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Han H, Cui J, Zhou D, Hua D, Peng W, Lin M, Zhang Y, Li F, Gong X, Zhang J. Single-stranded RNA as primers of terminal deoxynucleotidyl transferase for template-independent DNA polymerization. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Lu X, Li J, Li C, Lou Q, Peng K, Cai B, Liu Y, Yao Y, Lu L, Tian Z, Ma H, Wang W, Cheng J, Guo X, Jiang H, Ma Y. Enzymatic DNA Synthesis by Engineering Terminal Deoxynucleotidyl Transferase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaoyun Lu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shanxi 710072, China
- Zhonghe Gene Technology Co., Ltd., Tianjin 300308, China
| | - Jinlong Li
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Congyu Li
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Tianjin University of Science&Technology, Tianjin 300457, China
| | - Qianqian Lou
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Kai Peng
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bijun Cai
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ying Liu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yonghong Yao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lina Lu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zhenyang Tian
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hongwu Ma
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shanxi 710072, China
| | - Jian Cheng
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaoxian Guo
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Huifeng Jiang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Sadova AA, Panteleev DY, Pavlova GV. Zooming in: PAGE-Northern Blot Helps to Analyze Anti-Sense Transcripts Originating from Human rIGS under Transcriptional Stress. Noncoding RNA 2021; 7:ncrna7030050. [PMID: 34449671 PMCID: PMC8395900 DOI: 10.3390/ncrna7030050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
Ribosomal intergenic spacer (rIGS), located between the 45S rRNA coding arrays in humans, is a deep, unexplored source of small and long non-coding RNA molecules transcribed in certain conditions to help a cell generate a stress response, pass through a differentiation state or fine tune the functioning of the nucleolus as a ribosome biogenesis center of the cell. Many of the non-coding transcripts originating from the rIGS are not characterized to date. Here, we confirm the transcriptional activity of the region laying a 2 kb upstream of the rRNA promoter, and demonstrate its altered expression under transcriptional stress, induced by a wide range of known transcription inhibitors. We managed to show an increased variability of anti-sense transcripts in alpha-amanitin treated cells by applying the low-molecular RNA fraction extracted from agarose gel to PAGE-northern. Also, the fractioning of RNA by size using agarose gel slices occurred, being applicable for determining the sizes of target transcripts via RT-PCR.
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Affiliation(s)
- Anastasia A. Sadova
- Academic Chair of Biochemistry and Molecular Biology, Faculty of General Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia; (D.Y.P.); (G.V.P.)
- Correspondence:
| | - Dmitry Y. Panteleev
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia; (D.Y.P.); (G.V.P.)
| | - Galina V. Pavlova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia; (D.Y.P.); (G.V.P.)
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Department of X-ray and Radioisotope Diagnostic Methods, Burdenko Neurosurgical Institute, 125047 Moscow, Russia
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4
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Schaudy E, Lietard J, Somoza MM. Sequence Preference and Initiator Promiscuity for De Novo DNA Synthesis by Terminal Deoxynucleotidyl Transferase. ACS Synth Biol 2021; 10:1750-1760. [PMID: 34156829 PMCID: PMC8291772 DOI: 10.1021/acssynbio.1c00142] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The untemplated activity
of terminal deoxynucleotidyl transferase
(TdT) represents its most appealing feature. Its use is well established
in applications aiming for extension of a DNA initiator strand, but
a more recent focus points to its potential in enzymatic de
novo synthesis of DNA. Whereas its low substrate specificity
for nucleoside triphosphates has been studied extensively, here we
interrogate how the activity of TdT is modulated by the nature of
the initiating strands, in particular their length, chemistry, and
nucleotide composition. Investigation of full permutational libraries
of mono- to pentamers of d-DNA, l-DNA, and 2′O-methyl-RNA
of differing directionality immobilized to glass surfaces, and generated via photolithographic in situ synthesis,
shows that the efficiency of extension strongly depends on the nucleobase
sequence. We also show TdT being catalytically active on a non-nucleosidic
substrate, hexaethylene glycol. These results offer new perspectives
on constraints and strategies for de novo synthesis
of DNA using TdT regarding the requirements for initiation of enzymatic
generation of DNA.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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5
