1
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Sweeney KJ, Han X, Müller UF. A ribozyme that uses lanthanides as cofactor. Nucleic Acids Res 2023; 51:7163-7173. [PMID: 37326001 PMCID: PMC10415125 DOI: 10.1093/nar/gkad513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/10/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023] Open
Abstract
To explore how an early, RNA-based life form could have functioned, in vitro selection experiments have been used to develop catalytic RNAs (ribozymes) with relevant functions. We previously identified ribozymes that use the prebiotically plausible energy source cyclic trimetaphosphate (cTmp) to convert their 5'-hydroxyl group to a 5'-triphosphate. While these ribozymes were developed in the presence of Mg2+, we tested here whether lanthanides could also serve as catalytic cofactors because lanthanides are ideal catalytic cations for this reaction. After an in vitro selection in the presence of Yb3+, several active sequences were isolated, and the most active RNA was analyzed in more detail. This ribozyme required lanthanides for activity, with highest activity at a 10:1 molar ratio of cTmp : Yb3+. Only the four heaviest lanthanides gave detectable signals, indicating a high sensitivity of ribozyme catalysis to the lanthanide ion radius. Potassium and Magnesium did not facilitate catalysis alone but they increased the lanthanide-mediated kOBS by at least 100-fold, with both K+ and Mg2+ modulating the ribozyme's secondary structure. Together, these findings show that RNA is able to use the unique properties of lanthanides as catalytic cofactor. The results are discussed in the context of early life forms.
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Affiliation(s)
- Kevin J Sweeney
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Xu Han
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
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2
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Cardador CM, Muehlmann LA, Coelho CM, Silva LP, Garay AV, Carvalho AMDS, Bastos IMD, Longo JPF. Nucleotides Entrapped in Liposome Nanovesicles as Tools for Therapeutic and Diagnostic Use in Biomedical Applications. Pharmaceutics 2023; 15:873. [PMID: 36986734 PMCID: PMC10056227 DOI: 10.3390/pharmaceutics15030873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The use of nucleotides for biomedical applications is an old desire in the scientific community. As we will present here, there are references published over the past 40 years with this intended use. The main problem is that, as unstable molecules, nucleotides require some additional protection to extend their shelf life in the biological environment. Among the different nucleotide carriers, the nano-sized liposomes proved to be an effective strategic tool to overcome all these drawbacks related to the nucleotide high instability. Moreover, due to their low immunogenicity and easy preparation, the liposomes were selected as the main strategy for delivery of the mRNA developed for COVID-19 immunization. For sure this is the most important and relevant example of nucleotide application for human biomedical conditions. In addition, the use of mRNA vaccines for COVID-19 has increased interest in the application of this type of technology to other health conditions. For this review article, we will present some of these examples, especially focused on the use of liposomes to protect and deliver nucleotides for cancer therapy, immunostimulatory activities, enzymatic diagnostic applications, some examples for veterinarian use, and the treatment of neglected tropical disease.
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Affiliation(s)
- Camila Magalhães Cardador
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
| | | | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
| | - Luciano Paulino Silva
- Laboratório de Nanobiotecnologia (LNANO), Embrapa Recursos Genéticos e Biotecnologia, Brasilia 70770-917, DF, Brazil
| | - Aisel Valle Garay
- Molecular Biophysics Laboratory, Department of Cell Biology, Institute of Biological Science, University of Brasília (UnB), Brasília 70910-900, DF, Brazil
| | | | - Izabela Marques Dourado Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia (UnB), Brasilia 70910-900, DF, Brazil
| | - João Paulo Figueiró Longo
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
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3
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Guth-Metzler R, Bray MS, Frenkel-Pinter M, Suttapitugsakul S, Montllor-Albalate C, Bowman JC, Wu R, Reddi AR, Okafor CD, Glass JB, Williams LD. Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage. Nucleic Acids Res 2020; 48:8663-8674. [PMID: 32663277 PMCID: PMC7470983 DOI: 10.1093/nar/gkaa586] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the ribosome's early evolution in a high Fe2+ environment, and the continued use of Fe2+ by obligate anaerobes inhabiting high Fe2+ niches. Here, we show that (i) Fe2+ cleaves RNA by in-line cleavage, a non-oxidative mechanism that has not previously been shown experimentally for this metal, (ii) the first-order in-line rate constant with respect to divalent cations is >200 times greater with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification from cells grown under low O2 and high Fe2+ and (iv) a small fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent cations, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In total, these results expand the ancient role of iron in biochemistry and highlight a possible new mechanism of iron toxicity.
