1
|
Kennebeck MM, Kaminsky CK, Massa MA, Das PK, Boyd RD, Bishka M, Tricarico JT, Silverman SK. DNAzyme-Catalyzed Site-Specific N-Acylation of DNA Oligonucleotide Nucleobases. Angew Chem Int Ed Engl 2024; 63:e202317565. [PMID: 38157448 PMCID: PMC10873475 DOI: 10.1002/anie.202317565] [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: 11/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
We used in vitro selection to identify DNAzymes that acylate the exocyclic nucleobase amines of cytidine, guanosine, and adenosine in DNA oligonucleotides. The acyl donor was the 2,3,5,6-tetrafluorophenyl ester (TFPE) of a 5'-carboxyl oligonucleotide. Yields are as high as >95 % in 6 h. Several of the N-acylation DNAzymes are catalytically active with RNA rather than DNA oligonucleotide substrates, and eight of nine DNAzymes for modifying C are site-specific (>95 %) for one particular substrate nucleotide. These findings expand the catalytic ability of DNA to include site-specific N-acylation of oligonucleotide nucleobases. Future efforts will investigate the DNA and RNA substrate sequence generality of DNAzymes for oligonucleotide nucleobase N-acylation, toward a universal approach for site-specific oligonucleotide modification.
Collapse
Affiliation(s)
- Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Caroline K Kaminsky
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Maria A Massa
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Prakriti K Das
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Michelle Bishka
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - J Tomas Tricarico
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Scott K Silverman
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| |
Collapse
|
2
|
Chen Q, Zhang X, Shi J, Yan M, Zhou T. Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem Sci 2021; 46:790-804. [PMID: 34053843 PMCID: PMC8448906 DOI: 10.1016/j.tibs.2021.05.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation, RNA modifications, and protein-binding abilities. We summarize the mechanisms of tsRNA biogenesis and the impact of RNA modifications, and propose how thinking of tsRNA functionality from an evolutionary perspective urges the expansion of tsRNA research into a wider spectrum, including cross-tissue/cross-species regulation and harnessing of the 'tsRNA code' for precision medicine.
Collapse
Affiliation(s)
- Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Menghong Yan
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China; Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
| |
Collapse
|
3
|
Lee YH, Yu E, Park CM. Programmable site-selective labeling of oligonucleotides based on carbene catalysis. Nat Commun 2021; 12:1681. [PMID: 33727561 PMCID: PMC7966772 DOI: 10.1038/s41467-021-21839-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/03/2021] [Indexed: 11/08/2022] Open
Abstract
Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. Here we report chemo- and regioselective modification of oligonucleotides based on rhodium(I)-carbene catalysis in a programmable fashion. Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures. Moreover, high regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex. This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates.
Collapse
Affiliation(s)
- Yang-Ha Lee
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea
| | - Eunsoo Yu
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea
| | - Cheol-Min Park
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea.
| |
Collapse
|
4
|
Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
Collapse
Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| |
Collapse
|
5
|
Poudyal RR, Guth-Metzler RM, Veenis AJ, Frankel EA, Keating CD, Bevilacqua PC. Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates. Nat Commun 2019; 10:490. [PMID: 30700721 PMCID: PMC6353945 DOI: 10.1038/s41467-019-08353-4] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
Membraneless compartments, such as complex coacervates, have been hypothesized as plausible prebiotic micro-compartments due to their ability to sequester RNA; however, their compatibility with essential RNA World chemistries is unclear. We show that such compartments can enhance key prebiotically-relevant RNA chemistries. We demonstrate that template-directed RNA polymerization is sensitive to polycation identity, with polydiallyldimethylammonium chloride (PDAC) outperforming poly(allylamine), poly(lysine), and poly(arginine) in polycation/RNA coacervates. Differences in RNA diffusion rates between PDAC/RNA and oligoarginine/RNA coacervates imply distinct biophysical environments. Template-directed RNA polymerization is relatively insensitive to Mg2+ concentration when performed in PDAC/RNA coacervates as compared to buffer, even enabling partial rescue of the reaction in the absence of magnesium. Finally, we show enhanced activities of multiple nucleic acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generality of this approach, in which functional nucleic acids like aptamers and ribozymes, and in some cases key cosolutes localize within the coacervate microenvironments. Membraneless compartments have been theorized to be prebiotic micro-compartments as they spontaneously encapsulate RNA and proteins. Here, the authors report membraneless compartments can enhance RNA chemistries, affecting template directed RNA polymerization and stimulating nucleic acid enzymes.