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Citartan M. Aptamers as the powerhouse of dot blot assays. Talanta 2021; 232:122436. [PMID: 34074421 DOI: 10.1016/j.talanta.2021.122436] [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: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022]
Abstract
Dot blot assays have always been associated with antibodies as the main molecular recognition element, which are widely employed in a myriad of diagnostic applications. With the rising of aptamers as the equivalent molecular recognition elements of antibodies, dot blot assays are also one of the diagnostic avenues that should be scrutinized for their amenability with aptamers as the potential surrogates of antibodies. In this review, the stepwise procedures of an aptamer-based dot blot assays are underscored before reviewing the existing aptamer-based dot blot assays developed so far. Most of the applications center on monitoring the progress of SELEX and as the validatory assays to assess the potency of aptamer candidates. For the purpose of diagnostics, the current effort is still languid and as such possible suggestions to galvanize the move to spur the aptamer-based dot blot assays to a point-of-care arena are discussed.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Schnieders R, Keyhani S, Schwalbe H, Fürtig B. More than Proton Detection-New Avenues for NMR Spectroscopy of RNA. Chemistry 2020; 26:102-113. [PMID: 31454110 PMCID: PMC6973061 DOI: 10.1002/chem.201903355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleic acid oligonucleotides (RNAs) play pivotal roles in cellular function (riboswitches), chemical biology applications (SELEX-derived aptamers), cell biology and biomedical applications (transcriptomics). Furthermore, a growing number of RNA forms (long non-coding RNAs, circular RNAs) but also RNA modifications are identified, showing the ever increasing functional diversity of RNAs. To describe and understand this functional diversity, structural studies of RNA are increasingly important. However, they are often more challenging than protein structural studies as RNAs are substantially more dynamic and their function is often linked to their structural transitions between alternative conformations. NMR is a prime technique to characterize these structural dynamics with atomic resolution. To extend the NMR size limitation and to characterize large RNAs and their complexes above 200 nucleotides, new NMR techniques have been developed. This Minireview reports on the development of NMR methods that utilize detection on low-γ nuclei (heteronuclei like 13 C or 15 N with lower gyromagnetic ratio than 1 H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1 H coherences, detected by 13 C NMR spectroscopy. Furthermore, 13 C and 15 N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-γ nuclei detection experiments in RNA.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Sara Keyhani
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-Universität FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
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7
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Hegedüs É, Kókai E, Nánási P, Imre L, Halász L, Jossé R, Antunovics Z, Webb MR, El Hage A, Pommier Y, Székvölgyi L, Dombrádi V, Szabó G. Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:10649-10668. [PMID: 30445637 PMCID: PMC6237785 DOI: 10.1093/nar/gky743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022] Open
Abstract
Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.
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Affiliation(s)
- Éva Hegedüs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Endre Kókai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Imre
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Halász
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Rozenn Jossé
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (CCR-NCI), NIH, Bethesda, MD, USA
| | - Zsuzsa Antunovics
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | | | - Aziz El Hage
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (CCR-NCI), NIH, Bethesda, MD, USA
| | - Lóránt Székvölgyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Viktor Dombrádi
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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8
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Sarac I, Hollenstein M. Terminal Deoxynucleotidyl Transferase in the Synthesis and Modification of Nucleic Acids. Chembiochem 2019; 20:860-871. [PMID: 30451377 DOI: 10.1002/cbic.201800658] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Indexed: 12/26/2022]
Abstract
The terminal deoxynucleotidyl transferase (TdT) belongs to the X family of DNA polymerases. This unusual polymerase catalyzes the template-independent addition of random nucleotides on 3'-overhangs during V(D)J recombination. The biological function and intrinsic biochemical properties of the TdT have spurred the development of numerous oligonucleotide-based tools and methods, especially if combined with modified nucleoside triphosphates. Herein, we summarize the different applications stemming from the incorporation of modified nucleotides by the TdT. The structural, mechanistic, and biochemical properties of this polymerase are also discussed.
