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Hauptmann J, Hehne V, Balzer M, Bethge L, Wikstrom Lindholm M. Engineering miRNA features into siRNAs: Guide-strand bulges are compatible with gene repression. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:1116-1126. [PMID: 35251767 PMCID: PMC8881630 DOI: 10.1016/j.omtn.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/06/2022] [Indexed: 11/22/2022]
Abstract
Synthetic siRNA guide strands are typically designed with perfect complementarity to the passenger strand and the target mRNA. We examined whether siRNAs with intentional guide-strand bulges are functional in vitro and in vivo. Importantly, this was done by systematic shortening of the passenger strand, evaluating identical 19-mer guide-strand sequences but forcing them into conformations with 1- to 4-nt bulges after annealing. We demonstrate that guide-strand bulges can be well tolerated at several positions of unmodified and modified siRNAs. Beyond that, we show that GalNAc-conjugated siRNAs with bulges at certain positions of the guide strand repress transthyretin in murine primary hepatocytes and in vivo in mice. In vivo, a GalNAc-conjugated siRNA with a 1-nt bulge at position 14 of the guide strand was as active as the perfectly complementary siRNA. Finally, in a luciferase reporter system, mRNA target sequences were systematically shortened so that RNA-induced silencing complex activity could only occur with a guide-strand bulge. Here, luciferase reporters were repressed when 1- and 2-nt deletions of the reporter were applied to the edges of the sequence. We conclude that some guide-strand bulges versus target transcript can result in target repression and therefore should be evaluated as off-target risks.
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ElHefnawi M, Kim T, Kamar MA, Min S, Hassan NM, El-Ahwany E, Kim H, Zada S, Amer M, Windisch MP. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes. PLoS One 2016; 11:e0159211. [PMID: 27441640 PMCID: PMC4956106 DOI: 10.1371/journal.pone.0159211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022] Open
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide interventions.
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Affiliation(s)
- Mahmoud ElHefnawi
- Informatics and Systems Department, Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), Division of Engineering Research, National Research Centre, Cairo, Egypt
- Centre for Informatics, Nile University, Shiekh Zayed City, Egypt
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
- * E-mail: (MEH); (MPW)
| | - TaeKyu Kim
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Mona A. Kamar
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
| | - Saehong Min
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Nafisa M. Hassan
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
| | - Eman El-Ahwany
- Biology Department, American University in Cairo, New Cairo, Egypt
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Heeyoung Kim
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Suher Zada
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
- Biology Department, American University in Cairo, New Cairo, Egypt
| | - Marwa Amer
- Biology Department, American University in Cairo, New Cairo, Egypt
- Faculty of Biotechnology, Misr University for Science and Technology, 6 of October City, Egypt
| | - Marc P. Windisch
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
- * E-mail: (MEH); (MPW)
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Heinemann JA, Agapito-Tenfen SZ, Carman JA. A comparative evaluation of the regulation of GM crops or products containing dsRNA and suggested improvements to risk assessments. ENVIRONMENT INTERNATIONAL 2013; 55:43-55. [PMID: 23523853 DOI: 10.1016/j.envint.2013.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/08/2013] [Accepted: 02/22/2013] [Indexed: 05/20/2023]
Abstract
Changing the nature, kind and quantity of particular regulatory-RNA molecules through genetic engineering can create biosafety risks. While some genetically modified organisms (GMOs) are intended to produce new regulatory-RNA molecules, these may also arise in other GMOs not intended to express them. To characterise, assess and then mitigate the potential adverse effects arising from changes to RNA requires changing current approaches to food or environmental risk assessments of GMOs. We document risk assessment advice offered to government regulators in Australia, New Zealand and Brazil during official risk evaluations of GM plants for use as human food or for release into the environment (whether for field trials or commercial release), how the regulator considered those risks, and what that experience teaches us about the GMO risk assessment framework. We also suggest improvements to the process.
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Affiliation(s)
- Jack A Heinemann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Malhotra M, Nambiar S, Rengaswamy V, Prakash S. Small interfering ribonucleic acid design strategies for effective targeting and gene silencing. Expert Opin Drug Discov 2012; 6:269-89. [PMID: 22647204 DOI: 10.1517/17460441.2011.555394] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Gene silencing mediated by siRNAs is becoming a promising therapeutic approach. Although many strategies and technologies have been applied to siRNA design, a key issue lies in the selection of efficient design predictors. Furthermore, the development of systemic siRNA delivery strategies, which would enhance the therapeutic effect, remains a central issue. AREAS COVERED The review discusses the basic principles of the sequence-specific design criteria of functional siRNAs and possible chemical modifications. Some of the most recent advances in the development of siRNA design algorithms and delivery strategies are also presented. Emphasis is given to the important design rule sets and predictors which determine the functionality of an efficient siRNA. EXPERT OPINION The potential and limitations of efficient design predictors obtained from computational algorithms play a crucial role in the development of target-specific siRNAs. Furthermore, the future success of RNA interference therapeutics will depend on their ability to efficiently cross the physiological barriers, selectively target cells-of-interest and finally silence the gene-of-interest without any side effects.
