1
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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2
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Saon MS, Kirkpatrick CC, Znosko BM. Identification and characterization of RNA pentaloop sequence families. NAR Genom Bioinform 2023; 5:lqac102. [PMID: 36632613 PMCID: PMC9830547 DOI: 10.1093/nargab/lqac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/28/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
One of the current methods for predicting RNA tertiary structure is fragment-based homology, which predicts tertiary structure from secondary structure. For a successful prediction, this method requires a library of the tertiary structures of small motifs clipped from previously solved RNA 3D structures. Because of the limited number of available tertiary structures, it is not practical to find structures for all sequences of all motifs. Identifying sequence families for motifs can fill the gaps because all sequences within a family are expected to have similar structural features. Currently, a collection of well-characterized sequence families has been identified for tetraloops. Because of their prevalence and biological functions, pentaloop structures should also be well-characterized. In this study, 10 pentaloop sequence families are identified. For each family, the common and distinguishing structural features are highlighted. These sequence families can be used to predict the tertiary structure of pentaloop sequences for which a solved structure is not available.
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Affiliation(s)
- Md Sharear Saon
- Department of Chemistry, Saint Louis University, Saint Louis, MO 63103, USA
| | | | - Brent M Znosko
- To whom correspondence should be addressed. Tel: +1 314 977 8567; Fax: +1 314 977 2521;
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3
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Lu Q, Hu Y, Yin Li C, Kuang Y. Aptamer‐Array‐Guided Protein Assembly Enhances Synthetic mRNA Switch Performance. Angew Chem Int Ed Engl 2022; 61:e202207319. [PMID: 35703374 PMCID: PMC9544043 DOI: 10.1002/anie.202207319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 11/17/2022]
Abstract
Synthetic messenger RNA (mRNA) switches are powerful synthetic biological tools that can sense cellular molecules to manipulate cell fate. However, their performances are limited by high output signal noise due to leaky output protein expression. Here, we designed a readout control module that disables protein leakage from generating signal. Aptamer array on the switch guides the inactive output protein to self‐assemble into functional assemblies that generate output signal. Leaky protein expression fails to saturate the array, thus produces marginal signal. In this study, we demonstrated that switches with this module exhibit substantially lower signal noise and, consequently, higher input sensitivity and wider output range. Such switches are applicable for different types of input molecules and output proteins. The work here demonstrates a new type of spatially guided protein self‐assembly, affording novel synthetic mRNA switches that promise accurate cell manipulation for biomedical applications.
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Affiliation(s)
- Qiuyu Lu
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Yaxin Hu
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Yi Kuang
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
- HKUST Shenzhen Research Institute Shenzhen Guangdong China
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4
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Lu Q, Hu Y, Li CY, Kuang Y. Aptamer‐Array‐Guided Protein Assembly Enhances Synthetic mRNA Switch Performance. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Qiuyu Lu
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Yaxin Hu
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Cheuk Yin Li
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Yi Kuang
- Hong Kong University of Science and Technology Chemical and Biological Engineering Room 5578, Academic Bldg,Clear Water Bay 000000 Kowloon HONG KONG
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5
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Huang Z, Niu L. RNA aptamers for AMPA receptors. Neuropharmacology 2021; 199:108761. [PMID: 34509496 DOI: 10.1016/j.neuropharm.2021.108761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/07/2021] [Accepted: 08/19/2021] [Indexed: 12/16/2022]
Abstract
RNA aptamers are single-stranded RNA molecules, and they are selected against a target of interest so that they can bind to and modulate the activity of the target, such as inhibiting the target activity, with high potency and selectivity. Antagonists, such as RNA aptamers, acting on AMPA receptors, a major subtype of ionotropic glutamate receptors, are potential drug candidates for treatment of a number of CNS diseases that involve excessive receptor activation and/or elevated receptor expression. Here we review the approach to discover RNA aptamers targeting AMPA receptors from a random sequence library (∼1014 sequences) through a process called systematic evolution of ligands by exponential enrichment (SELEX). As compared with small-molecule compounds, RNA aptamers are a new class of regulatory agents with interesting and desirable pharmacological properties. Some AMPA receptor aptamers we have developed are presented in this review. The promises and challenges of translating RNA aptamers into potential drugs and treatment options are also discussed. This article is part of the special Issue on 'Glutamate Receptors - AMPA receptors'.
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Affiliation(s)
- Zhen Huang
- Chemistry Department, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY, USA
| | - Li Niu
- Chemistry Department, Center for Neuroscience Research, University at Albany, State University of New York (SUNY), Albany, NY, USA.
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6
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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7
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Demchuk AM, Patel TR. The biomedical and bioengineering potential of protein nanocompartments. Biotechnol Adv 2020; 41:107547. [PMID: 32294494 DOI: 10.1016/j.biotechadv.2020.107547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Protein nanocompartments (PNCs) are self-assembling biological nanocages that can be harnessed as platforms for a wide range of nanobiotechnology applications. The most widely studied examples of PNCs include virus-like particles, bacterial microcompartments, encapsulin nanocompartments, enzyme-derived nanocages (such as lumazine synthase and the E2 component of the pyruvate dehydrogenase complex), ferritins and ferritin homologues, small heat shock proteins, and vault ribonucleoproteins. Structural PNC shell proteins are stable, biocompatible, and tolerant of both interior and exterior chemical or genetic functionalization for use as vaccines, therapeutic delivery vehicles, medical imaging aids, bioreactors, biological control agents, emulsion stabilizers, or scaffolds for biomimetic materials synthesis. This review provides an overview of the recent biomedical and bioengineering advances achieved with PNCs with a particular focus on recombinant PNC derivatives.
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Affiliation(s)
- Aubrey M Demchuk
- Department of Neuroscience, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming, School of Medicine, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada; Li Ka Shing Institute of Virology and Discovery Lab, Faculty of Medicine & Dentistry, University of Alberta, 6-010 Katz Center for Health Research, Edmonton, AB T6G 2E1, Canada.
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Richardson KE, Adams MS, Kirkpatrick CC, Gohara DW, Znosko BM. Identification and Characterization of New RNA Tetraloop Sequence Families. Biochemistry 2019; 58:4809-4820. [PMID: 31714066 DOI: 10.1021/acs.biochem.9b00535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There is an abundance of RNA sequence information available due to the efforts of sequencing projects. However, current techniques implemented to solve the tertiary structures of RNA, such as NMR and X-ray crystallography, are difficult and time-consuming. Therefore, biophysical techniques are not able to keep pace with the abundance of sequence information available. Because of this, there is a need to develop quick and efficient ways to predict RNA tertiary structure from sequence. One promising approach is to identify structural patterns within previously solved 3D structures and apply these patterns to new sequences. RNA tetraloops are one of the most common naturally occurring secondary structure motifs. Here, we use RNA Characterization of Secondary Structure Motifs (CoSSMos), Dissecting the Spatial Structure of RNA (DSSR), and a bioinformatic approach to search for and characterize tertiary structure patterns among tetraloops. Not surprising, we identified the well-known GNRA and UNCG tetraloops, as well as the previously identified RNYA tetraloop. However, some previously identified characteristics of these families were not observed in this data set, and some new characteristics were identified. In addition, we also identified and characterized three new tetraloop sequence families: YGAR, UGGU, and RMSA. This new structural information sheds light on the tertiary structure of tetraloops and contributes to the efforts of RNA tertiary structure prediction from sequence.
