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Kim J. Circular RNAs: Novel Players in Cancer Mechanisms and Therapeutic Strategies. Int J Mol Sci 2024; 25:10121. [PMID: 39337606 PMCID: PMC11432211 DOI: 10.3390/ijms251810121] [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: 08/14/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that have emerged as pivotal players in gene regulation. Our understanding of circRNAs has greatly expanded over the last decade, with studies elucidating their biology and exploring their therapeutic applications. In this review, we provide an overview of the current understanding of circRNA biogenesis, outline their mechanisms of action in cancer, and assess their clinical potential as biomarkers. Furthermore, we discuss circRNAs as a potential therapeutic strategy, including recent advances in circRNA production and translation, along with proof-of-concept preclinical studies of cancer vaccines.
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Affiliation(s)
- Jimi Kim
- Department of Life Sciences, Gachon University, Seongnam 13120, Republic of Korea;
- Department of Health Science and Technology, GAIHST, Lee Gil Ya Cancer and Diabetes Institute, Incheon 21999, Republic of Korea
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2
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Petersen KV, Tesauro C, Hede MS, Pages C, Marcussen LB, Keller JG, Bugge M, Holm K, Bjergbæk L, Stougaard M, Wejse C, Knudsen BR. Rolling Circle Enhanced Detection of Specific Restriction Endonuclease Activities in Crude Cell Extracts. SENSORS (BASEL, SWITZERLAND) 2022; 22:7763. [PMID: 36298113 PMCID: PMC9608553 DOI: 10.3390/s22207763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Restriction endonucleases are expressed in all bacteria investigated so far and play an essential role for the bacterial defense against viral infections. Besides their important biological role, restriction endonucleases are of great use for different biotechnological purposes and are indispensable for many cloning and sequencing procedures. Methods for specific detection of restriction endonuclease activities can therefore find broad use for many purposes. In the current study, we demonstrate proof-of-concept for a new principle for the detection of restriction endonuclease activities. The method is based on rolling circle amplification of circular DNA products that can only be formed upon restriction digestion of specially designed DNA substrates. By combining the activity of the target restriction endonuclease with the highly specific Cre recombinase to generate DNA circles, we demonstrate specific detection of selected restriction endonuclease activities even in crude cell extracts. This is, to our knowledge, the first example of a sensor system that allows activity measurements of restriction endonucleases in crude samples. The presented sensor system may prove valuable for future characterization of bacteria species or strains based on their expression of restriction endonucleases as well as for quantification of restriction endonuclease activities directly in extracts from recombinant cells.
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Affiliation(s)
- Kamilla Vandsø Petersen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
| | | | | | - Camilla Pages
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Lærke Bay Marcussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Josephine Geertsen Keller
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Bugge
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Lotte Bjergbæk
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Christian Wejse
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
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Luo J, Chen H, An R, Liang X. Efficient preparation of AppDNA/AppRNA by T4 DNA ligase aided by a DNA involving mismatched mini-hairpin structure at its 3′ side. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jian Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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Liang X, Fujioka K, Asanuma H. Nick sealing by T4 DNA ligase on a modified DNA template: tethering a functional molecule on D-threoninol. Chemistry 2011; 17:10388-96. [PMID: 21815224 DOI: 10.1002/chem.201100215] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Indexed: 01/15/2023]
Abstract
Efficient DNA nick sealing catalyzed by T4 DNA ligase was carried out on a modified DNA template in which an intercalator such as azobenzene had been introduced. The intercalator was attached to a D-threoninol linker inserted into the DNA backbone. Although the structure of the template at the point of ligation was completely different from that of native DNA, two ODNs could be connected with yields higher than 90% in most cases. A systematic study of sequence dependence demonstrated that the ligation efficiency varied greatly with the base pairs adjacent to the azobenzene moiety. Interestingly, when the introduced azobenzene was photoisomerized to the cis form on subjection to UV light (320-380 nm), the rates of ligation were greatly accelerated for all sequences investigated. These unexpected ligations might provide a new approach for the introduction of functional molecules into long DNA strands in cases in which direct PCR cannot be used because of blockage of DNA synthesis by the introduced functional molecule. The biological significance of this unexpected enzymatic action is also discussed on the basis of kinetic analysis.
