PAGE) technique facilitates the imaging of the triplex formation, because carefully designed free RNA duplex constructs and PNA bound triplexes often show different migration rates. Non-denaturing PAGE with ethidium bromide post staining is often an easy and informative technique for characterizing the binding affinities and specificities of PNA oligomers. Typically, multiple RNA hairpins or duplexes with single base pair mutations can be used to characterize PNA binding properties, such as binding affinities and specificities. 2-Aminopurine is an isomer of adenine (6-aminopurine); the 2-aminopurine fluorescence intensity is sensitive to local structural environment changes, and is suitable for the monitoring of triplex formation with the 2-aminopurine residue incorporated near the PNA binding site. 2-Aminopurine fluorescence titration can also be used to confirm the binding selectivity of modified PNAs towards targeted double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). UV-absorbance-detected thermal melting experiments allow the measurement of the thermal stability of PNA-RNA duplexes and PNA·RNA2 triplexes. Here, we describe the synthesis and purification of PNA oligomers incorporating modified residues, and describe biochemical and biophysical methods for characterization of the recognition of RNA duplexes by the modified PNAs.
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Affiliation(s)
- Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University;
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Tähtinen V, Granqvist L, Murtola M, Strömberg R, Virta P. 19 F NMR Spectroscopic Analysis of the Binding Modes in Triple-Helical Peptide Nucleic Acid (PNA)/MicroRNA Complexes. Chemistry 2017; 23:7113-7124. [PMID: 28370485 DOI: 10.1002/chem.201700601] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 12/21/2022]
Abstract
Triplex-forming peptide nucleic acids (TFPNAs) were targeted to double-helical regions of 19 F-labeled RNA hairpin models (a UA-rich duplex with a hexaethylene glycol (heg) loop and a microRNA model, miR-215). In addition to conventional UV- and circular dichroism (CD)-based detection, binding was monitored by 19 F NMR spectroscopy. Detailed information on the stoichiometry and transition between the triple-helical peptide nucleic acid (PNA)/RNA and (PNA)2 /RNA binding modes could be obtained. γ-(R)-Hydroxymethyl-modified thymine-1-yl- and 2-aminopyridin-3-yl-acetyl derivatives of TFPNAs were additionally synthesized, which were targeted to the same RNA models, and the effect of the γ-(R)-hydroxymethyl group on binding was studied. An appropriate pattern of γ-(R)-hydroxymethyl modifications reduced the stability of the ternary complex and preferred stoichiometric binding to the miR-215 model.
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Affiliation(s)
- Ville Tähtinen
- Department of Chemistry, University of Turku, Turku, 20014, Finland
| | - Lotta Granqvist
- Department of Chemistry, University of Turku, Turku, 20014, Finland
| | - Merita Murtola
- Department of Chemistry, University of Turku, Turku, 20014, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83, Huddinge, Stockholm, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83, Huddinge, Stockholm, Sweden
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, 20014, Finland
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35
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Hnedzko D, McGee DW, Karamitas YA, Rozners E. Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids. RNA (NEW YORK, N.Y.) 2017; 23:58-69. [PMID: 27742909 PMCID: PMC5159649 DOI: 10.1261/rna.058362.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/08/2016] [Indexed: 05/07/2023]
Abstract
Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research, and biotechnology. However, specific recognition of structured RNA is challenging, and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well-suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 107 M-1) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same sequence (Ka = 0.05 to 1.1 × 107 M-1). The binding of double-stranded RNA by M-modified PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 104 M-1 sec-1) compared to the notoriously slow triple helix formation by oligodeoxynucleotides (kon ∼ 103 M-1 sec-1). M-modified PNA-peptide conjugates were not cytotoxic and were efficiently delivered in the cytosol of HEK293 cells at 10 µM. Surprisingly, M-modified PNAs without peptide conjugation were also taken up by HEK293 cells, which, to the best of our knowledge, is the first example of heterocyclic base modification that enhances the cellular uptake of PNA. Our results suggest that M-modified PNA-peptide conjugates are promising probes for sequence-selective recognition of double-stranded RNA in live cells and other biological systems.