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Affiliation(s)
- Katherine E Richardson
- Department of Chemistry , Saint Louis University , Saint Louis , Missouri 63103 , United States
| | - Miranda S Adams
- Department of Chemistry , Saint Louis University , Saint Louis , Missouri 63103 , United States
| | - Charles C Kirkpatrick
- Department of Chemistry , Saint Louis University , Saint Louis , Missouri 63103 , United States
| | - David W Gohara
- Department of Biochemistry and Molecular Biology , Saint Louis University , Saint Louis , Missouri 63103 , United States
| | - Brent M Znosko
- Department of Chemistry , Saint Louis University , Saint Louis , Missouri 63103 , United States
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9
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O’Leary CA, Andrews RJ, Tompkins VS, Chen JL, Childs-Disney JL, Disney MD, Moss WN. RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression. PLoS One 2019; 14:e0213758. [PMID: 31206539 PMCID: PMC6576772 DOI: 10.1371/journal.pone.0213758] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022] Open
Abstract
The MYC gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting MYC expression, we analyzed secondary structures in the MYC mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished by calculating folding metrics across the MYC sequence using a sliding analysis window and generating unique consensus base pairing models weighted by their lower-than-random predicted folding energy. A series of 30 motifs were identified, primarily in the 5' and 3' untranslated regions, which show evidence of structural conservation and compensating mutations across vertebrate MYC homologs. This analysis was able to recapitulate known elements found within an internal ribosomal entry site, as well as discover a novel element in the 3' UTR that is unusually stable and conserved. This novel motif was shown to affect MYC expression, potentially via the modulation of miRNA target accessibility or other trans-regulatory factors. In addition to providing basic insights into mechanisms that regulate MYC expression, this study provides numerous, potentially druggable RNA targets for the MYC gene, which is considered “undruggable” at the protein level.
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Affiliation(s)
- Collin A. O’Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Van S. Tompkins
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States of America
| | | | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
- * E-mail:
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10
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Lin TX, Lai PX, Mao JY, Chu HW, Unnikrishnan B, Anand A, Huang CC. Supramolecular Aptamers on Graphene Oxide for Efficient Inhibition of Thrombin Activity. Front Chem 2019; 7:280. [PMID: 31157200 PMCID: PMC6532589 DOI: 10.3389/fchem.2019.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/05/2019] [Indexed: 01/08/2023] Open
Abstract
Graphene oxide (GO), a two-dimensional material with a high aspect ratio and polar functional groups, can physically adsorb single-strand DNA through different types of interactions, such as hydrogen bonding and π-π stacking, making it an attractive nanocarrier for nucleic acids. In this work, we demonstrate a strategy to target exosites I and II of thrombin simultaneously by using programmed hybrid-aptamers for enhanced anticoagulation efficiency and stability. The targeting ligand is denoted as Supra-TBA15/29 (supramolecular TBA15/29), containing TBA15 (a 15-base nucleotide, targeting exosite I of thrombin) and TBA29 (a 29-base nucleotide, targeting exosite II of thrombin), and it is designed to allow consecutive hybridization of TBA15 and TBA29 to form a network of TBAs (i.e., supra-TBA15/29). The programmed hybrid-aptamers (Supra-TBA15/29) were self-assembled on GO to further boost anticoagulation activity by inhibiting thrombin activity, and thus suppress the thrombin-induced fibrin formation from fibrinogen. The Supra-TBA15/29-GO composite was formed mainly through multivalent interaction between poly(adenine) from Supra-TBA15/29 and GO. We controlled the assembly of Supra-TBA15/29 on GO by regulating the preparation temperature and the concentration ratio of Supra-TBA15/29 to GO to optimize the distance between TBA15 and TBA29 units, aptamer density, and aptamer orientation on the GO surfaces. The dose-dependent thrombin clotting time (TCT) delay caused by Supra-TBA15/29-GO was >10 times longer than that of common anticoagulant drugs including heparin, argatroban, hirudin, and warfarin. Supra-TBA15/29-GO exhibits high biocompatibility, which has been proved by in vitro cytotoxicity and hemolysis assays. In addition, the thromboelastography of whole-blood coagulation and rat-tail bleeding assays indicate the anticoagulation ability of Supra-TBA15/29-GO is superior to the most widely used anticoagulant (heparin). Our highly biocompatible Supra-TBA15/29-GO with strong multivalent interaction with thrombin [dissociation constant (K d) = 1.9 × 10-11 M] shows great potential as an effective direct thrombin inhibitor for the treatment of hemostatic disorders.
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Affiliation(s)
- Ting-Xuan Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Pei-Xin Lai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ju-Yi Mao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Han-Wei Chu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Binesh Unnikrishnan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Anisha Anand
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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11
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Twarock R, Stockley PG. RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy. Annu Rev Biophys 2019; 48:495-514. [PMID: 30951648 PMCID: PMC7612295 DOI: 10.1146/annurev-biophys-052118-115611] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses, entities composed of nucleic acids, proteins, and in some cases lipids lack the ability to replicate outside their target cells. Their components self-assemble at the nanoscale with exquisite precision-a key to their biological success in infection. Recent advances in structure determination and the development of biophysical tools such as single-molecule spectroscopy and noncovalent mass spectrometry allow unprecedented access to the detailed assembly mechanisms of simple virions. Coupling these techniques with mathematical modeling and bioinformatics has uncovered a previously unsuspected role for genomic RNA in regulating formation of viral capsids, revealing multiple, dispersed RNA sequence/structure motifs [packaging signals (PSs)] that bind cognate coat proteins cooperatively. The PS ensemble controls assembly efficiency and accounts for the packaging specificity seen in vivo. The precise modes of action of the PSs vary between viral families, but this common principle applies across many viral families, including major human pathogens. These insights open up the opportunity to block or repurpose PS function in assembly for both novel antiviral therapy and gene/drug/vaccine applications.