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Affiliation(s)
- Xingguo Liang
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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Leslie DC, Sohrabi A, Ikonomi P, McKee ML, Landers JP. Size-based separations as an important discriminator in development of proximity ligation assays for protein or organism detection. Electrophoresis 2010; 31:1615-22. [PMID: 20419707 DOI: 10.1002/elps.201000008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proximity ligation is a powerful technique to measure minute concentrations of target protein with high specificity, and it has been demonstrated to be effective on a wide variety of protein targets. The proximity ligation assay (PLA) technique is shown to be compromised by the amplification of a nonspecific fluorescent product that is not indicative of protein presence, which was previously unidentified in a published procedure. This result illuminates the complexity of designing the optimal PLA and the possibility of using a size-based separation to increase the reliability of PLAs in general. Nucleic acid controls were developed to optimize the assay, which led to a novel end-point detection method that exploits microchip electrophoresis to size the products. This method provides a greater ability to distinguish a between the target protein's signal and noise in a PLA. The utility of the PLA is demonstrated by the detection of human pathogenic Escherichia coli O157:H7 bacteria, a pathogen at the root of many recent life-threatening food poisoning outbreaks. The results of the PLA show a detection limit of 100 E. coli O157:H7 cells with minimal cross-reactivity with gram positive control Staphylococcus aureus bacteria. The advantages of miniaturizing this process are the 100-fold reduction in volume, greatly reducing reagent requirements, and doubling of the thermocycling speed via noncontact infrared heating. This work, consequently, adds to the understanding of background fluorescence in PLAs, provides a method for evaluating nonspecific amplification, and shows that a qualitative PCR response indicative of the presence protein can be achieved with PLA.
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Affiliation(s)
- Daniel C Leslie
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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One-base excess adaptor ligation method for walking uncloned genomic DNA. Appl Microbiol Biotechnol 2007; 78:173-80. [PMID: 18071644 DOI: 10.1007/s00253-007-1289-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 11/14/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
This report describes a novel and efficient method for walking the sequence of a genomic deoxyribonucleic acid (DNA) from a known region to an unknown region based on an oligodeoxynucleotide (oligo) cassette-mediated polymerase chain reaction technique. In this method, genomic DNA is digested by a restriction enzyme that generates a sticky 5'-end, followed by ligation of a one-base excess oligo-adaptor using T4 DNA ligase. The adaptor consists of two complementary oligos that form the same sticky end as the digested genomic DNA fragments, except that the 5'-overhang base overlaps the corresponding 3'-end base of the restriction site. This overhanging terminal base prevents ligation between the adaptors, and the appropriate molar ratio of adaptor to genomic DNA enables specific amplification of the target sequence. T4 DNA ligase catalyzes both the ligation of the phosphorylated overhang base of the adaptor to genomic DNA and the excision of the corresponding 3'-terminal base of the genomic DNA. This sequence-specific exonuclease activity of T4 DNA ligase was confirmed by ligation of an alternative adaptor in which the 5'-terminal base was not consistent with the corresponding 3'-terminal base. Using this technique, the 3'- and 5'-flanking sequences of the catalase gene of the ciliate Paramecium bursaria were determined.