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Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Yannis A Karamitas
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
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36
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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37
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Sato T, Sato Y, Nishizawa S. Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA. J Am Chem Soc 2016; 138:9397-400. [PMID: 27442229 DOI: 10.1021/jacs.6b05554] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA.
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Affiliation(s)
- Takaya Sato
- 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
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
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38
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Hnedzko D, McGee DW, Rozners E. Synthesis and properties of peptide nucleic acid labeled at the N-terminus with HiLyte Fluor 488 fluorescent dye. Bioorg Med Chem 2016; 24:4199-4205. [PMID: 27430566 DOI: 10.1016/j.bmc.2016.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/02/2016] [Accepted: 07/05/2016] [Indexed: 11/16/2022]
Abstract
Fluorescently labeled peptide nucleic acids (PNAs) are important tools in fundamental research and biomedical applications. However, synthesis of labeled PNAs, especially using modern and expensive dyes, is less explored than similar preparations of oligonucleotide dye conjugates. Herein, we present a simple procedure for labeling of the PNA N-terminus with HiLyte Fluor 488 as the last step of solid phase PNA synthesis. A minimum excess of 1.25equiv of activated carboxylic acid achieved labeling yields close to 90% providing a good compromise between the price of dye and the yield of product and significant improvement over previous literature procedures. The HiLyte Fluor 488-labeled PNAs retained the RNA binding ability and in live cell fluorescence microscopy experiments were brighter and significantly more photostable than PNA labeled with carboxyfluorescein. In contrast to fluorescein-labeled PNA, the fluorescence of PNAs labeled with HiLyte Fluor 488 was independent of pH in the biologically relevant range of 5-8. The potential of HiLyte Fluor 488-labeling for studies of PNA cellular uptake and distribution was demonstrated in several cell lines.
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Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, United States
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, The State University of New York, Binghamton, NY 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, United States.
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39
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Cheruiyot SK, Rozners E. Fluorescent 2-Aminopyridine Nucleobases for Triplex-Forming Peptide Nucleic Acids. Chembiochem 2016; 17:1558-62. [PMID: 27223320 DOI: 10.1002/cbic.201600182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 01/18/2023]
Abstract
Development of new fluorescent peptide nucleic acids (PNAs) is important for fundamental research and practical applications. The goal of this study was the design of fluorogenic nucleobases for incorporation in triplex-forming PNAs. The underlying design principle was the use of a protonation event that accompanied binding of a 2-aminopyridine (M) nucleobase to a G-C base pair as an on switch for a fluorescence signal. Two fluorogenic nucleobases, 3-(1-phenylethynyl)-M and phenylpyrrolo-M, were designed, synthesized and studied. The new M derivatives provided modest enhancement of fluorescence upon protonation but showed reduced RNA binding affinity and quenching of fluorescence signal upon triple-helix formation with cognate double-stranded RNA. Our study illustrates the principal challenges of design and provides guidelines for future improvement of fluorogenic PNA nucleobases. The 3-(1-phenylethynyl)-M may be used as a fluorescent nucleobase to study PNA-RNA triple-helix formation.
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Affiliation(s)
- Samwel K Cheruiyot
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA.