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Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology, and York Cross-disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, United Kingdom;
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
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12
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Tapp MJN, Slocik JM, Dennis PB, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Identify DNA Aptamers. ACS COMBINATORIAL SCIENCE 2018; 20:585-593. [PMID: 30189130 DOI: 10.1021/acscombsci.8b00048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Competition-enhanced ligand screening (CompELS) was employed to rapidly screen through large DNA libraries to identify single-stranded, oligonucleotide-based ligands called aptamers that bind to a nonbiological target. This previously unreported aptamer screening approach involves the repeated introduction of unenriched random sequence populations during the biopanning process, but avoids iterative elution and polymerase chain reaction (PCR) amplification steps inherent to traditional SELEX (systematic evolution of ligands by exponential enrichment) screening. In this study, 25 aptamers were identified against a gold surface via CompELS and evaluated to identify patterns in primary structures and predicted secondary structures. Following a final one-round competition experiment with the 25 identified aptamers, one particular aptamer sequence (1N) emerged as the most competitive adsorbate species for the gold substrate. Binding analysis indicated at least an order of magnitude difference in the binding affinity of 1N ( Kd = 5.6 × 10-10 M) compared to five other high affinity aptamer candidates ( Kd = 10-8-10-9 M) from identical secondary structure families. Collectively, these studies introduce a rapid, reliable screening and ranking platform along with a classification scheme well-suited for identifying and characterizing aptamers for nonbiological as well as biological targets.
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Affiliation(s)
| | - Joseph M. Slocik
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Patrick B. Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R. Naik
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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13
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Valencia-Reséndiz DG, Palomino-Vizcaino G, Tapia-Vieyra JV, Benítez-Hess ML, Leija-Montoya AG, Alvarez-Salas LM. Inhibition of Human Papillomavirus Type 16 Infection Using an RNA Aptamer. Nucleic Acid Ther 2018; 28:97-105. [PMID: 29437522 DOI: 10.1089/nat.2017.0687] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Human papillomavirus type 16 (HPV16) DNA has been found in ∼50% of cervical tumors worldwide. HPV infection starts with the binding of the virus capsid to heparan sulfate (HS) receptors exposed on the surface of epithelial basal layer keratinocytes. Previously, our group isolated a high-affinity RNA aptamer (Sc5c3) specific for HPV16 L1 virus-like particles (VLPs). In this study, we report the inhibition of HPV16 infection by Sc5c3 in a pseudovirus (PsVs) model. 293TT cells were infected by HPV16 PsVs containing the yellow fluorescent protein (YFP) as reporter gene. Incubation of HPV16 PsVs with Sc5c3 before infection resulted in a dose-dependent decrease in YFP fluorescence, suggesting infection inhibition. Aptamer degradation by RNase A restored PsVs infectivity, supporting the previous observation that Sc5c3 aptamer can inhibit infection. VLP mutants with removed HS binding sites were used in binding assays to elucidate the Sc5c3 blocking mechanism; however, no binding difference was observed between wild-type and mutant VLPs, suggesting that pseudoinfection inhibition relies on mechanisms additional to electrostatic HS binding site interaction. A DNA/RNA Sc5c3 version also inhibited HPV PsVs infection, suggesting that a modified, nuclease-resistant Sc5c3 may be used to inhibit HPV16 infection in vivo.
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Affiliation(s)
- Diana Gabriela Valencia-Reséndiz
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Giovanni Palomino-Vizcaino
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Juana Virginia Tapia-Vieyra
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - María Luisa Benítez-Hess
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Ana Gabriela Leija-Montoya
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Luis Marat Alvarez-Salas
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
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14
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Mapping the Universe of RNA Tetraloop Folds. Biophys J 2017; 113:257-267. [PMID: 28673616 DOI: 10.1016/j.bpj.2017.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 11/22/2022] Open
Abstract
We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.
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15
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Poudel L, Twarock R, Steinmetz NF, Podgornik R, Ching WY. Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA. J Phys Chem B 2017; 121:6321-6330. [PMID: 28581757 DOI: 10.1021/acs.jpcb.7b02569] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MS2 presents a well-studied example of a single-stranded RNA virus for which the genomic RNA plays a pivotal role in the virus assembly process based on the packaging signal-mediated mechanism. Packaging signals (PSs) are multiple dispersed RNA sequence/structure motifs varying around a central recognition motif that interact in a specific way with the capsid protein in the assembly process. Although the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimental protocols, we approach this problem using large-scale ab initio computation centered on critical aspects of the consensus protein-RNA interactions recognition motif. DFT calculations are carried out on two nucleoprotein complexes: wild-type and mutated (PDB IDs: 1ZDH and 5MSF ). The calculated partial charge distribution of residues and the strength of hydrogen bonding (HB) between them enabled us to locate the exact binding sites with the strongest HBs, identified to be LYS43-A-4, ARG49-C-13, TYR85-C-5, and LYS61-C-5, due to the change in the sequence of the mutated RNA.
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Affiliation(s)
- Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City , Kansas City, Missouri 64110, United States
| | - Reidun Twarock
- Department of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York , York YO10 5DD, United Kingdom
| | | | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute , SI-1000 Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana , SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City , Kansas City, Missouri 64110, United States
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16
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In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus. Nature 2016; 541:112-116. [PMID: 27992877 PMCID: PMC5701785 DOI: 10.1038/nature20589] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/26/2016] [Indexed: 12/11/2022]
Abstract
Genome packaging into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike dsDNA viruses which pump their genome into a preformed capsid1-3, ssRNA viruses, such as bacteriophage MS2, co-assemble their capsid with genome4-7; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via host “sex” pilus (F-pilus)8 and is the first fully-sequenced organism9 and a model system for studies of gene translational regulations10,11, RNA-protein interactions12-14, and RNA virus assembly15-17. Its positive-sense ssRNA genome of 3569 bases is enclosed in a capsid with one maturation protein (MP) monomer and 89 coat protein (CP) dimers arranged in a T=3 icosahedral lattice18,19. MP is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection8, but how the genome is organized and delivered are not known. Here we show the MS2 structure at 3.6Å resolution determined by electron-counting cryo electron microscopy (cryoEM) and asymmetric reconstruction. We traced ~80% backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-CP interactions among 15 of these stem-loops with diverse sequences. The stem-loop at 3’ end of the genome interacts extensively with the MP, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus, and joins 89 CP-dimers to form a capsid. This first atomic description of genome-capsid interactions in a spherical ssRNA virus provides insights into genome delivery via host “sex” pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires imaginations about links between nucleoprotein complexes and the origin of viruses.
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17
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Pumpens P, Renhofa R, Dishlers A, Kozlovska T, Ose V, Pushko P, Tars K, Grens E, Bachmann MF. The True Story and Advantages of RNA Phage Capsids as Nanotools. Intervirology 2016; 59:74-110. [DOI: 10.1159/000449503] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
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18
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Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, Lybrand TP, Frydman C, Monteiro RQ, Gomer RH, Nawrot B, Yang X. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res 2016; 44:8052-64. [PMID: 27566147 PMCID: PMC5041495 DOI: 10.1093/nar/gkw725] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/12/2022] Open
Abstract
RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.