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Affiliation(s)
- Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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9
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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10
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:12017-12021. [PMID: 30007102 DOI: 10.1002/anie.201807125] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 02/04/2023]
Abstract
The investigation of non-coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo-enzymatic RNA synthesis containing photoactivatable or 13 C,15 N-labelled nucleosides. All four ribonucleotides containing ortho-nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C-nucleotides and 13 C,15 N-labelled nucleotides were incorporated position-specifically in high yields. We applied this approach for the synthesis of light-inducible 2'dG-sensing riboswitch variants and detected ligand-induced structural reorganization upon irradiation by NMR spectroscopy. This chemo-enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid-phase synthesis.
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Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
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11
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Zhang D, Hu J, Yang XY, Wu Y, Su W, Zhang CY. Target-initiated synthesis of fluorescent copper nanoparticles for the sensitive and label-free detection of bleomycin. NANOSCALE 2018; 10:11134-11142. [PMID: 29873380 DOI: 10.1039/c8nr02780c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluorescent copper nanoparticles (CuNPs) have received great attention due to their distinct characteristics of facile synthesis, tunable fluorescence emission, high photostability, and biological compatibility, and they have been widely used for chemical and biological analyses. Bleomycins (BLMs) are widely used antitumor agents for the clinical treatment of various cancers. Here, we develop a sensitive and label-free fluorescence method for the quantitative detection of BLM on the basis of BLM-initiated enzymatic polymerization-mediated synthesis of fluorescent CuNPs. We design two hairpin DNAs: one (Hp1) for the recognition of BLM and the other (Hp2) for signal amplification. In the presence of BLM, it may recognize and cleave the 5'-GC-3' site of the Hp1 stem, releasing the 8-17 DNAzyme fragment. The resultant 8-17 DNAzyme fragments may bind with the loop of Hp2 to form a partial double-stranded DNA (dsDNA) duplex, initiating the cyclic cleavage of Hp2 in the presence of Zn2+-dependent DNAzymes and generating numerous new DNA fragments with the free 3'-OH terminal, which can induce the formation of a poly(thymine) (poly-T) sequence with the assistance of terminal deoxynucleotidyl transferase (TdTase). Subsequently, the ploy-T sequence may function as the template for the synthesis of CuNPs with strong fluorescence emission. This method shows good selectivity and high sensitivity with a detection limit as low as 8.1 × 10-16 M, and it exhibits good performance in serum samples. Moreover, this method has distinct advantages of simplicity and low cost, holding great potential in clinical diagnosis and biomedical research.
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Affiliation(s)
- Dandan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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12
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Hanhijärvi KJ, Ziedaite G, Bamford DH, Hæggström E, Poranen MM. Single-molecule measurements of viral ssRNA packaging. RNA (NEW YORK, N.Y.) 2017; 23:119-129. [PMID: 27803153 PMCID: PMC5159644 DOI: 10.1261/rna.057471.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Genome packaging of double-stranded RNA (dsRNA) phages has been widely studied using biochemical and molecular biology methods. We adapted the existing in vitro packaging system of one such phage for single-molecule experimentation. To our knowledge, this is the first attempt to study the details of viral RNA packaging using optical tweezers. Pseudomonas phage φ6 is a dsRNA virus with a tripartite genome. Positive-sense (+) single-stranded RNA (ssRNA) genome precursors are packaged into a preformed procapsid (PC), where negative strands are synthesized. We present single-molecule measurements of the viral ssRNA packaging by the φ6 PC. Our data show that packaging proceeds intermittently in slow and fast phases, which likely reflects differences in the unfolding of the RNA secondary structures of the ssRNA being packaged. Although the mean packaging velocity was relatively low (0.07-0.54 nm/sec), packaging could reach 4.62 nm/sec during the fast packaging phase.