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40
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Endoh T, Hnedzko D, Rozners E, Sugimoto N. Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; Japan
| | - Dziyana Hnedzko
- Department of Chemistry; Binghamton University; The State University of New York; Binghamton NY 13902 USA
| | - Eriks Rozners
- Department of Chemistry; Binghamton University; The State University of New York; Binghamton NY 13902 USA
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
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41
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Endoh T, Hnedzko D, Rozners E, Sugimoto N. Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells. Angew Chem Int Ed Engl 2015; 55:899-903. [PMID: 26473504 DOI: 10.1002/anie.201505938] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/08/2015] [Indexed: 11/11/2022]
Abstract
Compounds that bind specifically to double-stranded regions of RNA have potential as regulators of structure-based RNA function; however, sequence-selective recognition of double-stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA-RNA triplexes. Herein, we demonstrate that a 9-mer PNA forms a sequence-specific PNA-RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5' untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex-forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double-stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein-RNA interactions.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan
| | - Dziyana Hnedzko
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
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42
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Tähtinen V, Granqvist L, Virta P. Synthesis of C-5, C-2' and C-4'-neomycin-conjugated triplex forming oligonucleotides and their affinity to DNA-duplexes. Bioorg Med Chem 2015; 23:4472-4480. [PMID: 26118338 DOI: 10.1016/j.bmc.2015.06.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/18/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
Neomycin-conjugated homopyrimidine oligo 2'-deoxyribonucleotides have been synthesized on a solid phase and their potential as triplex forming oligonucleotides (TFOs) with DNA-duplexes has been studied. For the synthesis of the conjugates, C-5, C-2' and C-4'-tethered alkyne-modified nucleoside derivatives were used as an integral part of the standard automated oligonucleotide chain elongation. An azide-derived neomycin was then conjugated to the incorporated terminal alkynes by Cu(I)-catalyzed 1,3-dipolar cycloaddition (the click chemistry). Concentrated ammonia released the desired conjugates in acceptable purity and yields. The site of conjugation was expectedly important for the Hoogsteen-face recognition: C-5-conjugation showed a notable positive effect, whereas the influence of the C-2' and C-4'-modification remained marginal. In addition to conventional characterization methods (UV- and CD-spectroscopy), (19)F NMR spectroscopy was applied for the monitoring of triplex/duplex/single strand-conversions.
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Affiliation(s)
- Ville Tähtinen
- Department of Chemistry, University of Turku, 20014 Turku, Finland
| | - Lotta Granqvist
- Department of Chemistry, University of Turku, 20014 Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
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43
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Bartolami E, Gilles A, Dumy P, Ulrich S. Synthesis of α-PNA containing a functionalized triazine as nucleobase analogue. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Paolantoni D, Cantel S, Dumy P, Ulrich S. A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies. Int J Mol Sci 2015; 16:3609-25. [PMID: 25667976 PMCID: PMC4346916 DOI: 10.3390/ijms16023609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 12/16/2022] Open
Abstract
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.
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Affiliation(s)
- Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
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45
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Hnedzko D, Cheruiyot SK, Rozners E. Using triple-helix-forming Peptide nucleic acids for sequence-selective recognition of double-stranded RNA. ACTA ACUST UNITED AC 2014; 58:4.60.1-23. [PMID: 25199637 DOI: 10.1002/0471142700.nc0460s58] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Non-coding RNAs play important roles in regulation of gene expression. Specific recognition and inhibition of these biologically important RNAs that form complex double-helical structures will be highly useful for fundamental studies in biology and practical applications in medicine. This protocol describes a strategy developed in our laboratory for sequence-selective recognition of double-stranded RNA (dsRNA) using triple-helix-forming peptide nucleic acids (PNAs) that bind in the major grove of the RNA helix. The strategy developed uses chemically modified nucleobases, such as 2-aminopyridine (M), which enables strong triple-helical binding under physiologically relevant conditions, and 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E), which enable recognition of isolated pyrimidines in the purine-rich strand of the RNA duplex. Detailed protocols for preparation of modified PNA monomers, solid-phase synthesis, HPLC purification of PNA oligomers, and measuring dsRNA binding affinity using isothermal titration calorimetry are included.
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Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York
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Devi G, Zhou Y, Zhong Z, Toh DFK, Chen G. RNA triplexes: from structural principles to biological and biotech applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:111-28. [DOI: 10.1002/wrna.1261] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 06/30/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
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