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Affiliation(s)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Karen Mercier
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Jonas Nascimento Conde
- Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Daniella M Mizurini
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Fatima-Ezzahra Hibti
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Tom Hassell
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Feng-Wu Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Carlos Martinez
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Anil K Sood
- Departments of Gynecologic Oncology and Cancer Biology, and Center for RNAi and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Terry P Lybrand
- Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Chiraz Frydman
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Robson Q Monteiro
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
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19
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Koning RI, Gomez-Blanco J, Akopjana I, Vargas J, Kazaks A, Tars K, Carazo JM, Koster AJ. Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ. Nat Commun 2016; 7:12524. [PMID: 27561669 PMCID: PMC5007439 DOI: 10.1038/ncomms12524] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/11/2016] [Indexed: 01/22/2023] Open
Abstract
In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes. Using cryo-electron microscopy and single particle analysis we determined the asymmetric virion structure of bacteriophage MS2, which includes 178 copies of the coat protein, a single copy of the A-protein and the RNA genome. This reveals that in situ, the viral RNA genome can adopt a defined conformation. The RNA forms a branched network of stem-loops that almost all allocate near the capsid inner surface, while predominantly binding to coat protein dimers that are located in one-half of the capsid. This suggests that genomic RNA is highly involved in genome packaging and virion assembly. MS2 is a single-stranded RNA bacteriophage that infects its host via adsorption to bacterial pili. Here the authors visualize the MS2 virion with asymmetric cryo-EM reconstruction, revealing that the genome of MS2 adopts a specific structure of asymmetrically distributed stem-loops connected to the capsid.
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Affiliation(s)
- Roman I Koning
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.,Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Josue Gomez-Blanco
- Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, Madrid 28049, Spain
| | - Inara Akopjana
- Biomedical Research and Study Centre, Ratsupites 1, LV-1067 Riga, Latvia
| | - Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, Madrid 28049, Spain
| | - Andris Kazaks
- Biomedical Research and Study Centre, Ratsupites 1, LV-1067 Riga, Latvia
| | - Kaspars Tars
- Biomedical Research and Study Centre, Ratsupites 1, LV-1067 Riga, Latvia
| | - José María Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, Madrid 28049, Spain
| | - Abraham J Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.,Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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20
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Bjerregaard N, Andreasen PA, Dupont DM. Expected and unexpected features of protein-binding RNA aptamers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:744-757. [PMID: 27173731 DOI: 10.1002/wrna.1360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022]
Abstract
RNA molecules with high affinity to specific proteins can be isolated from libraries of up to 1016 different RNA sequences by systematic evolution of ligands by exponential enrichment (SELEX). These so-called protein-binding RNA aptamers are often interesting, e.g., as modulators of protein function for therapeutic use, for probing the conformations of proteins, for studies of basic aspects of nucleic acid-protein interactions, etc. Studies on the interactions between RNA aptamers and proteins display a number of expected and unexpected features, including the chemical nature of the interacting RNA-protein surfaces, the conformation of protein-bound aptamer versus free aptamer, the conformation of aptamer-bound protein versus free protein, and the effects of aptamers on protein function. Here, we review current insights into the details of RNA aptamer-protein interactions. WIREs RNA 2016, 7:744-757. doi: 10.1002/wrna.1360 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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21
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Gelinas AD, Davies DR, Janjic N. Embracing proteins: structural themes in aptamer-protein complexes. Curr Opin Struct Biol 2016; 36:122-32. [PMID: 26919170 DOI: 10.1016/j.sbi.2016.01.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 01/17/2023]
Abstract
Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity.
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Affiliation(s)
- Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States
| | - Douglas R Davies
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States.
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22
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016; 428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
Abstract
Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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Affiliation(s)
- Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefani Middleton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Robert Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric Dykeman
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - James Ford
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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23
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Stockley PG, White SJ, Dykeman E, Manfield I, Rolfsson O, Patel N, Bingham R, Barker A, Wroblewski E, Chandler-Bostock R, Weiß EU, Ranson NA, Tuma R, Twarock R. Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid. BACTERIOPHAGE 2016; 6:e1157666. [PMID: 27144089 PMCID: PMC4836477 DOI: 10.1080/21597081.2016.1157666] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Using RNA-coat protein crosslinking we have shown that the principal RNA recognition surface on the interior of infectious MS2 virions overlaps with the known peptides that bind the high affinity translational operator, TR, within the phage genome. The data also reveal the sequences of genomic fragments in contact with the coat protein shell. These show remarkable overlap with previous predictions based on the hypothesis that virion assembly is mediated by multiple sequences-specific contacts at RNA sites termed Packaging Signals (PSs). These PSs are variations on the TR stem-loop sequence and secondary structure. They act co-operatively to regulate the dominant assembly pathway and ensure cognate RNA encapsidation. In MS2, they also trigger conformational change in the dimeric capsomere creating the A/B quasi-conformer, 60 of which are needed to complete the T=3 capsid. This is the most compelling demonstration to date that this ssRNA virus, and by implications potentially very many of them, assemble via a PS-mediated assembly mechanism.
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Affiliation(s)
- Peter G. Stockley
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Simon J. White
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Eric Dykeman
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Iain Manfield
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, University of Iceland Biomedical Center, Reykjavik, Iceland
| | - Nikesh Patel
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Richard Bingham
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Amy Barker
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Emma Wroblewski
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | - Eva U. Weiß
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Neil A. Ranson
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Roman Tuma
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Reidun Twarock
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
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24
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Kopra K, Syrjänpää M, Hänninen P, Härmä H. Non-competitive aptamer-based quenching resonance energy transfer assay for homogeneous growth factor quantification. Analyst 2015; 139:2016-23. [PMID: 24611155 DOI: 10.1039/c3an01814h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A non-competitive homogeneous, single-label quenching resonance energy transfer (QRET) assay for protein quantification is now presented using lanthanide-chelate labeled nucleic acid aptamers. A labeled ssDNA aptamer binding to a growth factor has been successfully used to provide luminescence signal protection of the lanthanide label. The QRET technology has previously been applied to competitive assay formats, but now for the first time a direct non-competitive assay is presented. The QRET system is based on the protection of the Eu(iii)-chelate from a soluble quencher molecule when the aptamer interacts with a specific target protein. The direct QRET assay is possible as the aptamer structure itself cannot protect the Eu(iii)-label from quenching. The dynamic range for the optimized vascular endothelial growth factor (VEGF) assay is 0.25-10 nM. A successful quantification of the basic fibroblast growth factor (bFGF) is also demonstrated using the same QRET assay format with a dynamic range of 0.75-50 nM. These assays evidently show the suitability of the direct QRET technique to simple and efficient detection of large biomolecules. The QRET assay can potentially be applied as a detection platform for any other protein targets with a known aptamer sequence.