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Affiliation(s)
- Rebecca Guth-Metzler
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Marcus S Bray
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Moran Frenkel-Pinter
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | | | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer B Glass
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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4
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Sun H, Cai S, Wang C, Chen Y, Yang R. Recent Progress of Nanozymes in the Detection of Pathogenic Microorganisms. Chembiochem 2020; 21:2572-2584. [PMID: 32352212 DOI: 10.1002/cbic.202000126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/11/2020] [Indexed: 12/17/2022]
Abstract
Infectious diseases are among the world's principal health problems. It is crucial to develop rapid, accurate and cost-effective methods for the detection of pathogenic microorganisms. Recently, considerable progress has been achieved in the field of inorganic enzyme mimics (nanozymes). Compared with natural enzymes, nanozymes have higher stability and lower cost. More interestingly, their properties can be designed for various demands. Herein, we introduce the latest research progress on the detection of pathogenic microorganisms by using various nanozymes. We also discuss the current challenges of nanozymes in biosensing and provide some strategies to overcome these barriers.
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Affiliation(s)
- Huiyuan Sun
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, UCAS, Beijing, 100190, P. R. China.,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Shuangfei Cai
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, UCAS, Beijing, 100190, P. R. China
| | - Chen Wang
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, UCAS, Beijing, 100190, P. R. China
| | - Yongxiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Rong Yang
- CAS Key Lab for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, UCAS, Beijing, 100190, P. R. China.,Sino-Danish College, UCAS, Sino-Danish Center for Education and Research, Beijing, 100190, P. R. China
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5
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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6
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Ma L, Liu J. Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology. iScience 2020; 23:100815. [PMID: 31954323 PMCID: PMC6962706 DOI: 10.1016/j.isci.2019.100815] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023] Open
Abstract
Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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7
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020; 59:3573-3577. [PMID: 31867832 DOI: 10.1002/anie.201915675] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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8
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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9
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Tian R, Zhang B, Zhao M, Zou H, Zhang C, Qi Y, Ma Q. Fluorometric enhancement of the detection of H 2O 2 using different organic substrates and a peroxidase-mimicking polyoxometalate. RSC Adv 2019; 9:12209-12217. [PMID: 35515876 PMCID: PMC9063527 DOI: 10.1039/c9ra00505f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/01/2019] [Indexed: 12/20/2022] Open
Abstract
Simple, sensitive and stable fluorometric sensors based on the polyoxotungstate intrinsic peroxidase (Na10[α-SiW9O34]) induced fluorescent enhancement of benzoic acid (BA), thiamine (TH) and 3-(4-hydroxyphenyl)propionic acid (HPPA) for the detection of hydrogen peroxide (H2O2) are developed for the first time. In three assays, the three non-fluorescent substrates BA, TH and HPPA were oxidized with the ·OH radicals decomposed from H2O2 under the catalysis of Na10[α-SiW9O34] under basic pH conditions. The optimal conditions for the detection of H2O2 were evaluated and possible mechanisms are also discussed. The fluorescence intensity increases were linearly related to the concentration of H2O2 in the ranges 1 × 10-8 to 1.6 × 10-6, 1.6 × 10-6 to 1 × 10-4, and 1 × 10-5to 2.5 × 10-4 M with BA, TH, and HPPA as substrates, respectively. Detection limits for the three systems were found to be 6.7 × 10-9, 2.2 × 10-7 and 9.6 × 10-6 M (3σ), respectively. The RSD values ranged from 2.57% to 4.66%, 0.82% to 4.06%, and 1.08% to 2.75%, respectively. The rates of recoveries were between 99.73% and 113.06%, 95.20% and 104.22%, and 95.28% and 128.76%, respectively. Moreover, the effects of interference were studied. The proposed work was successfully applied to the determination of H2O2 in water and a sensitive, rapid and easy to operate assay was built, which has great potential applications in environmental science.
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Affiliation(s)
- Rui Tian
- School of Public Health, Jilin University Changchun Jilin 130021 China +86-431-85619441
| | - Boyu Zhang
- School of Public Health, Jilin University Changchun Jilin 130021 China +86-431-85619441
| | - Mingming Zhao
- School of Public Health, Jilin University Changchun Jilin 130021 China +86-431-85619441
| | - Hangjin Zou
- School of Public Health, Jilin University Changchun Jilin 130021 China +86-431-85619441
| | - Chuhan Zhang
- School of Public Health, Jilin University Changchun Jilin 130021 China +86-431-85619441
| | - Yanfei Qi
- School of Public Health, Jilin University Changchun Jilin 130021 China +86-431-85619441
| | - Qiang Ma
- Department of Analytical Chemistry, College of Chemistry, Jilin University Changchun 130012 China
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10
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Sigel A, Operschall BP, Sigel RKO, Sigel H. Metal ion complexes of nucleoside phosphorothioates reflecting the ambivalent properties of lead(ii). NEW J CHEM 2018. [DOI: 10.1039/c7nj04989g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lead(ii)-lone pair leads to ambivalency: hemidirected (distorted, non-spherical) coordination spheres result from electronegative O-coordination and holodirected (symmetric, spherical) ones from less electronegative S-coordination.