Collapse
Affiliation(s)
- Raghav R Poudyal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Rebecca M Guth-Metzler
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew J Veenis
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Erica A Frankel
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,The Dow Chemical Company, 400 Arcola Road, Collegeville, PA, 19426, USA
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
6
|
Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Nat Commun 2018; 9:2283. [PMID: 29891903 PMCID: PMC5995956 DOI: 10.1038/s41467-018-04691-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19–21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50–80 kDa, 175–250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs. Large RNAs and ribonucleoprotein complexes have shown potential as novel therapeutic agents, but their targeted delivery to cells is still challenging. Here the authors present a modular aptamer nanostructure for intracellular delivery of RNAs up to 250 nucleotides to cancer cells.
Collapse
|
7
|
Poudyal R, Cakmak FP, Keating CD, Bevilacqua PC. Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry. Biochemistry 2018; 57:2509-2519. [PMID: 29560725 PMCID: PMC7276092 DOI: 10.1021/acs.biochem.8b00081] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This Perspective focuses on RNA in biological and nonbiological compartments resulting from liquid-liquid phase separation (LLPS), with an emphasis on origins of life. In extant cells, intracellular liquid condensates, many of which are rich in RNAs and intrinsically disordered proteins, provide spatial regulation of biomolecular interactions that can result in altered gene expression. Given the diversity of biogenic and abiogenic molecules that undergo LLPS, such membraneless compartments may have also played key roles in prebiotic chemistries relevant to the origins of life. The RNA World hypothesis posits that RNA may have served as both a genetic information carrier and a catalyst during the origin of life. Because of its polyanionic backbone, RNA can undergo LLPS by complex coacervation in the presence of polycations. Phase separation could provide a mechanism for concentrating monomers for RNA synthesis and selectively partition longer RNAs with enzymatic functions, thus driving prebiotic evolution. We introduce several types of LLPS that could lead to compartmentalization and discuss potential roles in template-mediated non-enzymatic polymerization of RNA and other related biomolecules, functions of ribozymes and aptamers, and benefits or penalties imparted by liquid demixing. We conclude that tiny liquid droplets may have concentrated precious biomolecules and acted as bioreactors in the RNA World.
Collapse
Affiliation(s)
- Raghav Poudyal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Fatma Pir Cakmak
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
8
|
Poudyal RR, Benslimane M, Lokugamage MP, Callaway MK, Staller S, Burke DH. Selective Inactivation of Functional RNAs by Ribozyme-Catalyzed Covalent Modification. ACS Synth Biol 2017; 6:528-534. [PMID: 28139121 DOI: 10.1021/acssynbio.6b00222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diverse functions of RNA provide numerous opportunities for programming biological circuits. We describe a new strategy that uses ribozyme K28min to covalently tag a specific nucleobase within an RNA or DNA target strand to regulate and selectively inactivate those nucleic acids. K28min variants with appropriately reprogrammed internal guide sequences efficiently tagged multiple sites from an mRNA and from aptamer and ribozyme targets. Upon covalent modification by the corresponding K28min variant, an ATP-binding aptamer lost all affinity for ATP, and the fluorogenic Mango aptamer lost its ability to activate fluorescence of its dye ligand. Modifying a hammerhead ribozyme near the catalytic core led to loss of almost all of its substrate-cleaving activity, but modifying the same hammerhead ribozyme within a tertiary stabilizing element that reduces magnesium dependence only impaired substrate cleavage at low magnesium concentration. Thus, ribozyme-mediated covalent modification can be used both to selectively inactivate and to fine-tune the activities of targeted functional RNAs, analogous to the effects of post-translational modifications of proteins. Ribozyme-catalyzed covalent modification could therefore be developed to regulate nucleic acids components of synthetic and natural circuits.
Collapse
Affiliation(s)
- Raghav R. Poudyal
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Malak Benslimane
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Melissa P. Lokugamage
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Mackenzie K. Callaway
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Seth Staller
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Donald H. Burke
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| |
Collapse
|