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Affiliation(s)
- Kari Kopra
- Laboratory of Biophysics, Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Tykistökatu 6 A 5th floor, FI-20520 Turku, Finland.
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25
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A novel method to produce armored double-stranded DNA by encapsulation of MS2 viral capsids. Appl Microbiol Biotechnol 2015; 99:7047-57. [PMID: 25981999 PMCID: PMC7079959 DOI: 10.1007/s00253-015-6664-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/21/2015] [Accepted: 05/01/2015] [Indexed: 02/08/2023]
Abstract
With the rapid development of molecular diagnostic techniques, there is a growing need for quality controls and standards with favorable properties to monitor the entire detection process. In this study, we describe a novel method to produce armored hepatitis B virus (HBV) and human papillomavirus (HPV) DNA for use in nucleic acid tests, which was confirmed to be stable, homogeneous, noninfectious, nuclease resistant, and safe for shipping. We demonstrated that MS2 bacteriophage could successfully package double-stranded DNA of 1.3-, 3-, 3.5-, and 6.5-kb length into viral capsids with high reassembly efficiency. This is the first application of RNA bacteriophage MS2 as a platform to encapsulate double-stranded DNA, forming virus-like particles (VLPs) which were indistinguishable from native MS2 capsids in size and morphology. Moreover, by analyzing the interaction mechanism of pac site and the MS2 coat protein (CP), we found that in addition to the recognized initiation signal TR-RNA, TR-DNA can also trigger spontaneous reassembly of CP dimers, providing a more convenient and feasible method of assembly. In conclusion, this straightforward and reliable manufacturing approach makes armored DNA an ideal control and standard for use in clinical laboratory tests and diagnostics, possessing prospects for broad application, especially providing a new platform for the production of quality controls for DNA viruses.
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26
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Cheng F, He Y, Xing XJ, Tan DD, Lin Y, Pang DW, Tang HW. A gold nanoparticle-based label free colorimetric aptasensor for adenosine deaminase detection and inhibition assay. Analyst 2015; 140:1572-7. [PMID: 25597304 DOI: 10.1039/c4an02070g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel strategy for the fabrication of a colorimetric aptasensor using label free gold nanoparticles (AuNPs) is proposed in this work, and the strategy has been employed for the assay of adenosine deaminase (ADA) activity. The aptasensor consists of adenosine (AD) aptamer, AD and AuNPs. The design of the biosensor takes advantage of the special optical properties of AuNPs and the interaction between AuNPs and single-strand DNA. In the absence of ADA, the AuNPs are aggregated and are blue in color under appropriate salt concentration because of the grid structure of an AD aptamer when binding to AD, while in the presence of the analyte, AuNPs remain dispersed with red color under the same concentration of salt owing to ADA converting AD into inosine which has no affinity with the AD aptamer, thus allowing quantitative investigation of ADA activity. The present strategy is simple, cost-effective, selective and sensitive for ADA with a detection limit of 1.526 U L(-1), which is about one order of magnitude lower than that previously reported. In addition, a very low concentration of the inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA) could generate a distinguishable response. Therefore, the AuNP-based colorimetric biosensor has great potential in the diagnosis of ADA-relevant diseases and drug screening.
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Affiliation(s)
- Fen Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, and Wuhan Institute of Biotechnology, Wuhan University, Wuhan, 430072, P. R. China.
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27
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Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
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Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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28
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Kennedy AB, Vowles JV, d'Espaux L, Smolke CD. Protein-responsive ribozyme switches in eukaryotic cells. Nucleic Acids Res 2014; 42:12306-21. [PMID: 25274734 PMCID: PMC4231745 DOI: 10.1093/nar/gku875] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic devices that directly detect and respond to intracellular concentrations of proteins are important synthetic biology tools, supporting the design of biological systems that target, respond to or alter specific cellular states. Here, we develop ribozyme-based devices that respond to protein ligands in two eukaryotic hosts, yeast and mammalian cells, to regulate the expression of a gene of interest. Our devices allow for both gene-ON and gene-OFF response upon sensing the protein ligand. As part of our design process, we describe an in vitro characterization pipeline for prescreening device designs to identify promising candidates for in vivo testing. The in vivo gene-regulatory activities in the two types of eukaryotic cells correlate with in vitro cleavage activities determined at different physiologically relevant magnesium concentrations. Finally, localization studies with the ligand demonstrate that ribozyme switches respond to ligands present in the nucleus and/or cytoplasm, providing new insight into their mechanism of action. By extending the sensing capabilities of this important class of gene-regulatory device, our work supports the implementation of ribozyme-based devices in applications requiring the detection of protein biomarkers.
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Affiliation(s)
- Andrew B Kennedy
- Department of Bioengineering, 443 Via Ortega, MC 4245 Stanford University, Stanford, CA 94305, USA
| | - James V Vowles
- Division of Chemistry and Chemical Engineering, 1200 E. California Boulevard, MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leo d'Espaux
- Division of Chemistry and Chemical Engineering, 1200 E. California Boulevard, MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina D Smolke
- Department of Bioengineering, 443 Via Ortega, MC 4245 Stanford University, Stanford, CA 94305, USA
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29
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A quantitative framework for the forward design of synthetic miRNA circuits. Nat Methods 2014; 11:1147-53. [PMID: 25218181 DOI: 10.1038/nmeth.3100] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/30/2014] [Indexed: 11/08/2022]
Abstract
Synthetic genetic circuits incorporating regulatory components based on RNA interference (RNAi) have been used in a variety of systems. A comprehensive understanding of the parameters that determine the relationship between microRNA (miRNA) and target expression levels is lacking. We describe a quantitative framework supporting the forward engineering of gene circuits that incorporate RNAi-based regulatory components in mammalian cells. We developed a model that captures the quantitative relationship between miRNA and target gene expression levels as a function of parameters, including mRNA half-life and miRNA target-site number. We extended the model to synthetic circuits that incorporate protein-responsive miRNA switches and designed an optimized miRNA-based protein concentration detector circuit that noninvasively measures small changes in the nuclear concentration of β-catenin owing to induction of the Wnt signaling pathway. Our results highlight the importance of methods for guiding the quantitative design of genetic circuits to achieve robust, reliable and predictable behaviors in mammalian cells.
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30
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Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP. Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis. Nucleic Acids Res 2014; 42:10795-808. [PMID: 25140011 PMCID: PMC4176348 DOI: 10.1093/nar/gku743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.