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Affiliation(s)
- Astrid Sigel
- Department of Chemistry
- Inorganic Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Bert P. Operschall
- Department of Chemistry
- Inorganic Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | | | - Helmut Sigel
- Department of Chemistry
- Inorganic Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
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11
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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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12
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Nakano SI, Watabe T, Sugimoto N. Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions. Chemphyschem 2017; 18:3614-3619. [DOI: 10.1002/cphc.201700882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/13/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
| | - Takaaki Watabe
- Department of Nanobiochemistry; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
- Department of Chemistry; Faculty of Science and Engineering; Konan University; 8-9-1, Okamoto, Higashinada-ku Kobe 658-8501 Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20, Minatojima-minamimachi, Chuo-ku Kobe 650-0047 Japan
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13
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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14
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Drosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration. Sci Rep 2017; 7:41559. [PMID: 28139767 PMCID: PMC5282483 DOI: 10.1038/srep41559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022] Open
Abstract
Endoribonucleases participate in almost every step of eukaryotic RNA metabolism, acting either as degradative or biosynthetic enzymes. We previously identified the founding member of the Eukaryotic EndoU ribonuclease family, whose components display unique biochemical features and are flexibly involved in important biological processes, such as ribosome biogenesis, tumorigenesis and viral replication. Here we report the discovery of the CG3303 gene product, which we named DendoU, as a novel family member in Drosophila. Functional characterisation revealed that DendoU is essential for Drosophila viability and nervous system activity. Pan-neuronal silencing of dendoU resulted in fly immature phenotypes, highly reduced lifespan and dramatic motor performance defects. Neuron-subtype selective silencing showed that DendoU is particularly important in cholinergic circuits. At the molecular level, we unveiled that DendoU is a positive regulator of the neurodegeneration-associated protein dTDP-43, whose downregulation recapitulates the ensemble of dendoU-dependent phenotypes. This interdisciplinary work, which comprehends in silico, in vitro and in vivo studies, unveils a relevant role for DendoU in Drosophila nervous system physio-pathology and highlights that DendoU-mediated neurotoxicity is, at least in part, contributed by dTDP-43 loss-of-function.
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15
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Teramoto N, Imanishi Y, Ito Y. In Vitro Selection of Ligase Ribozymes Containing 2'-Amino Groups. J BIOACT COMPAT POL 2016. [DOI: 10.1177/088391150001500402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Novel ribozymes containing 2'-amino groups in the side chains were in vitro selected to accelerate their ligation reaction rates with oligodeoxynucleotides. The ligation rate of random sequenced RNAs in the starting pool was accelerated by incorporation of 2'-amino-2'-deoxyuridine and N6-(6-aminohexyl)adenosine. The incorporation of the amino group enhanced the activity of non-selected RNAs independent of the incorporation site. In vitro selection using 2'-amino-2'-deoxyuridine instead of uridine produced more active ribozymes. In this case, the activity of ribozyme was reduced when N6-(6-aminohexyl)adenosine was incorporated into the selected RNAs instead of natural adenosine. The presence of amino groups as well as the incorporation site affected the activity of the in vitro selected ribozyme. It seems that RNAs with tertiary structures suitable for the ligation reaction were selected by the in vitro method.
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Affiliation(s)
- Naozumi Teramoto
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 660-8501 Japan
| | - Yukio Imanishi
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0101 Japan
| | - Yoshihiro Ito
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, Tokushima 770-8506 Japan
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16
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The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev 2016; 8:11-23. [PMID: 28510143 DOI: 10.1007/s12551-015-0188-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023] Open
Abstract
Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.
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17
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Saran R, Liu J. A comparison of two classic Pb2+-dependent RNA-cleaving DNAzymes. Inorg Chem Front 2016. [DOI: 10.1039/c5qi00125k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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18
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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19
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Saran R, Chen Q, Liu J. Searching for a DNAzyme Version of the Leadzyme. J Mol Evol 2015; 81:235-44. [PMID: 26458991 DOI: 10.1007/s00239-015-9702-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022]
Abstract