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Affiliation(s)
| | - Gabija Ziedaite
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Edward Hæggström
- Department of Physics, University of Helsinki, Helsinki 00014, Finland
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
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13
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Liu S, Wei W, Sun X, Wang L. Ultrasensitive electrochemical DNAzyme sensor for lead ion based on cleavage-induced template-independent polymerization and alkaline phosphatase amplification. Biosens Bioelectron 2016; 83:33-8. [DOI: 10.1016/j.bios.2016.04.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/28/2016] [Accepted: 04/11/2016] [Indexed: 11/16/2022]
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14
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Takahara M, Hayashi K, Goto M, Kamiya N. Enzymatic conjugation of multiple proteins on a DNA aptamer in a tail-specific manner. Biotechnol J 2016; 11:814-23. [PMID: 27119459 DOI: 10.1002/biot.201500560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/09/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Conjugation of single-strand DNA aptamers and enzymes has been of great significance in bioanalytical and biomedical applications because of the unlimited functions provided by DNA aptamer direction. Therefore, we developed efficient tailing of a DNA aptamer, with end-specific conjugation of multiple enzymes, through enzymatic catalysis. Terminal deoxynucleotidyl transferase (TdT) added multiple Z-Gln-Gly (Z-QG) moieties to the 3'-end of a DNA aptamer via the addition of Z-QG-modified deoxyuridine triphosphate (Z-QG-dUTP) and deoxynucleoside triphosphates (dNTPs). The resultant (Z-QG)m -(dN)l-aptamer, whose Z-QGs with dN spacers served as stickers for microbial transglutaminase (MTG), were crosslinked between the Z-QGs on the DNA and a substrate peptide sequence containing lysine (K), fused to a recombinant enzyme (i.e. bacterial alkaline phosphatase; BAP) by MTG. The incorporation efficiency of Z-QG moieties on the aptamer tail and the subsequent conjugation efficiency with multiple enzyme molecules were dramatically altered by the presence of dNTPs, revealing that a combination of Z-QG-dUTP/dTTP comprised the best labeling efficiency and corresponding properties during analytical performance. Thus, a novel optimized platform for designing (BAP)n -(dT)l-DNA aptamers was demonstrated for the first time in this article, offering unique opportunities for tailoring new types of covalent protein-nucleic acid conjugates in a controllable way.
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Affiliation(s)
- Mari Takahara
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan
| | - Kounosuke Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan.,Hitachi Aloka Medical, Ltd, Tokyo, Mure, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, Motooka, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan. .,Center for Future Chemistry, Kyushu University, Fukuoka, Motooka, Japan.
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15
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Rublack N, Müller S. Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme. Beilstein J Org Chem 2014; 10:1906-13. [PMID: 25246949 PMCID: PMC4168874 DOI: 10.3762/bjoc.10.198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/30/2014] [Indexed: 11/23/2022] Open
Abstract
Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.
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Affiliation(s)
- Nico Rublack
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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16
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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17
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Tailing DNA aptamers with a functional protein by two-step enzymatic reaction. J Biosci Bioeng 2013; 116:660-5. [PMID: 23806788 DOI: 10.1016/j.jbiosc.2013.05.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/13/2013] [Accepted: 05/15/2013] [Indexed: 11/23/2022]
Abstract
An efficient, quantitative synthetic strategy for aptamer-enzyme conjugates was developed by using a two-step enzymatic reaction. Terminal deoxynucleotidyl transferase (TdT) was used to first incorporate a Z-Gln-Gly (QG) modified nucleotide which can act as a glutamine donor for a subsequent enzymatic reaction, to the 3'-OH of a DNA aptamer. Microbial transglutaminase (MTG) then catalyzed the cross-linking between the Z-QG modified aptamers and an enzyme tagged with an MTG-reactive lysine containing peptide. The use of a Z-QG modified dideoxynucleotide (Z-QG-ddUTP) or a deoxyuridine triphosphate (Z-QG-dUTP) in the TdT reaction enables the controlled introduction of a single or multiple MTG reactive residues. This leads to the preparation of enzyme-aptamer and (enzyme)n-aptamer conjugates with different detection limits of thrombin, a model analyte, in a sandwich enzyme-linked aptamer assay (ELAA). Since the combination of two enzymatic reactions yields high site-specificity and requires only short peptide substrates, the methodology should be useful for the labeling of DNA/RNA aptamers with proteins.
