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Lei Y, Li C, Ji X, Sun H, Liu X, Mao Z, Chen W, Qing Z, Liu J. Lowering Entropic Barriers in Triplex DNA Switches Facilitating Biomedical Applications at Physiological pH. Angew Chem Int Ed Engl 2024; 63:e202402123. [PMID: 38453654 DOI: 10.1002/anie.202402123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/09/2024]
Abstract
Triplex DNA switches are attractive allosteric tools for engineering smart nanodevices, but their poor triplex-forming capacity at physiological conditions limited the practical applications. To address this challenge, we proposed a low-entropy barrier design to facilitate triplex formation by introducing a hairpin duplex linker into the triplex motif, and the resulting triplex switch was termed as CTNSds. Compared to the conventional clamp-like triplex switch, CTNSds increased the triplex-forming ratio from 30 % to 91 % at pH 7.4 and stabilized the triple-helix structure in FBS and cell lysate. CTNSds was also less sensitive to free-energy disturbances, such as lengthening linkers or mismatches in the triple-helix stem. The CTNSds design was utilized to reversibly isolate CTCs from whole blood, achieving high capture efficiencies (>86 %) at pH 7.4 and release efficiencies (>80 %) at pH 8.0. Our approach broadens the potential applications of DNA switches-based switchable nanodevices, showing great promise in biosensing and biomedicine.
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Affiliation(s)
- Yanli Lei
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Chuangchuang Li
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xinyue Ji
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Haiyan Sun
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xiaowen Liu
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, 410083, China
| | - Zenghui Mao
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, 410083, China
| | - Weiju Chen
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2 L 3G1, Canada
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2
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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3
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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Munyaradzi O, Rundell S, Bong D. Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA. Chembiochem 2022; 23:e202100707. [PMID: 35167719 PMCID: PMC9136932 DOI: 10.1002/cbic.202100707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Indexed: 11/07/2022]
Abstract
We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.
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Affiliation(s)
- Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
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Devari S, Bhunia D, Bong D. Synthesis of bifacial Peptide Nucleic Acids with diketopiperazine backbones. Synlett 2022; 33:965-968. [DOI: 10.1055/a-1802-6873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report herein synthesis of bifacial peptide nucleic acids (bPNAs) with novel diketopiperazine (DKP) backbones that display unnatural melamine (M) bases as well as native bases. To examine the structure-function scope of diketopiperazine bPNAs, we synthesized a set of bPNAs using diaminopropionic acid, diaminobutyric acid, ornithine and lysine derivatives to display the base-tripling motifs, which result in 1, 2, 3, and 4 carbons linking alpha carbon to sidechain amine, respectively. Thermal denaturation of DNA hybrids with these bPNAs revealed that the optimal sidechain linkage was 4 carbons, corresponding to the lysine derivative. Accordingly, monomers displaying two bases per sidechain were prepared via double reductive alkylation of the ε-amine of Fmoc-Lysine with acetaldehyde derivatives of adenine, cytidine, uridine and melamine. With these building blocks in hand, diketopiperazine bPNAs were prepared to display a combination of native and synthetic (melamine) bases. Preliminary melting studies indicate binding signatures of cytidine and melamine-displaying bPNAs to T-rich DNAs, though full characterization of this behavior is ongoing. We anticipate that the straightforward synthetic methodology developed herein will enable further studies on noncanonical nucleic acid hybridization with diketopiperazine backbones.
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Affiliation(s)
- Shekaraiah Devari
- Chemistry & Biochemistry, The Ohio State University, Columbus, United States
| | - Debmalya Bhunia
- Chemistry & Biochemistry, The Ohio State University, Columbus, United States
| | - Dennis Bong
- Chemistry & Biochemistry, The Ohio State University, Columbus, United States
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6
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Kumar V, Rozners E. Fluorobenzene Nucleobase Analogues for Triplex-Forming Peptide Nucleic Acids. Chembiochem 2022; 23:e202100560. [PMID: 34889020 PMCID: PMC8935525 DOI: 10.1002/cbic.202100560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/24/2021] [Indexed: 02/06/2023]
Abstract
2,4-Difluorotoluene is a nonpolar isostere of thymidine that has been used as a powerful mechanistic probe to study the role of hydrogen bonding in nucleic acid recognition and interactions with polymerases. In the present study, we evaluated five fluorinated benzenes as nucleobase analogues in peptide nucleic acids designed for triple helical recognition of double helical RNA. We found that analogues having para and ortho fluorine substitution patterns (as in 2,4-difluorotoluene) selectively stabilized Hoogsteen triplets with U-A base pairs. The results were consistent with attractive electrostatic interactions akin to non-canonical F to H-N and C-H to N hydrogen bonding. The fluorinated nucleobases were not able to stabilize Hoogsteen-like triplets with pyrimidines in either G-C or A-U base pairs. Our results illustrate the ability of fluorine to engage in non-canonical base pairing and provide insights into triple helical recognition of RNA.