The leadzyme refers to a small ribozyme that cleaves a RNA substrate in the presence of Pb(2+). In an optimized form, the enzyme strand contains only two unpaired nucleotides. Most RNA-cleaving DNAzymes are much longer. Two classical Pb(2+)-dependent DNAzymes, 8-17 and GR5, both contain around 15 nucleotides in the enzyme loop. This is also the size of most RNA-cleaving DNAzymes that use other metal ions for their activity. Such large enzyme loops make spectroscopic characterization difficult and so far no high-resolution structural information is available for active DNAzymes. The goal of this work is to search for DNAzymes with smaller enzyme loops. A simple replacement of the ribonucleotides in the leadzyme by deoxyribonucleotides failed to produce an active enzyme. A Pb(2+)-dependent in vitro selection combined with deep sequencing was then performed. After sequence alignment and DNA folding, a new DNAzyme named PbE22 was identified, which contains only 5 nucleotides in the enzyme catalytic loop. The biochemical characteristics of PbE22 were compared with those of the leadzyme and the two classical Pb(2+)-dependent DNAzymes. The rate of PbE22 rises with increase in Pb(2+) concentration, being 1.7 h(-1) in the presence of 100 μM Pb(2+) and reaching 3.5 h(-1) at 500 µM Pb(2+). The log of PbE22 rate rises linearly in a pH-dependent fashion (20 µM Pb(2+)) with a slope of 0.74. In addition, many other abundant sequences in the final library were studied. These sequences are quite varied in length and nucleotide composition, but some contain a few conserved nucleotides consistent with the GR5 structure. Interestingly, some sequences are active with Pb(2+) but none of them were active with even 50 mM Mg(2+), which is reminiscent of the difference between the GR5 and 8-17 DNAzymes.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Qingyun Chen
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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20
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Qi X, Xia T. Structure, dynamics, and mechanism of the lead-dependent ribozyme. Biomol Concepts 2015; 2:305-14. [PMID: 25962038 DOI: 10.1515/bmc.2011.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/06/2011] [Indexed: 12/24/2022] Open
Abstract
Leadzyme is a small catalytic RNA that was identified by in vitro selection for Pb2+-dependent cleavage from a tRNA library. Leadzyme employs a unique two-step Pb2+-specific mechanism to cleave within its active site. NMR and crystal structures of the active site revealed different folding patterns, but neither features the in-line alignment for attack by the 2'-OH nucleophilic group. These experimentally determined structures most likely represent ground states and are catalytically inactive. There are significant dynamics of the active site and the motif samples multiple conformations at the ground states. Various metal ion binding sites have been identified, including one that may be occupied by a catalytic Pb2+. Based on functional group analysis, a computational model of the transition state has been proposed. This model features a unique base triple that is consistent with sequence and functional group requirements for catalysis. This structure is likely only populated transiently, but imposing appropriate conformational constraints may significantly stabilize this state thereby promoting catalysis. Other ions may inhibit the cleavage by competing for the Pb2+ binding site, or by stabilizing the ground state thereby suppressing its transition to the catalytically active conformation. Some rare earth ions can enhance the reaction via an unknown mechanism. Because of its unique chemistry and dynamic behavior, leadzyme can continue to serve as an excellent model system for teaching us RNA biology and chemistry.
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21
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Abstract
The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.
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22
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Heyer EE, Ozadam H, Ricci EP, Cenik C, Moore MJ. An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments. Nucleic Acids Res 2014; 43:e2. [PMID: 25505164 PMCID: PMC4288154 DOI: 10.1093/nar/gku1235] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Deep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs. Our approach works across a wide range of input amounts (400 pg to 200 ng), is easy to follow and produces a library in 2–3 days at relatively low reagent cost, all while giving the user complete control over every step. Because all enzymatic reactions were optimized and driven to apparent completion, sequence diversity and species abundance in the input sample are well preserved.
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Affiliation(s)
- Erin E Heyer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Hakan Ozadam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emiliano P Ricci
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Can Cenik
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
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23
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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24
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Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. Small, highly active DNAs that hydrolyze DNA. J Am Chem Soc 2013; 135:9121-9. [PMID: 23679108 PMCID: PMC3763483 DOI: 10.1021/ja403585e] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (k(obs)) of ~1 min(-1) when incubated near neutral pH in the presence of Zn(2+). Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn(2+), pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.
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Affiliation(s)
- Hongzhou Gu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
| | - Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Daniel F. Berenson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
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25
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Auyeung VC, Ulitsky I, McGeary SE, Bartel DP. Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 2013; 152:844-58. [PMID: 23415231 DOI: 10.1016/j.cell.2013.01.031] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/28/2012] [Accepted: 01/14/2013] [Indexed: 12/26/2022]
Abstract
To use microRNAs to downregulate mRNA targets, cells must first process these ~22 nt RNAs from primary transcripts (pri-miRNAs). These transcripts form RNA hairpins important for processing, but additional determinants must distinguish pri-miRNAs from the many other hairpin-containing transcripts expressed in each cell. Illustrating the complexity of this recognition, we show that most Caenorhabditis elegans pri-miRNAs lack determinants required for processing in human cells. To find these determinants, we generated many variants of four human pri-miRNAs, sequenced millions that retained function, and compared them with the starting variants. Our results confirmed the importance of pairing in the stem and revealed three primary-sequence determinants, including an SRp20-binding motif (CNNC) found downstream of most pri-miRNA hairpins in bilaterian animals, but not in nematodes. Adding this and other determinants to C. elegans pri-miRNAs imparted efficient processing in human cells, thereby confirming the importance of primary-sequence determinants for distinguishing pri-miRNAs from other hairpin-containing transcripts.