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18
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Tjong V, Yu H, Hucknall A, Chilkoti A. Direct fluorescence detection of RNA on microarrays by surface-initiated enzymatic polymerization. Anal Chem 2012. [PMID: 23194025 DOI: 10.1021/ac303132j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the first demonstration of surface-initiated enzymatic polymerization (SIEP) for the direct detection of RNA in a fluorescence microarray format. This new method incorporates multiple fluorophores into an RNA strand using the two-step sequential and complementary reactions catalyzed by yeast poly(A) polymerase (PaP) to incorporate deoxyadenosine triphosphate (dATP) at the 3'-OH of an RNA molecule, followed by terminal deoxynucleotidyl transferase (TdT) to catalyze the sequential addition of a mixture of natural and fluorescent deoxynucleotides (dNTPs) at the 3'-OH of an RNA-DNA hybrid. We found that the 3'-end of RNA can be efficiently converted into DNA (∼50% conversion) by polymerization of dATP using yeast PaP, and the short DNA strand appended to the end of the RNA by PaP acts as the initiator for the TdT-catalyzed polymerization of longer DNA strands from a mixture of natural and fluorescent dNTPs that contain up to ∼45 Cy3 fluorophores per 1 kb DNA. We obtained an ∼2 pM limit of detection (LOD) and a 3 log-linear dynamic range for hybridization of a short 21 base-long RNA target to an immobilized peptide nucleic acid probe, while fragmented mRNA targets from three different full length mRNA transcripts yielded a ∼10 pM LOD with a similar dynamic range in a microarray format.
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Affiliation(s)
- Vinalia Tjong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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19
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Winz ML, Samanta A, Benzinger D, Jäschke A. Site-specific terminal and internal labeling of RNA by poly(A) polymerase tailing and copper-catalyzed or copper-free strain-promoted click chemistry. Nucleic Acids Res 2012; 40:e78. [PMID: 22344697 PMCID: PMC3378897 DOI: 10.1093/nar/gks062] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The modification of RNA with fluorophores, affinity tags and reactive moieties is of enormous utility for studying RNA localization, structure and dynamics as well as diverse biological phenomena involving RNA as an interacting partner. Here we report a labeling approach in which the RNA of interest—of either synthetic or biological origin—is modified at its 3′-end by a poly(A) polymerase with an azido-derivatized nucleotide. The azide is later on conjugated via copper-catalyzed or strain-promoted azide–alkyne click reaction. Under optimized conditions, a single modified nucleotide of choice (A, C, G, U) containing an azide at the 2′-position can be incorporated site-specifically. We have identified ligases that tolerate the presence of a 2′-azido group at the ligation site. This azide is subsequently reacted with a fluorophore alkyne. With this stepwise approach, we are able to achieve site-specific, internal backbone-labeling of de novo synthesized RNA molecules.
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Affiliation(s)
- Marie-Luise Winz
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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20
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Zhao B, Gong Z, Ma Z, Wang D, Jin Y. Simple and sensitive microRNA labeling by terminal deoxynucleotidyl transferase. Acta Biochim Biophys Sin (Shanghai) 2012; 44:129-35. [PMID: 22189512 DOI: 10.1093/abbs/gmr115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) constitute a critically important class of non-translated, small RNAs, which post-transcriptionally regulate gene expression via one of the multiple mechanisms. To profile miRNA expression, microarrays have been extensively applied to the high-throughput detection of miRNAs. Here, we described a novel 3'-end miRNA-labeling method for microarray detection by terminal-deoxynucleotidyl transferase (TdT). TdT can catalyze the formation of polynucleotides at RNA receptor molecule with deoxycytidine triphosphate (dCTP). Using this activity, miRNA was successfully labeled by adding fluorescence dCTPs to its 3'-end. This labeling method was very simple and sensitive. The TdT-labeling method can detect as little as 0.04 fmol of synthetic small RNA, and produce precise and accurate measurements that span a linear dynamic range from 0.04 to 5 fmol of synthetic small RNA. The high consistency of miRNA expression data between our TdT method and real-time polymerase chain reaction analysis indicated the reliability and accuracy of the TdT method. Taken together, these results emphasize the immense potential application of the TdT-labeling method for sensitive and high-throughput microarray analysis of miRNA expression.
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Affiliation(s)
- Botao Zhao
- School of Life Sciences, Shanghai University, China.