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Affiliation(s)
- Vipin Kumar
- 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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7
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Liang Y, Miao S, Mao J, Devari S, Gonzalez M, Bong D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry 2022; 28:e202103616. [PMID: 34693570 PMCID: PMC8758549 DOI: 10.1002/chem.202103616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 01/12/2023]
Abstract
We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Jie Mao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Maricarmen Gonzalez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
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Rundell S, Munyaradzi O, Bong D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs. Biochemistry 2021; 61:85-91. [PMID: 34955016 DOI: 10.1021/acs.biochem.1c00693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
General design principles for recognition at noncanonical interfaces of DNA and RNA remain elusive. Triplex hybridization of bifacial peptide nucleic acids (bPNAs) with oligo-T/U DNAs and RNAs is a robust recognition platform that can be used to define structure-function relationships in synthetic triplex formation. To this end, a set of minimal (mw < 1 kD) bPNA variants was synthesized to probe the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on hybridization with short, unstructured T-rich DNA and U-rich RNAs. Thermodynamic parameters extracted from optical melting analyses of bPNA variant hybrids indicated that there are two bPNA backbone modifications that significantly improve hybridization: alternating (d, l) configuration in open-chain dipeptides and homochiral dipeptide cyclization to diketopiperazine. Further, binding to DNA is preferred over RNA for all bPNA variants. Thymine-uracil substitutions in DNA substrates revealed that the methyl group of thymine accounts for 71% of ΔΔGDNA-RNA for open-chain bPNAs but only 40% of ΔΔGDNA-RNA for diketopiperazine bPNA, suggesting a greater sensitivity to RNA conformation and more optimized stacking in the cyclic bPNA. Together, these data reveal pressure points for tuning triplex hybridization at the chiral centers of bPNA, backbone conformation, stacking effects at the base triple, and the nucleic acid substrate itself. A structural blueprint for enhancing bPNA targeting of both DNA and RNA substrates includes syndiotactic base presentation (as found in homochiral diketopiperazines and d, l peptides), expansion of base stacking, and further investigation of bPNA backbone preorganization.
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Affiliation(s)
- Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
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9
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Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D. Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop. ACS Chem Biol 2021; 16:1600-1609. [PMID: 34382766 DOI: 10.1021/acschembio.1c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Debmalya Bhunia
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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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: 31] [Impact Index Per Article: 10.3] [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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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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Meena CL, Singh D, Kizhakeetil B, Prasad M, George M, Tothadi S, Sanjayan GJ. Triazine-Based Janus G-C Nucleobase as a Building Block for Self-Assembly, Peptide Nucleic Acids, and Smart Polymers. J Org Chem 2021; 86:3186-3195. [PMID: 33523657 DOI: 10.1021/acs.joc.0c02530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This communication reports on the utility of a triazine-based self-assembling system, reminiscent of a Janus G-C nucleobase, as a building block for developing (1) supramolecular polymers, (2) peptide nucleic acids (PNAs), and (3) smart polymers. The strategically positioned self-complementary triple H-bonding arrays DDA and AAD facilitate efficient self-assembly, leading to a linear supramolecular polymer.
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Affiliation(s)
- Chhuttan L Meena
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Dharmendra Singh
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Bhavya Kizhakeetil
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Manasa Prasad
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Malini George
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Srinu Tothadi
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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14
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Liang Y, Miao S, Mao J, DeSantis C, Bong D. Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs. Biochemistry 2020; 59:2410-2418. [PMID: 32519542 DOI: 10.1021/acs.biochem.0c00362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we demonstrate context-dependent molecular recognition of DNA by synthetic bPNA iron and copper complexes, using oxidative backbone cleavage as a chemical readout for binding. Oligoethylenimine bPNAs displaying iron·EDTA or copper·phenanthroline sites were found to be efficient chemical nucleases for designed and native structured DNAs with T-rich single-stranded domains. Cleavage reactivity depends strongly on structural context, as strikingly demonstrated with DNA substrates of the form (GGGTTA)n. This repeat sequence from the human telomere is known to switch between parallel and antiparallel G-quadruplex (G4) topologies with a change from potassium to sodium buffer: notably, bPNA-copper complexes efficiently cleave long repeat sequences into ∼22-nucleotide portions in sodium, but not potassium, buffer. We hypothesize preferential cleavage of the antiparallel topology (Na+) over the parallel topology (K+) due to the greater accessibility of the TTA loop to bPNA in the antiparallel (Na+) form. Similar ion-sensitive telomere shortening upon treatment with bPNA nucleases can be observed in both isolated and intracellular DNA from PC3 cells by quantitative polymerase chain reaction. Live cell treatment was accompanied by accelerated cellular senescence, as expected for significant telomere shortening. Taken together, the loop-targeting approach of bPNA chemical nucleases complements prior intercalation strategies targeting duplex and quadruplex DNA. Structurally sensitive loop targeting enables discrimination between similar target sequences, thus expanding bPNA targeting beyond simple oligo-T sequences. In addition, bPNA nucleases are cell membrane permeable and therefore may be used to target native intracellular substrates. In addition, these data indicate that bPNA scaffolds can be a platform for new synthetic binders to particular nucleic acid structural motifs.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiqin Miao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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