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Affiliation(s)
- Milya Davlieva
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - James Donarski
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Jiachen Wang
- Department of Physics, East China Normal University, 200062 Shanghai, P. R. China
| | - Yousif Shamoo
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - Edward P Nikonowicz
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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31
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Analysis of stacking overlap in nucleic acid structures: algorithm and application. J Comput Aided Mol Des 2014; 28:851-67. [DOI: 10.1007/s10822-014-9767-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
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32
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Crystal structure of the bacteriophage Qβ coat protein in complex with the RNA operator of the replicase gene. J Mol Biol 2013; 426:1039-49. [PMID: 24035813 DOI: 10.1016/j.jmb.2013.08.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/20/2022]
Abstract
The coat proteins of single-stranded RNA bacteriophages specifically recognize and bind to a hairpin structure in their genome at the beginning of the replicase gene. The interaction serves to repress the synthesis of the replicase enzyme late in infection and contributes to the specific encapsidation of phage RNA. While this mechanism is conserved throughout the Leviviridae family, the coat protein and operator sequences from different phages show remarkable variation, serving as prime examples for the co-evolution of protein and RNA structure. To better understand the protein-RNA interactions in this virus family, we have determined the three-dimensional structure of the coat protein from bacteriophage Qβ bound to its cognate translational operator. The RNA binding mode of Qβ coat protein shares several features with that of the widely studied phage MS2, but only one nucleotide base in the hairpin loop makes sequence-specific contacts with the protein. Unlike in other RNA phages, the Qβ coat protein does not utilize an adenine-recognition pocket for binding a bulged adenine base in the hairpin stem but instead uses a stacking interaction with a tyrosine side chain to accommodate the base. The extended loop between β strands E and F of Qβ coat protein makes contacts with the lower part of the RNA stem, explaining the greater length dependence of the RNA helix for optimal binding to the protein. Consequently, the complex structure allows the proposal of a mechanism by which the Qβ coat protein recognizes and discriminates in favor of its cognate RNA.
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33
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Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
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Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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34
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Chen Y, Varani G. Engineering RNA-binding proteins for biology. FEBS J 2013; 280:3734-54. [PMID: 23742071 DOI: 10.1111/febs.12375] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 12/20/2022]
Abstract
RNA-binding proteins play essential roles in the regulation of gene expression. Many have modular structures and combine relatively few common domains in various arrangements to recognize RNA sequences and/or structures. Recent progress in engineering the specificity of the PUF class RNA-binding proteins has shown that RNA-binding domains may be combined with various effector or functional domains to regulate the metabolism of targeted RNAs. Designer RNA-binding proteins with tailored sequence specificity will provide valuable tools for biochemical research as well as potential therapeutic applications. In this review, we discuss the suitability of various RNA-binding domains for engineering RNA-binding specificity, based on the structural basis for their recognition. We also compare various protein engineering and design methods applied to RNA-binding proteins, and discuss future applications of these proteins.
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Affiliation(s)
- Yu Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195-1700, USA.
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35
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Dykeman EC, Stockley PG, Twarock R. Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome. J Mol Biol 2013; 425:3235-49. [PMID: 23763992 DOI: 10.1016/j.jmb.2013.06.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 11/29/2022]
Abstract
The current paradigm for assembly of single-stranded RNA viruses is based on a mechanism involving non-sequence-specific packaging of genomic RNA driven by electrostatic interactions. Recent experiments, however, provide compelling evidence for sequence specificity in this process both in vitro and in vivo. The existence of multiple RNA packaging signals (PSs) within viral genomes has been proposed, which facilitates assembly by binding coat proteins in such a way that they promote the protein-protein contacts needed to build the capsid. The binding energy from these interactions enables the confinement or compaction of the genomic RNAs. Identifying the nature of such PSs is crucial for a full understanding of assembly, which is an as yet untapped potential drug target for this important class of pathogens. Here, for two related bacterial viruses, we determine the sequences and locations of their PSs using Hamiltonian paths, a concept from graph theory, in combination with bioinformatics and structural studies. Their PSs have a common secondary structure motif but distinct consensus sequences and positions within the respective genomes. Despite these differences, the distributions of PSs in both viruses imply defined conformations for the packaged RNA genomes in contact with the protein shell in the capsid, consistent with a recent asymmetric structure determination of the MS2 virion. The PS distributions identified moreover imply a preferred, evolutionarily conserved assembly pathway with respect to the RNA sequence with potentially profound implications for other single-stranded RNA viruses known to have RNA PSs, including many animal and human pathogens.
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Affiliation(s)
- Eric C Dykeman
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, UK
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36
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Stockley PG, Ranson NA, Twarock R. A new paradigm for the roles of the genome in ssRNA viruses. Future Virol 2013. [DOI: 10.2217/fvl.12.84] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recent work with RNA phages and an ssRNA plant satellite virus challenges the widely held view that the sequences and structures of genomic RNAs are unimportant for virion assembly. In the T=3 phages, RNA–coat protein interactions occur throughout the genome, defining the quasiconformers of their protein shells. In the plant virus, there are multiple packaging signals dispersed throughout the genome that overcome electrostatic barriers to protein self-assembly. Both viral coat proteins cause the solution structures of their cognate genomes to collapse into a form that is readily encapsidated in a two-stage assembly process. Such similar behavior in two structurally unrelated viral protein folds implies that this might be a conserved feature of many viral assembly reactions. These results suggest a highly defined structure for the RNA in the virions, consistent with recent structural studies. They also have implications both for subsequent genome release during infection and for the evolution of viral sequences.
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Affiliation(s)
- Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Reidun Twarock
- Departments of Biology & Mathematics, York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
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37
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Stockley PG, Twarock R, Bakker SE, Barker AM, Borodavka A, Dykeman E, Ford RJ, Pearson AR, Phillips SEV, Ranson NA, Tuma R. Packaging signals in single-stranded RNA viruses: nature's alternative to a purely electrostatic assembly mechanism. J Biol Phys 2013; 39:277-87. [PMID: 23704797 PMCID: PMC3662417 DOI: 10.1007/s10867-013-9313-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/11/2013] [Indexed: 11/29/2022] Open
Abstract
The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA–coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology.
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Affiliation(s)
- Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT UK
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38
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Persson M, Tars K, Liljas L. PRR1 coat protein binding to its RNA translational operator. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:367-72. [DOI: 10.1107/s0907444912047464] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/19/2012] [Indexed: 11/10/2022]
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39
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Ruigrok VJB, Levisson M, Hekelaar J, Smidt H, Dijkstra BW, van der Oost J. Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches. Int J Mol Sci 2012; 13:10537-10552. [PMID: 22949878 PMCID: PMC3431876 DOI: 10.3390/ijms130810537] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 12/11/2022] Open
Abstract
Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.