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21
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Yu WH, Høvik H, Olsen I, Chen T. Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays. BMC Mol Biol 2011; 12:3. [PMID: 21235785 PMCID: PMC3031212 DOI: 10.1186/1471-2199-12-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/14/2011] [Indexed: 01/08/2023] Open
Abstract
Background With lower manufacturing cost, high spot density, and flexible probe design, genomic tiling microarrays are ideal for comprehensive transcriptome studies. Typically, transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. To address this issue, we have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. This paper describes this method and its application to the mapping of transcriptome profiles. Results RNA extracted from laboratory cultures of Porphyromonas gingivalis was fluorescently labeled with an alkylation reagent and hybridized directly to probes on genomic tiling microarrays specifically designed for this periodontal pathogen. The generated transcriptome profile was strand-specific and produced signals close to background level in most antisense regions of the genome. In contrast, high levels of signal were detected in the antisense regions when the hybridization was done with cDNA. Five antisense areas were tested with independent strand-specific RT-PCR and none to negligible amplification was detected, indicating that the strong antisense cDNA signals were experimental artifacts. Conclusions An efficient method was developed for mapping transcriptome profiles specific to both coding strands of a bacterial genome. This method chemically labels and uses extracted RNA directly in microarray hybridization. The generated transcriptome profile was free of cDNA artifactual signals. In addition, this method requires fewer processing steps and is potentially more sensitive in detecting small amount of RNA compared to conventional end-labeling methods due to the incorporation of more fluorescent molecules per RNA fragment.
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Affiliation(s)
- Wen-Han Yu
- Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
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22
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Synthesis of biotin-AMP conjugate for 5' biotin labeling of RNA through one-step in vitro transcription. Nat Protoc 2009; 3:1848-61. [PMID: 18989262 DOI: 10.1038/nprot.2008.185] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Biotin-labeled RNA has found broad applications in chemistry, biology and biomedicine. In this protocol, we describe a simple procedure for 5' RNA biotin labeling by one-step in vitro transcription. A biotin-AMP (adenosine 5'-monophosphate) conjugate, biotin-HDAAMP (adenosine 5'-(6-aminohexyl) phosphoramide; where HDA is 1,6-hexanediamine), is chemically synthesized. Transcription initiation by biotin-HDAAMP under the T7 phi 2.5 promoter produces 5' biotin-labeled RNA with high labeling efficiency. The procedure is especially useful for biotin labeling of RNA that is larger than 60 nucleotides. In addition, the protocol provides an attractive alternative to chemical synthesis of biotin-labeled small RNA of less than 60 nucleotides, particularly when the desired quantity of RNA is low. The whole procedure, from chemical syntheses to isolated biotin-labeled RNA, can be completed within 2 weeks.
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23
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Zheng D, Liu X, Zhou Y. 3GC cloning: PCR products cloning mediated by terminal deoxynucleotidyl transferase. Anal Biochem 2008; 378:108-10. [PMID: 18440295 DOI: 10.1016/j.ab.2008.03.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 03/30/2008] [Accepted: 03/31/2008] [Indexed: 10/22/2022]
Abstract
We have developed a PCR product cloning strategy called 3GC cloning. Through this strategy, PCR products tailed with more than three homopolymeric deoxycytidines (dCs) at the 3' ends by terminal deoxynucleotidyl transferase (TdT) would anneal complementarily with three-deoxyguanosine (dG) protruding ends of 3G vector, which was generated through coupled SfiI cleavage at both recognition sites. Redundant overhangs at insert-vector junctions after ligation would be trimmed off and repaired in bacteria, and the length of such junction was only three G/C pairs. Any chain lengths of three or more nucleotides, which are able to serve as substrates for TdT, could theoretically be cloned by this strategy.
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Affiliation(s)
- Dong Zheng
- Laboratory of Genetics and Molecular Biology, Northeast Forestry University, Harbin 150040, China
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24
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Vilfan ID, Kamping W, van den Hout M, Candelli A, Hage S, Dekker NH. An RNA toolbox for single-molecule force spectroscopy studies. Nucleic Acids Res 2007; 35:6625-39. [PMID: 17905817 PMCID: PMC2095808 DOI: 10.1093/nar/gkm585] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/15/2007] [Accepted: 07/17/2007] [Indexed: 01/29/2023] Open
Abstract
Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk biochemical studies. Next, the incorporation of modified nucleotides into the RNA construct is required for its surface immobilization. In addition, RNA constructs for single-molecule studies are commonly assembled from different single-stranded RNA molecules, demanding good control of hybridization or ligation. Finally, precautions to prevent RNase- and divalent cation-dependent RNA digestion must be taken. The rather limited selection of molecular biology tools adapted to the manipulation of RNA molecules, as well as the sensitivity of RNA to degradation, make RNA construct preparation a challenging task. We briefly illustrate the types of single-molecule force spectroscopy experiments that can be performed on RNA, and then present an overview of the toolkit of molecular biology techniques at one's disposal for the assembly of such RNA constructs. Within this context, we evaluate the molecular biology protocols in terms of their effectiveness in producing long and stable RNA constructs.