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Affiliation(s)
- Vincent C Auyeung
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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26
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Wei H, Wang E. Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes. Chem Soc Rev 2013; 42:6060-93. [DOI: 10.1039/c3cs35486e] [Citation(s) in RCA: 2267] [Impact Index Per Article: 206.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Giel-Pietraszuk M, Barciszewski J. Hydrostatic and osmotic pressure study of the RNA hydration. Mol Biol Rep 2012; 39:6309-18. [PMID: 22314910 PMCID: PMC3310992 DOI: 10.1007/s11033-012-1452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/23/2012] [Indexed: 11/17/2022]
Abstract
The tertiary structure of nucleic acids results from an equilibrium between electrostatic interactions of phosphates, stacking interactions of bases, hydrogen bonds between polar atoms and water molecules. Water interactions with ribonucleic acid play a key role in its structure formation, stabilization and dynamics. We used high hydrostatic pressure and osmotic pressure to analyze changes in RNA hydration. We analyzed the lead catalyzed hydrolysis of tRNAPhe from S. cerevisiae as well as hydrolytic activity of leadzyme. Pb(II) induced hydrolysis of the single phosphodiester bond in tRNAPhe is accompanied by release of 98 water molecules, while other molecule, leadzyme releases 86.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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28
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Erat MC, Coles J, Finazzo C, Knobloch B, Sigel RK. Accurate analysis of Mg2+ binding to RNA: From classical methods to a novel iterative calculation procedure. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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29
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Suga H, Futai K, Jin K. Metal Ion Requirements in Artificial Ribozymes that Catalyze Aminoacylation and Redox Reactions. STRUCTURAL AND CATALYTIC ROLES OF METAL IONS IN RNA 2011; 9:277-97. [DOI: 10.1039/9781849732512-00277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The means of in vitro selection has yielded a number of artificial ribozymes with functions that have not been discovered as yet in modern biological systems. Like naturally occurring ribozymes, most artificial ribozymes also use metal ions for the support of catalysis. Here we choose two such ribozymes, flexizyme and ribox, that exhibit specific activities of tRNA aminoacylation and redox chemistry, respectively, and comprehensively summarize the roles of metal ions in conjunction with their structure and function.
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Affiliation(s)
- Hiroaki Suga
- Department of Chemistry School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo Japan
- Department of Chemistry and Biotechnology School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo Japan
- Research Center for Advanced Science and Technology The University of Tokyo, 4-6-1 Komaba, Meguro-ku 153-8904 Tokyo Japan
| | - Kazuki Futai
- Research Center for Advanced Science and Technology The University of Tokyo, 4-6-1 Komaba, Meguro-ku 153-8904 Tokyo Japan
| | - Koichiro Jin
- Department of Chemistry and Biotechnology School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo Japan
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30
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31
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32
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Esakova O, Perederina A, Quan C, Berezin I, Krasilnikov AS. Substrate recognition by ribonucleoprotein ribonuclease MRP. RNA (NEW YORK, N.Y.) 2011; 17:356-64. [PMID: 21173200 PMCID: PMC3022284 DOI: 10.1261/rna.2393711] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/15/2010] [Indexed: 05/22/2023]
Abstract
The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5' ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed.
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Affiliation(s)
- Olga Esakova
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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33
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Johnson-Buck AE, McDowell SE, Walter NG. Metal ions: supporting actors in the playbook of small ribozymes. Met Ions Life Sci 2011; 9:175-96. [PMID: 22010272 DOI: 10.1039/9781849732512-00175] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the 1980s, several small RNA motifs capable of chemical catalysis have been discovered. These small ribozymes, composed of between approximately 40 and 200 nucleotides, have been found to play vital roles in the replication of subviral and viral pathogens, as well as in gene regulation in prokaryotes, and have recently been discovered in noncoding eukaryotic RNAs. All of the known natural small ribozymes - the hairpin, hammerhead, hepatitis delta virus, Varkud satellite, and glmS ribozymes--catalyze the same self-cleavage reaction as RNase A, resulting in two products, one bearing a 2'-3' cyclic phosphate and the other a 5'-hydroxyl group. Although originally thought to be obligate metalloenzymes like the group I and II self-splicing introns, the small ribozymes are now known to support catalysis in a wide variety of cations that appear to be only indirectly involved in catalysis. Nevertheless, under physiologic conditions, metal ions are essential for the proper folding and function of the small ribozymes, the most effective of these being magnesium. Metal ions contribute to catalysis in the small ribozymes primarily by stabilizing the catalytically active conformation, but in some cases also by activating RNA functional groups for catalysis, directly participating in catalytic acid-base chemistry, and perhaps by neutralizing the developing negative charge of the transition state. Although interactions between the small ribozymes and cations are relatively nonspecific, ribozyme activity is quite sensitive to the types and concentrations of metal ions present in solution, suggesting a close evolutionary relationship between cellular metal ion homeostasis and cation requirements of catalytic RNAs, and perhaps RNA in general.
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Affiliation(s)
- Alexander E Johnson-Buck
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109-1055, USA.
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34
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Kumar A, Sharma S, Maurya RA. Single Nucleotide-Catalyzed Biomimetic Reductive Amination. Adv Synth Catal 2010. [DOI: 10.1002/adsc.201000178] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Manapat ML, Chen IA, Nowak MA. The basic reproductive ratio of life. J Theor Biol 2009; 263:317-27. [PMID: 20034501 DOI: 10.1016/j.jtbi.2009.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/26/2009] [Accepted: 12/16/2009] [Indexed: 11/16/2022]
Abstract
Template-directed polymerization of nucleotides is believed to be a pathway for the replication of genetic material in the earliest cells. We assume that activated monomers are produced by prebiotic chemistry. These monomers can undergo spontaneous polymerization, a system that we call "prelife." Adding template-directed polymerization changes the equilibrium structure of prelife if the rate constants meet certain criteria. In particular, if the basic reproductive ratio of sequences of a certain length exceeds one, then those sequences can attain high abundance. Furthermore, if many sequences replicate, then the longest sequences can reach high abundance even if the basic reproductive ratios of all sequences are less than one. We call this phenomenon "subcritical life." Subcritical life suggests that sequences long enough to be ribozymes can become abundant even if replication is relatively inefficient. Our work on the evolution of replication has interesting parallels to infection dynamics. Life (replication) can be seen as an infection of prelife.