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Affiliation(s)
- Vincent J. B. Ruigrok
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Mark Levisson
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Johan Hekelaar
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands; E-Mails: (J.H.); (B.W.D.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands; E-Mails: (J.H.); (B.W.D.)
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
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40
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Bleckley S, Schroeder SJ. Incorporating global features of RNA motifs in predictions for an ensemble of secondary structures for encapsidated MS2 bacteriophage RNA. RNA (NEW YORK, N.Y.) 2012; 18:1309-1318. [PMID: 22645379 PMCID: PMC3383962 DOI: 10.1261/rna.032326.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 05/02/2012] [Indexed: 06/01/2023]
Abstract
The secondary structure of encapsidated MS2 genomic RNA poses an interesting RNA folding challenge. Cryoelectron microscopy has demonstrated that encapsidated MS2 RNA is well-ordered. Models of MS2 assembly suggest that the RNA hairpin-protein interactions and the appropriate placement of hairpins in the MS2 RNA secondary structure can guide the formation of the correct icosahedral particle. The RNA hairpin motif that is recognized by the MS2 capsid protein dimers, however, is energetically unfavorable, and thus free energy predictions are biased against this motif. Computer programs called Crumple, Sliding Windows, and Assembly provide useful tools for prediction of viral RNA secondary structures when the traditional assumptions of RNA structure prediction by free energy minimization may not apply. These methods allow incorporation of global features of the RNA fold and motifs that are difficult to include directly in minimum free energy predictions. For example, with MS2 RNA the experimental data from SELEX experiments, crystallography, and theoretical calculations of the path for the series of hairpins can be incorporated in the RNA structure prediction, and thus the influence of free energy considerations can be modulated. This approach thoroughly explores conformational space and generates an ensemble of secondary structures. The predictions from this new approach can test hypotheses and models of viral assembly and guide construction of complete three-dimensional models of virus particles.
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Affiliation(s)
- Samuel Bleckley
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Susan J. Schroeder
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
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41
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Bunka DHJ, Lane SW, Lane CL, Dykeman EC, Ford RJ, Barker AM, Twarock R, Phillips SEV, Stockley PG. Degenerate RNA packaging signals in the genome of Satellite Tobacco Necrosis Virus: implications for the assembly of a T=1 capsid. J Mol Biol 2011; 413:51-65. [PMID: 21839093 DOI: 10.1016/j.jmb.2011.07.063] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/20/2011] [Accepted: 07/26/2011] [Indexed: 11/26/2022]
Abstract
Using a recombinant, T=1 Satellite Tobacco Necrosis Virus (STNV)-like particle expressed in Escherichia coli, we have established conditions for in vitro disassembly and reassembly of the viral capsid. In vivo assembly is dependent on the presence of the coat protein (CP) N-terminal region, and in vitro assembly requires RNA. Using immobilised CP monomers under reassembly conditions with "free" CP subunits, we have prepared a range of partially assembled CP species for RNA aptamer selection. SELEX directed against the RNA-binding face of the STNV CP resulted in the isolation of several clones, one of which (B3) matches the STNV-1 genome in 16 out of 25 nucleotide positions, including across a statistically significant 10/10 stretch. This 10-base region folds into a stem-loop displaying the motif ACAA and has been shown to bind to STNV CP. Analysis of the other aptamer sequences reveals that the majority can be folded into stem-loops displaying versions of this motif. Using a sequence and secondary structure search motif to analyse the genomic sequence of STNV-1, we identified 30 stem-loops displaying the sequence motif AxxA. The implication is that there are many stem-loops in the genome carrying essential recognition features for binding STNV CP. Secondary structure predictions of the genomic RNA using Mfold showed that only 8 out of 30 of these stem-loops would be formed in the lowest-energy structure. These results are consistent with an assembly mechanism based on kinetically driven folding of the RNA.
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Affiliation(s)
- David H J Bunka
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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42
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Zhang K, Zhu X, Wang J, Xu L, Li G. Strategy to fabricate an electrochemical aptasensor: application to the assay of adenosine deaminase activity. Anal Chem 2010; 82:3207-11. [PMID: 20345118 DOI: 10.1021/ac902771k] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel strategy for the fabrication of electrochemical aptasensor is proposed in this work, and the strategy has been employed to develop an aptasensor for the assay of adenosine deaminase activity. While a well-designed oligonucleotide containing three functional regions (an adenosine aptamer region, a G-quadruplex halves region, and a linker region) is adopted in our strategy as the core element, the enzymatic reaction of adenosine catalyzed by adenosine deaminase plays a key role as well in the regulation of the binding of the G-quadruplex halves with hemin, the electroactive probe, which is to reflect the activity of the enzyme indirectly but accurately. The detection limit of the fabrication biosensor can be lowered to 0.2 U mL(-1) of adenosine deaminase, and 1 nM of the inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine hydrochloride is enough to present distinguishable electrochemical response. Moreover, since the electroactive probe is not required to be bound with the oligonucleotide, this strategy may integrate the advantages of both the labeled and label-free strategies.
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Affiliation(s)
- Kai Zhang
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
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43
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Abstract
Structural 3D motifs in RNA play an important role in the RNA stability and function. Previous studies have focused on the characterization and discovery of 3D motifs in RNA secondary and tertiary structures. However, statistical analyses of the distribution of 3D motifs along the RNA appear to be lacking. Herein, we present a novel strategy for evaluating the distribution of 3D motifs along the RNA chain and those motifs whose distributions are significantly non-random are identified. By applying it to the X-ray structure of the large ribosomal subunit from Haloarcula marismortui, helical motifs were found to cluster together along the chain and in the 3D structure, whereas the known tetraloops tend to be sequentially and spatially dispersed. That the distribution of key structural motifs such as tetraloops differ significantly from a random one suggests that our method could also be used to detect novel 3D motifs of any size in sufficiently long/large RNA structures. The motif distribution type can help in the prediction and design of 3D structures of large RNA molecules.