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Affiliation(s)
| | | | | | | | | | - Nynke H. Dekker
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, The Netherlands
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25
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Cho S, Lee SH, Chung WJ, Kim YK, Lee YS, Kim BG. Microbead-based affinity chromatography chip using RNA aptamer modified with photocleavable linker. Electrophoresis 2005; 25:3730-9. [PMID: 15565696 DOI: 10.1002/elps.200406103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A microbead-based affinity chromatography chip (micro-BACC) controlling hundreds of nanoliters of reaction volume was developed to separate and analyze hepatitis C virus (HCV) RNA polymerase protein by immobilization of an RNA aptamer on beads. A photocleavable linker was conjugated in between the beads and the aptamer to elute the bound RNA polymerase from the RNA aptamer in one step by UV irradiation, resulting in an efficient method to elute and identify the target molecule bound on RNA using a mass spectrometer. This linker showed a cleavage activity over 70% upon UV irradiation at 1050 mW/cm2 for more than 5 min. The photoelution method could prevent the target molecule from contaminations in affinity chromatography caused by elution solutions of high salt concentration, extreme pH and detergent, respectively. In this chip, sample reagents up to 800 nL could be metered quantitatively into the bead chamber using a nanoliter dispenser working, based on surface-guided flow control and pneumatic control by external air pressure on the chip. RNA polymerase eluted after UV irradiation was successfully analyzed by trypsin treatment without additional purification. As a result, using the aptamer, we could detect RNA polymerase from 800 nL hepatitis C patient serum containing 96 fmol HCV RNA polymerase. The detection limit of this system was estimated to be 9.6 fmol HCV RNA polymerase.
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Affiliation(s)
- Suhyung Cho
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Korea
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26
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Chung WJ, Kim MS, Cho S, Park SS, Kim JH, Kim YK, Kim BG, Lee YS. Microaffinity purification of proteins based on photolytic elution: Toward an efficient microbead affinity chromatography on a chip. Electrophoresis 2005; 26:694-702. [PMID: 15690422 DOI: 10.1002/elps.200410005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A bead affinity chromatography system, which was based on the photolytic elution method, was integrated into a glass-silicon microchip to purify specific target proteins. CutiCore beads, which were coupled with a photo-cleavable ligand, such as biotin and an RNA aptamer, were introduced into a filter chamber in the microchip. The protein mixture containing target protein labeled with fluorescein isothiocyanate (FITC) was then passed through the packed affinity beads in the microchamber by pressure-driven flow. During the process, the adsorbed protein on the bead was monitored by fluorescence. The concentrated target protein on the affinity bead was released by simple irradiation with UV light at a wavelength of 360 nm, and subsequently eluted with the phosphate buffer flow. The eluted target protein was quantitatively detected via the fluorescence intensity measurements at the downstream of the capillary connected to the outlet of the microchip. The microaffinity purification allowed for a successful method for the identification of specific target proteins from a protein mixture. In addition, the feasibility of this system for use as a diagnosis chip was demonstrated.