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Affiliation(s)
- Meenakshi Malhotra
- McGill University, Artificial Cells and Organs Research Center, Departments of Biomedical Engineering and Physiology, Biomedical Technology and Cell Therapy Research Laboratory, Faculty of Medicine, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada +1 514 398 3676 ; +1 514 398 7461 ;
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Naito Y, Ui-Tei K. siRNA Design Software for a Target Gene-Specific RNA Interference. Front Genet 2012; 3:102. [PMID: 22701467 PMCID: PMC3371628 DOI: 10.3389/fgene.2012.00102] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/20/2012] [Indexed: 01/05/2023] Open
Abstract
RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA suppresses the expression of the intended gene whose transcript possesses perfect complementarity to the siRNA guide strand. Hence, its silencing effect has been assumed to be extremely specific. However, accumulated evidences revealed that siRNA could downregulate unintended genes with partial complementarities mainly to the seven-nucleotide seed region of siRNA. This phenomenon is referred to as off-target effect. We have revealed that the capability to induce off-target effect is strongly correlated to the thermodynamic stability in siRNA seed-target duplex. For understanding accurate target gene function and successful therapeutic application, it may be critical to select a target gene-specific siRNA with minimized off-target effect. Here we present our siRNA design software for a target-specific RNAi. In addition, we also introduce the software programs open to the public for designing functional siRNAs.
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Affiliation(s)
- Yuki Naito
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo Tokyo, Japan
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Nejepinska J, Flemr M, Svoboda P. Control of the interferon response in RNAi experiments. Methods Mol Biol 2012; 820:133-61. [PMID: 22131030 DOI: 10.1007/978-1-61779-439-1_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA interference (RNAi) and interferons have been an uneasy marriage. Ever since the discovery of RNAi in mammals, the interferon response has been a feared problem. While RNAi became an efficient and widespread method for gene silencing in mammals, numerous studies recognized several obstacles, including undesirable activation of the interferon response, which need to be overcome to achieve a specific and robust RNAi effect. The aim of this text is to provide theoretical and practical information for scientists who want to control interferon response and other adverse effects in their RNAi experiments.
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Affiliation(s)
- Jana Nejepinska
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
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Thakur N, Qureshi A, Kumar M. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res 2012; 40:D230-6. [PMID: 22139916 PMCID: PMC3245049 DOI: 10.1093/nar/gkr1147] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/04/2011] [Accepted: 11/09/2011] [Indexed: 12/22/2022] Open
Abstract
RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb.
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Affiliation(s)
| | | | - Manoj Kumar
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh-160036, India
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Designing of highly effective complementary and mismatch siRNAs for silencing a gene. PLoS One 2011; 6:e23443. [PMID: 21853133 PMCID: PMC3154470 DOI: 10.1371/journal.pone.0023443] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 07/17/2011] [Indexed: 11/19/2022] Open
Abstract
In past, numerous methods have been developed for predicting efficacy of short interfering RNA (siRNA). However these methods have been developed for predicting efficacy of fully complementary siRNA against a gene. Best of author's knowledge no method has been developed for predicting efficacy of mismatch siRNA against a gene. In this study, a systematic attempt has been made to identify highly effective complementary as well as mismatch siRNAs for silencing a gene. Support vector machine (SVM) based models have been developed for predicting efficacy of siRNAs using composition, binary and hybrid pattern siRNAs. We achieved maximum correlation 0.67 between predicted and actual efficacy of siRNAs using hybrid model. All models were trained and tested on a dataset of 2182 siRNAs and performance was evaluated using five-fold cross validation techniques. The performance of our method desiRm is comparable to other well-known methods. In this study, first time attempt has been made to design mutant siRNAs (mismatch siRNAs). In this approach we mutated a given siRNA on all possible sites/positions with all possible nucleotides. Efficacy of each mutated siRNA is predicted using our method desiRm. It is well known from literature that mismatches between siRNA and target affects the silencing efficacy. Thus we have incorporated the rules derived from base mismatches experimental data to find out over all efficacy of mutated or mismatch siRNAs. Finally we developed a webserver, desiRm (http://www.imtech.res.in/raghava/desirm/) for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.