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Affiliation(s)
- Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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44
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Basnak G, Morton VL, Rolfsson Ó, Stonehouse NJ, Ashcroft AE, Stockley PG. Viral genomic single-stranded RNA directs the pathway toward a T=3 capsid. J Mol Biol 2010; 395:924-36. [PMID: 19913556 PMCID: PMC4785722 DOI: 10.1016/j.jmb.2009.11.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/02/2009] [Accepted: 11/05/2009] [Indexed: 11/20/2022]
Abstract
The molecular mechanisms controlling genome packaging by single-stranded RNA viruses are still largely unknown. It is necessary in most cases for the protein to adopt different conformations at different positions on the capsid lattice in order to form a viral capsid from multiple copies of a single protein. We showed previously that such quasi-equivalent conformers of RNA bacteriophage MS2 coat protein dimers (CP(2)) can be switched by sequence-specific interaction with a short RNA stem-loop (TR) that occurs only once in the wild-type phage genome. In principle, multiple switching events are required to generate the phage T=3 capsid. We have therefore investigated the sequence dependency of this event using two RNA aptamer sequences selected to bind the phage coat protein and an analogous packaging signal from phage Qbeta known to be discriminated against by MS2 coat protein both in vivo and in vitro. All three non-cognate stem-loops support T=3 shell formation, but none shows the kinetic-trapping effect seen when TR is mixed with equimolar CP(2). We show that this reflects the fact that they are poor ligands compared with TR, failing to saturate the coat protein under the assay conditions, ensuring that sufficient amounts of both types of dimer required for efficient assembly are present in these reactions. Increasing the non-cognate RNA concentration restores the kinetic trap, confirming this interpretation. We have also assessed the effects of extending the TR stem-loop at the 5' or 3' end with short genomic sequences. These longer RNAs all show evidence of the kinetic trap, reflecting the fact that they all contain the TR sequence and are more efficient at promoting capsid formation than TR. Mass spectrometry has shown that at least two pathways toward the T=3 shell occur in TR-induced assembly reactions: one via formation of a 3-fold axis and another that creates an extended 5-fold complex. The longer genomic RNAs suppress the 5-fold pathway, presumably as a consequence of steric clashes between multiply bound RNAs. Reversing the orientation of the extension sequences with respect to the TR stem-loop produces RNAs that are poor assembly initiators. The data support the idea that RNA-induced protein conformer switching occurs throughout assembly of the T=3 shell and show that both positional and sequence-specific effects outside the TR stem-loop can have significant impacts on the precise assembly pathway followed.
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Affiliation(s)
- Gabriella Basnak
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Victoria L. Morton
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nicola J. Stonehouse
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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45
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Dykeman E, Stockley P, Twarock R. Dynamic Allostery Controls Coat Protein Conformer Switching during MS2 Phage Assembly. J Mol Biol 2010; 395:916-23. [DOI: 10.1016/j.jmb.2009.11.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 11/02/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
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46
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Plevka P, Tars K, Liljas L. Structure and stability of icosahedral particles of a covalent coat protein dimer of bacteriophage MS2. Protein Sci 2009; 18:1653-61. [PMID: 19521994 PMCID: PMC2776953 DOI: 10.1002/pro.184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Particles formed by the bacteriophage MS2 coat protein mutants with insertions in their surface loops induce a strong immune response against the inserted epitopes. The covalent dimers created by fusion of two copies of the coat protein gene are more tolerant to various insertions into the surface loops than the single subunits. We determined a 4.7-A resolution crystal structure of an icosahedral particle assembled from covalent dimers and compared its stability with wild-type virions. The structure resembled the wild-type virion except for the intersubunit linker regions. The covalent dimer orientation was random with respect to both icosahedral twofold and quasi-twofold symmetry axes. A fraction of the particles was unstable in phosphate buffer because of assembly defects. Our results provide a structural background for design of modified covalent coat protein dimer subunits for use in immunization.
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Affiliation(s)
- Pavel Plevka
- Department of Cell and Molecular Biology, Uppsala UniversitySE-751 24 Uppsala, Sweden,*Correspondence to: Department of Cell and Molecular Biology, Uppsala University, Box 596, S751 24 Uppsala, Sweden. E-mail:
| | - Kaspars Tars
- Latvian Biomedical Research and Study CentreLV 1067 Riga, Latvia
| | - Lars Liljas
- Department of Cell and Molecular Biology, Uppsala UniversitySE-751 24 Uppsala, Sweden
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47
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Zhang Y, Zhao X, Mu Y. Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation. J Chem Theory Comput 2009; 5:1146-54. [DOI: 10.1021/ct8004276] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yufen Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, and State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P.R. China
| | - Xian Zhao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, and State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P.R. China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, and State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P.R. China
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48
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A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure. Biochem Biophys Res Commun 2008; 378:168-73. [PMID: 19000653 PMCID: PMC7117394 DOI: 10.1016/j.bbrc.2008.10.160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 10/24/2008] [Indexed: 12/11/2022]
Abstract
Recent studies suggest that some RNA-binding proteins facilitate the folding of non-cognate RNAs. Here, we report that bacteriophage MS2 coat protein (MS2 CP) bound and promoted the catalytic activity of Candida group I ribozyme. Cloning of the MS2-bound RNA segments showed that this protein primarily interacts with the P5ab-P5 structure. Ultraviolet cross-linking and the T1 footprinting assay further showed that MS2 binding stabilized tertiary interactions, including the conserved L9-P5 interaction, and led to a more compact core structure. This mechanism is similar to that of the yeast mitochondrial tyrosyl-tRNA synthetase on other group I introns, suggesting that different RNA-binding proteins may use common mechanisms to support RNA structures.
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49
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Persson M, Tars K, Liljas L. The Capsid of the Small RNA Phage PRR1 Is Stabilized by Metal Ions. J Mol Biol 2008; 383:914-22. [DOI: 10.1016/j.jmb.2008.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 06/16/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
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50
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Gell C, Sabir T, Westwood J, Rashid A, Smith DAM, Harris SA, Stockley PG. Single-molecule fluorescence resonance energy transfer assays reveal heterogeneous folding ensembles in a simple RNA stem-loop. J Mol Biol 2008; 384:264-78. [PMID: 18805425 DOI: 10.1016/j.jmb.2008.08.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 08/25/2008] [Accepted: 08/27/2008] [Indexed: 11/30/2022]
Abstract
We have examined the folding ensembles present in solution for a series of RNA oligonucleotides that encompass the replicase translational operator stem-loop of the RNA bacteriophage MS2. Single-molecule (SM) fluorescence assays suggest that these RNAs exist in solution as ensembles of differentially base-paired/base-stacked states at equilibrium. There are two distinct ensembles for the wild-type sequence, implying the existence of a significant free energy barrier between "folded" and "unfolded" ensembles. Experiments with sequence variants are consistent with an unfolding mechanism in which interruptions to base-paired duplexes, in this example by the single-stranded loop and a single-base bulge in the base-paired stem, as well as the free ends, act as nucleation points for unfolding. The switch between folded and unfolded ensembles is consistent with a transition that occurs when all base-pairing and/or base-stacking interactions that would orientate the legs of the RNA stem are broken. Strikingly, a U-to-C replacement of a residue in the loop, which creates a high-affinity form of the operator for coat protein binding, results in dramatically different (un)folding behaviour, revealing distinct subpopulations that are either stabilised or destabilised with respect to the wild-type sequence. This result suggests additional reasons for selection against the C-variant stem-loop in vivo and provides an explanation for the increased affinity.
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Affiliation(s)
- Christopher Gell
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS29JT, UK
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