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Affiliation(s)
- Woo-Jae Chung
- School of Chemical Engineering, Seoul National University, Kwanak-Gu, Seoul, Korea
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27
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Hwang B, Cho JS, Yeo HJ, Kim JH, Chung KM, Han K, Jang SK, Lee SW. Isolation of specific and high-affinity RNA aptamers against NS3 helicase domain of hepatitis C virus. RNA (NEW YORK, N.Y.) 2004; 10:1277-1290. [PMID: 15247433 PMCID: PMC1370617 DOI: 10.1261/rna.7100904] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Accepted: 05/12/2004] [Indexed: 05/24/2023]
Abstract
Hepatitis C virus (HCV)-encoded nonstructural protein 3 (NS3) possesses protease, NTPase, and helicase activities, which are considered essential for viral proliferation. Thus, HCV NS3 is a good putative therapeutic target protein for the development of anti-HCV agents. In this study, we isolated specific RNA aptamers to the helicase domain of HCV NS3 from a combinatorial RNA library with 40-nucleotide random sequences using in vitro selection techniques. The isolated RNAs were observed to very avidly bind the HCV helicase with an apparent Kd of 990 pM in contrast to original pool RNAs with a Kd of >1 microM. These RNA ligands appear to impede binding of substrate RNA to the HCV helicase and can act as potent decoys to competitively inhibit helicase activity with high efficiency compared with poly(U) or tRNA. The minimal binding domain of the ligands was determined to evaluate the structural features of the isolated RNA molecules. Interestingly, part of binding motif of the RNA aptamers consists of similar secondary structure to the 3'-end of HCV negative-strand RNA. Moreover, intracellular NS3 protein can be specifically detected in situ with the RNA aptamers, indicating that the selected RNAs are very specific to the HCV NS3 helicase. Furthermore, the RNA aptamers partially inhibited RNA synthesis of HCV subgenomic replicon in Huh-7 hepatoma cell lines. These results suggest that the RNA aptamers selected in vitro could be useful not only as therapeutic and diagnostic agents of HCV infection but also as a powerful tool for the study of HCV helicase mechanism.
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Affiliation(s)
- Byounghoon Hwang
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, San8 Hannam-Dong, Yongsan-Gu, Seoul 140-714, Korea
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28
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Cole K, Truong V, Barone D, McGall G. Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes. Nucleic Acids Res 2004; 32:e86. [PMID: 15205470 PMCID: PMC443553 DOI: 10.1093/nar/gnh085] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Direct labeling of RNA is an expedient method for labeling large quantities (e.g. micrograms) of target RNA for microarray analysis. We have developed an efficient labeling system that uses T4 RNA ligase to attach a 3'-biotinylated donor molecule to target RNA. Microarray analyses indicate that directly labeled RNA is uniformly labeled, has higher signal intensity than comparable labeling methods and achieves high transcript detection sensitivity. The labeled donor molecule we have developed allows the attachment of multiple biotins, which increases target signal intensity up to 30%. We have used this direct-labeling method to detect previously discovered class predictor genes for two types of cancer: acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). In order to test the sensitivity of direct RNA labeling, we analyzed the AML and ALL expression profiles for predictor genes that were previously found to show elevated expression in the disease state. Direct labeling of AML poly(A) RNA detects 90% of the class predictor genes that are detected by the IVT-based target amplification method used to discover the genes. These results indicate that the detection sensitivity, simplicity (single tube reaction) and speed (2 h) of this direct labeling protocol may be ideal for diagnostic applications that do not require target amplification.
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Affiliation(s)
- Kyle Cole
- Affymetrix Inc., 3380 Central Expressway, Santa Clara, CA 95051, USA.
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29
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You KM, Lee SH, Im A, Lee SB. Aptamers as functional nucleic acids:In vitro selection and biotechnological applications. BIOTECHNOL BIOPROC E 2003. [DOI: 10.1007/bf02940259] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Sobczak K, Krzyzosiak WJ. RNA structure analysis assisted by capillary electrophoresis. Nucleic Acids Res 2002; 30:e124. [PMID: 12434006 PMCID: PMC137181 DOI: 10.1093/nar/gnf123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although most capillary electrophoresis (CE) applications in the nucleic acid field performed so far address DNA analysis, various RNA assays by CE have also been done. Both natural and synthetic RNAs have been examined to evaluate their quantities, sizes and interactions. In this report, we show a novel application of CE in RNA research for the analysis of RNA stable conformers. First, we present a successful adaptation of two different enzymatic methods for the 3'-end labeling of RNAs with commercially available fluorescent probes. Then, we show the high performance of CE with laser-induced fluorescence detection (CE-LIF) assisting the structural studies of transcripts. Using the example of regulatory elements present in the breast cancer gene transcript BRCA1, we demonstrate-by direct comparisons-the advantages of CE-LIF over the traditional slab-gel electrophoresis. These include a better and more reproducible separation of conformers, shorter analysis time and higher detection sensitivity.
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Affiliation(s)
- Krzysztof Sobczak
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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