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Affiliation(s)
- Michael L Manapat
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
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36
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Kadakkuzha BM, Zhao L, Xia T. Conformational distribution and ultrafast base dynamics of leadzyme. Biochemistry 2009; 48:3807-9. [PMID: 19301929 DOI: 10.1021/bi900256q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The dynamic nature of ribozymes represents a significant challenge in elucidating their structure-dynamics-function relationship. Here, using femtosecond time-resolved spectroscopy and other biophysical tools, we demonstrate that the active site of leadzyme does not have a unique structure, but rather samples an ensemble of conformations that undergo picosecond structural changes. Various base modifications have a profound context-dependent impact on the catalysis.
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Affiliation(s)
- Beena M Kadakkuzha
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083-0688, USA
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37
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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38
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Laneve P, Gioia U, Ragno R, Altieri F, Di Franco C, Santini T, Arceci M, Bozzoni I, Caffarelli E. The tumor marker human placental protein 11 is an endoribonuclease. J Biol Chem 2008; 283:34712-9. [PMID: 18936097 PMCID: PMC3259861 DOI: 10.1074/jbc.m805759200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 10/16/2008] [Indexed: 01/19/2023] Open
Abstract
Human PP11 (placental protein 11) was previously described as a serine protease specifically expressed in the syncytiotrophoblast and in numerous tumor tissues. Several PP11-like proteins were annotated in distantly related organisms, such as worms and mammals, suggesting their involvement in evolutionarily conserved processes. Based on sequence similarity, human PP11 was included in a protein family whose characterized members are XendoU, a Xenopus laevis endoribonuclease involved in small nucleolar RNA processing, and Nsp15, an endoribonuclease essential for coronavirus replication. Here we show that the bacterially expressed human PP11 displays RNA binding capability and cleaves single stranded RNA in a Mn(2+)-dependent manner at uridylates, to produce molecules with 2',3'-cyclic phosphate ends. These features, together with structural and mutagenesis analyses, which identified the potential active site residues, reveal striking parallels to the amphibian XendoU and assign a ribonuclease function to PP11. This newly discovered enzymatic activity places PP11-like proteins in a completely new perspective.
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Affiliation(s)
- Pietro Laneve
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Ubaldo Gioia
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Rino Ragno
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Fabio Altieri
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Carmen Di Franco
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Tiziana Santini
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Massimo Arceci
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Irene Bozzoni
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Elisa Caffarelli
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
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39
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Lippert B. Ligand-pKaShifts through Metals: Potential Relevance to Ribozyme Chemistry. Chem Biodivers 2008; 5:1455-1474. [DOI: 10.1002/cbdv.200890135] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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40
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Knobloch B, Nawrot B, Okruszek A, Sigel RKO. Discrimination in metal-ion binding to RNA dinucleotides with a non-bridging oxygen or sulfur in the phosphate diester link. Chemistry 2008; 14:3100-9. [PMID: 18270983 DOI: 10.1002/chem.200701491] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replacement of a non-bridging oxygen in the phosphate diester bond by a sulfur has become quite popular in nucleic acid research and is often used as a probe, for example, in ribozymes, where the normally essential Mg(2+) is partly replaced by a thiophilic metal ion to reactivate the system. Despite these widely applied rescue experiments no detailed studies exist quantifying the affinity of metal ions to such terminal sulfur atoms. Therefore, we performed potentiometric pH titrations to determine the binding properties of pUp((S))U(3-) towards Mg(2+), Mn(2+), Zn(2+), Cd(2+), and Pb(2+), and compared these data with those previously obtained for the corresponding pUpU(3-) complexes. The primary binding site in both dinucleotides is the terminal phosphate group. Theoretically, also the formation of 10-membered chelates involving the terminal oxygen or sulfur atoms of the (thio)phosphate bridge is possible with both ligands. The results show that Mg(2+) and Mn(2+) exist as open (op) isomers binding to both dinucleotides only at the terminal phosphate group. Whereas Cd(pUpU)(-) only exists as Cd(pUpU)(-)(op), Cd(pUp((S))U)(-) is present to about 64 % as the S-coordinated macrochelate, Cd(pUp((S))U)(-)(cl/PS). Zn(2+) forms with pUp((S))U(3-) three isomeric species, that is, Zn(pUp((S))U)(-)(op), Zn(pUp((S))U)(-)(cl/PO), and Zn(pUp((S))U)(-)(cl/PS), which occur to about 33, 12 (O-bound), and 55 %, respectively. Pb(2+) forms the 10-membered chelate with both nucleotides involving only the terminal oxygen atoms of the (thio)phosphate bridge, that is, no indication of S binding was discovered in this case. Hence, Zn(2+) and Cd(2+) show pronounced thiophilic properties, whereas Mg(2+), Mn(2+), and Pb(2+) coordinate to the oxygen, macrochelate formation being of relevance with Pb(2+) only.