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An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design. BMC Res Notes 2011; 4:168. [PMID: 21619643 PMCID: PMC3117723 DOI: 10.1186/1756-0500-4-168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 05/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The "off-target" silencing effect hinders the development of siRNA-based therapeutic and research applications. Existing solutions for finding possible locations of siRNA seats within a large database of genes are either too slow, miss a portion of the targets, or are simply not designed to handle a very large number of queries. We propose a new approach that reduces the computational time as compared to existing techniques. FINDINGS The proposed method employs tree-based storage in a form of a modified truncated suffix tree to sort all possible short string substrings within given set of strings (i.e. transcriptome). Using the new algorithm, we pre-computed a list of the best siRNA locations within each human gene ("siRNA seats"). siRNAs designed to reside within siRNA seats are less likely to hybridize off-target. These siRNA seats could be used as an input for the traditional "set-of-rules" type of siRNA designing software. The list of siRNA seats is available through a publicly available database located at http://web.cos.gmu.edu/~gmanyam/siRNA_db/search.php CONCLUSIONS In attempt to perform top-down prediction of the human siRNA with minimized off-target hybridization, we developed an efficient algorithm that employs suffix tree based storage of the substrings. Applications of this approach are not limited to optimal siRNA design, but can also be useful for other tasks involving selection of the characteristic strings specific to individual genes. These strings could then be used as siRNA seats, as specific probes for gene expression studies by oligonucleotide-based microarrays, for the design of molecular beacon probes for Real-Time PCR and, generally, any type of PCR primers.
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Sakurai K, Chomchan P, Rossi JJ. Silencing of gene expression in cultured cells using small interfering RNAs. ACTA ACUST UNITED AC 2010; Chapter 27:Unit 27.1.1-28. [PMID: 20521232 DOI: 10.1002/0471143030.cb2701s47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The discovery of RNA interference (RNAi) and related small RNA-mediated regulatory pathways has significantly altered the understanding of gene regulation in eukaryotic cells. In the RNAi pathway, small interfering RNAs (siRNAs) approximately 21 to 23 nucleotides in length serve as the regulatory molecules that guide and induce sequence-specific gene silencing. The use of siRNA-mediated silencing as a tool for investigating gene function is well established in cultured mammalian cells. This unit provides basic approaches to explore the field of RNAi, and hopes to address the importance of optimizing transfection conditions after empirical determinations in order to understand various degrees of silencing efficiency.
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Affiliation(s)
- Kumi Sakurai
- Beckman Research Institute of City of Hope, Duarte, California, USA
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Palanichamy JK, Mehndiratta M, Bhagat M, Ramalingam P, Das B, Das P, Sinha S, Chattopadhyay P. Silencing of integrated human papillomavirus-16 oncogenes by small interfering RNA-mediated heterochromatization. Mol Cancer Ther 2010; 9:2114-22. [PMID: 20587668 DOI: 10.1158/1535-7163.mct-09-0977] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Double-stranded RNAs or small interfering RNAs (siRNA) targeting the promoters of genes are known to cause gene knockdown by a process known as transcriptional gene silencing (TGS). We screened multiple siRNAs homologous to one of the NF-1 binding sites in the human papillomavirus-16 (HPV-16) enhancer and identified one siRNA which causes specific TGS of the HPV-16 oncogenes E6 and E7 when transfected into two HPV-16-positive cell lines siHa and CaSki. This phenomenon was specific to the HPV-16 enhancer with no effect on the HPV-18 enhancer. TGS was associated with heterochromatization of the targeted region of the enhancer but no DNA methylation was noted during the time period studied. The choice of target in the enhancer was important as siRNAs differing by one or two bases showed no suppression of downstream gene expression. A low copy number enhancer-associated transcript was detected in the cell lines studied and its level decreased significantly after treatment with the siRNA that caused TGS. This supports the RNA:RNA model described previously for TGS. This siRNA which causes simultaneous silencing of E6 as well as E7 oncogenes by an epigenetic mechanism might be useful as a therapeutic modality for HPV-16-positive cervical and other epithelial cancers.
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Abstract
RNA interference mediated by short interfering RNA (siRNA) molecules represents a powerful genetic tool with an increasing interest as potential therapeutics. Current bioinformatic approaches to design functional siRNA molecules take into account both empirical and rational approaches to identify selectable characteristics of active and specific siRNA molecules and focusing the downstream events in the RNAi pathway, such as target messenger RNA accessibility. The design of effective siRNA molecules is the key to successful experimentation with RNAi. Here, we show advanced siRNA design parameters and options for highly efficient siRNA candidate search.
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Naito Y, Yoshimura J, Morishita S, Ui-Tei K. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics 2009; 10:392. [PMID: 19948054 PMCID: PMC2791777 DOI: 10.1186/1471-2105-10-392] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 11/30/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring perfect complementarity between the siRNA guide strand and the target mRNA, was believed to be extremely specific. However, a recent growing body of evidence has suggested that siRNA could down-regulate unintended genes whose transcripts possess complementarity to the 7-nt siRNA seed region. This off-target gene silencing may often provide incongruous results obtained from knockdown experiments, leading to misinterpretation. Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value. RESULTS We present siDirect 2.0, an update of our web-based software siDirect, which provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. CONCLUSION siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in RefSeq. siDirect 2.0 is available at http://siDirect2.RNAi.jp/.
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Affiliation(s)
- Yuki Naito
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan.
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