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Peter Wo YY, Chaung FL, Wang CL, Pan FM. Improvement of inverse polymerase chain reaction by optimal dilution and acidic polypeptides. Anal Biochem 2007; 364:219-21. [PMID: 17362869 DOI: 10.1016/j.ab.2007.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 01/17/2007] [Accepted: 01/17/2007] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Yuan Peter Wo
- Department of Molecular Biology and Biochemistry and Graduate Institute of Biotechnology, National Chiayi University, Chiayi 600, Taiwan
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Abstract
T4 DNA ligase is one of the workhorses of molecular biology and used in various biotechnological applications. Here we report that this ligase, unlike Escherichia coli DNA ligase, Taq DNA ligase and Ampligase, is able to join the ends of single-stranded DNA in the absence of any duplex DNA structure at the ligation site. Such nontemplated ligation of DNA oligomers catalyzed by T4 DNA ligase occurs with a very low yield, as assessed by quantitative competitive PCR, between 10(-6) and 10(-4) at oligonucleotide concentrations in the range 0.1-10 nm, and thus is insignificant in many molecular biological applications of T4 DNA ligase. However, this side reaction may be of paramount importance for diagnostic detection methods that rely on template-dependent or target-dependent DNA probe ligation in combination with amplification techniques, such as PCR or rolling-circle amplification, because it can lead to nonspecific background signals or false positives. Comparison of ligation yields obtained with substrates differing in their strandedness at the terminal segments involved in ligation shows that an acceptor duplex DNA segment bearing a 3'-hydroxy end, but lacking a 5'-phosphate end, is sufficient to play a role as a cofactor in blunt-end ligation.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, MA 02215, USA.
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Mendel-Hartvig M, Kumar A, Landegren U. Ligase-mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase. Nucleic Acids Res 2004; 32:e2. [PMID: 14704359 PMCID: PMC373312 DOI: 10.1093/nar/gnh011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Branched nucleic acid strands exist as intermediates in certain biological reactions, and bifurcating DNA also presents interesting opportunities in biotechnological applications. We describe here how T4 DNA ligase can be used for efficient construction of DNA molecules having one 5' end but two distinct 3' ends that extend from the 2' and 3' carbons, respectively, of an internal nucleotide. The nature of the reaction products is investigated, and optimal reaction conditions are reported for the construction of branched oligonucleotides. We discuss the utility of these branched DNA nanostructures for gene detection.
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Affiliation(s)
- M J Moore
- Department of Biochemistry, W. M. Keck Institute for Cellular Visualization, Brandeis University, Waltham, Massachusetts 02454, USA
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Stefano JE, Genovese L, An Q, Lu L, McCarty J, Du Y, Stefano K, Burg JL, King W, Lane DJ. Rapid and sensitive detection of Chlamydia trachomatis using a ligatable binary RNA probe and Q beta replicase. Mol Cell Probes 1997; 11:407-26. [PMID: 9500810 DOI: 10.1006/mcpr.1997.0135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A simple assay format was developed for the direct detection of C. trachomatis rRNA utilizing ligation of recombinant MDV-1 probe RNA fragments hybridized to 23S rRNA after capture and release from a solid support. Assay background (equivalent to 10(4) targets) was suppressed by blocking sequences in the 5' MDV reporter probe fragment complementary to the 3' fragment by prehybridization of a DNA oligonucleotide. A pair of reporter fragments bearing a deletion within the region, obtained by a hydrid-selection-amplification protocol, yielded a low level of assay background which was reduced to < 2% with a blocker directed against the remaining pairing sequence. This probe set showed a sensitivity of 10(3) molecules of 23S rRNA (> 95% responding) and could detect a single elementary body (EB) of Chlamydia trachomatis or 1-10 EB added to a clinical matrix of pooled negative human cervical swab samples. The time of first appearance of amplification products by real-time fluorescence detection showed a linear response to log increases in the target level over a 10(5)-fold range, permitting the determination of target level within an order of magnitude. The assay showed approximately 10(9)-fold discrimination over Chlamydia pneumonae (TWAR) rRNA. High levels of cultured C. albicans, E. coli, S. aureus, or N. gonorrhoeae had no detectable effect on assay background or the ability to detect a single elementary body.
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