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Affiliation(s)
- Bernd Knobloch
- Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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41
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Abstract
Enzymatic catalysis by RNA was discovered 25 years ago, yet mechanistic insights are emerging only slowly. Thought to be metalloenzymes at first, some ribozymes proved more versatile than anticipated when shown to utilize their own functional groups for catalysis. Recent evidence suggests that some may also judiciously place structural water molecules to shuttle protons in acid-base catalyzed reactions.
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Affiliation(s)
- Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48019-1055, USA.
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42
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Abstract
It has been 40 years since Spiegelman and co-workers demonstrated how RNA molecules can be evolved in the test tube. This result established Darwinian evolution as a chemical process and paved the way for the many directed evolution experiments that followed. Chemists can benefit from reflecting on Spiegelman's studies and the subsequent advances, which have taken the field to the brink of the generation of life itself in the laboratory. This Review summarizes the concepts and methods for the directed evolution of RNA molecules in vitro.
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Affiliation(s)
- Gerald F Joyce
- Department of Chemistry and Molecular Biology, La Jolla, CA 92037, USA.
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44
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Anderson PC, Mecozzi S. Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques. J Comput Chem 2007; 27:1631-40. [PMID: 16900493 DOI: 10.1002/jcc.20459] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology.
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Affiliation(s)
- Peter C Anderson
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, USA
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45
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Anderson PC, Mecozzi S. Minimum sequence requirements for the binding of paromomycin to the rRNA decoding site A. Biopolymers 2007; 86:95-111. [PMID: 17323326 DOI: 10.1002/bip.20707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We have recently introduced a computational methodology that combines molecular dynamics (MD) simulations, free-energy calculations, and in vitro binding assays to predict the minimum RNA structural requirements for selective, high-affinity RNA binding to small-molecule ligands. Here, we show that this methodology can be applied to the conformationally flexible aminoglycoside antibiotic paromomycin. A RNA consisting of an 11-mer:10-mer duplex that contains one 16S ribosome RNA decoding A-site bound to paromomycin was simulated for 4 ns. The methodology predicts that the 11-mer:10-mer duplex binds to paromomycin with high affinity, whereas smaller RNA duplexes lose complex stability and the ability to bind paromomycin. The predicted high-affinity binding to paromomycin of the 11-mer:10-mer duplex was confirmed experimentally (EC(50) = 0.28 microM), as well as the inability of smaller complexes to bind. Our simulations show good agreement with experiment for dynamic and structural properties of the isolated A-site, including hydrogen-bonding networks and RNA structural rearrangements upon ligand binding. The results suggest that MD simulations can supplement in vitro methods as a tool for predicting minimum RNA-binding motifs for both small, rigid ligands, and large, flexible ligands when structural information is available.
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Affiliation(s)
- Peter C Anderson
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, USA
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46
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Wyszko E, Nowak M, Pospieszny H, Szymanski M, Pas J, Barciszewska MZ, Barciszewski J. Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum. FEBS J 2006; 273:5022-31. [PMID: 17032353 PMCID: PMC7163940 DOI: 10.1111/j.1742-4658.2006.05497.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 08/03/2006] [Accepted: 09/12/2006] [Indexed: 11/29/2022]
Abstract
We developed a new method for inhibiting tobacco mosaic virus infection in tobacco plants based on specific RNA hydrolysis induced by a leadzyme. We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16-mer oligoribonucleotide capable of forming a specific leadzyme motif with a five-nucleotide catalytic loop. The synthetic 16-mer RNA was applied with nontoxic, catalytic amount of lead to infected tobacco leaves. We observed inhibition of tobacco mosaic virus infection in tobacco leaves in vivo due to specific tobacco mosaic virus RNA cleavage effected by leadzyme. A significant reduction in tobacco mosaic virus accumulation was observed even when the leadzyme was applied up to 2 h after inoculation of leaves with tobacco mosaic virus. This process, called leadzyme interference, is determined by specific recognition and cleavage of the target site by the RNA catalytic strand in the presence of Pb(2+).
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Affiliation(s)
- Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Knobloch B, Suliga D, Okruszek A, Sigel RKO. Acid-base and metal-ion binding properties of the RNA dinucleotide uridylyl-(5'-->3')-[5']uridylate (pUpU3-). Chemistry 2006; 11:4163-70. [PMID: 15861476 DOI: 10.1002/chem.200500013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is well known that Mg2+ and other divalent metal ions bind to the phosphate groups of nucleic acids. Subtle differences in the coordination properties of these metal ions to RNA, especially to ribozymes, determine whether they either promote or inhibit catalytic activity. The ability of metal ions to coordinate simultaneously with two neighboring phosphate groups is important for ribozyme structure and activity. However, such an interaction has not yet been quantified. Here, we have performed potentiometric pH titrations to determine the acidity constants of the protonated dinucleotide H2(pUpU)-, as well as the binding properties of pUpU3- towards Mg2+, Mn2+, Cd2+, Zn2+, and Pb2+. Whereas Mg2+, Mn2+, and Cd2+ only bind to the more basic 5'-terminal phosphate group, Pb2+, and to a certain extent also Zn2+, show a remarkably enhanced stability of the [M(pUpU)]- complex. This can be attributed to the formation of a macrochelate by bridging the two phosphate groups within this dinucleotide by these metal ions. Such a macrochelate is also possible in an oligonucleotide, because the basic structural units are the same, despite the difference in charge. The formation degrees of the macrochelated species of [Zn(pUpU)]- and [Pb(pUpU)]- amount to around 25 and 90 %, respectively. These findings are important in the context of ribozyme and DNAzyme catalysis, and explain, for example, why the leadzyme could be selected in the first place, and why this artificial ribozyme is inhibited by other divalent metal ions, such as Mg2+.
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Affiliation(s)
- Bernd Knobloch
- Institute of Inorganic Chemistry, University of Zürich, Switzerland
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48
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Anderson PC, Mecozzi S. Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity. Nucleic Acids Res 2005; 33:6992-9. [PMID: 16377778 PMCID: PMC1322272 DOI: 10.1093/nar/gki992] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aptamers are nucleic acids developed by in vitro evolution techniques that bind to specific ligands with high affinity and selectivity. Despite such high affinity and selectivity, however, in vitro evolution does not necessarily reveal the minimum structure of the nucleic acid required for selective ligand binding. Here, we show that a 35mer RNA aptamer for the cofactor flavin mononucleotide (FMN) identified by in vitro evolution can be computationally evolved to a mere 14mer structure containing the original binding pocket and eight scaffolding nucleotides while maintaining its ability to bind in vitro selectively to FMN. Using experimental and computational methodologies, we found that the 14mer binds with higher affinity to FMN (KD ∼ 4 µM) than to flavin adenine dinucleotide (KD ∼ 12 µM) or to riboflavin (KD ∼ 13 µM),despite the negative charge of FMN. Different hydrogen-bond strengths resulting from differing ring-system electron densities associated with the aliphatic-chain charges appear to contribute to the selectivity observed for the binding of the 14mer to FMN and riboflavin. Our results suggest that high affinity and selectivity in ligand binding is not restricted to large RNAs, but can also be a property of extraordinarily short RNAs.
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Affiliation(s)
- Peter C. Anderson
- School of Pharmacy, University of Wisconsin777 Highland Avenue, Madison, WI 53705, USA
| | - Sandro Mecozzi
- School of Pharmacy, University of Wisconsin777 Highland Avenue, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin777 Highland Avenue, Madison, WI 53705, USA
- To whom correspondence should be addressed. Tel: +1 608 262 7810; Fax: +1 608 262 5345;
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Levy M, Griswold KE, Ellington AD. Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization. RNA (NEW YORK, N.Y.) 2005; 11:1555-62. [PMID: 16131588 PMCID: PMC1370839 DOI: 10.1261/rna.2121705] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We have used a compartmentalized in vitro selection method to directly select for ligase ribozymes that are capable of acting on and turning over separable oligonucleotide substrates. Starting from a degenerate pool, we selected a trans-acting variant of the Bartel class I ligase which statistically may have been the only active variant in the starting pool. The isolation of this sequence from the population suggests that this selection method is extremely robust at selecting optimal ribozymes and should, therefore, prove useful for the selection and optimization of other trans-acting nucleic acid catalysts capable of multiple turnover catalysis.
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Affiliation(s)
- Matthew Levy
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78751, USA
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50
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Fauzi H, Jack KD, Hines JV. In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding. Nucleic Acids Res 2005; 33:2595-602. [PMID: 15879350 PMCID: PMC1090546 DOI: 10.1093/nar/gki546] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with four bases in a 7 nt bulge of the antiterminator RNA. In vitro selection of randomized tRNA binding to Bacillus subtilis tyrS antiterminator model RNAs was used to determine what, if any, sequence trends there are for binding beyond the known base pair complementarity. The model antiterminator RNAs were selected for the wild-type tertiary fold of tRNA. While there were no obvious sequence correlations between the selected tRNAs, there were correlations between certain tertiary structural elements and binding efficiency to different antiterminator model RNAs. In addition, one antiterminator model selected primarily for a kissing tRNA T loop-antiterminator bulge interaction, while another antiterminator model resulted in no such selection. The selection results indicate that, at the level of tertiary structure, there are ideal matches between tRNAs and antiterminator model RNAs consistent with in vivo observations and that additional recognition features, beyond base pair complementarity, may play a role in the formation of the complex.
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Affiliation(s)
| | | | - Jennifer V. Hines
- To whom correspondence should be addressed. Tel: +1 740 517 8482; Fax: +1 740 593 0148;
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