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Klotz K, Radwan Y, Chakrabarti K. Dissecting Functional Biological Interactions Using Modular RNA Nanoparticles. Molecules 2022; 28:molecules28010228. [PMID: 36615420 PMCID: PMC9821959 DOI: 10.3390/molecules28010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Nucleic acid nanoparticles (NANPs) are an exciting and innovative technology in the context of both basic and biomedical research. Made of DNA, RNA, or their chemical analogs, NANPs are programmed for carrying out specific functions within human cells. NANPs are at the forefront of preventing, detecting, and treating disease. Their nucleic acid composition lends them biocompatibility that provides their cargo with enhanced opportunity for coordinated delivery. Of course, the NANP system of targeting specific cells and tissues is not without its disadvantages. Accumulation of NANPs outside of the target tissue and the potential for off-target effects of NANP-mediated cargo delivery present challenges to research and medical professionals and these challenges must be effectively addressed to provide safe treatment to patients. Importantly, development of NANPs with regulated biological activities and immunorecognition becomes a promising route for developing versatile nucleic acid therapeutics. In a basic research context, NANPs can assist investigators in fine-tuning the structure-function relationship of final formulations and in this review, we explore the practical applications of NANPs in laboratory and clinical settings and discuss how we can use established nucleic acid research techniques to design effective NANPs.
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Affiliation(s)
- Kaitlin Klotz
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Yasmine Radwan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
- Correspondence:
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Déraspe M, Boisvert S, Laviolette F, Roy PH, Corbeil J. Flexible protein database based on amino acid k-mers. Sci Rep 2022; 12:9101. [PMID: 35650262 PMCID: PMC9160020 DOI: 10.1038/s41598-022-12843-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/17/2022] [Indexed: 11/09/2022] Open
Abstract
Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that do not accommodate rich information on proteins and require additional pipelining steps for protein identification. We introduce kAAmer, a protein database engine based on amino-acid k-mers that provides efficient identification of proteins while supporting the incorporation of flexible annotations on these proteins. Moreover, the database is built to be used as a microservice, to be hosted and queried remotely.
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Affiliation(s)
- Maxime Déraspe
- Department of Molecular Medicine, Université Laval, Quebec, Canada.
- Big Data Research Center, Université Laval, Quebec, Canada.
| | | | - François Laviolette
- Big Data Research Center, Université Laval, Quebec, Canada
- Department of Computer Science, Université Laval, Quebec, Canada
| | - Paul H Roy
- Infectious Disease Research Centre, Université Laval, Quebec, Canada
| | - Jacques Corbeil
- Department of Molecular Medicine, Université Laval, Quebec, Canada
- Big Data Research Center, Université Laval, Quebec, Canada
- Centre NUTRISS, Université Laval, Quebec, Canada
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Mehmood M, Khan MJ, Khan MJ, Akhtar N, Mughal F, Shah STA, Hyder MZ, Farrakh S, Sadiq I. Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage. Mol Biol Rep 2022; 49:2059-2071. [PMID: 34993726 DOI: 10.1007/s11033-021-07024-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors affecting its world-wide growth and productivity. Among plant specific transcription factors, the association of HD-ZIPs with sesame drought responses at early seedling stage is not well-established yet and is very important to develop our molecular understanding on sesame drought tolerance. METHODS AND RESULTS In this study, total 61 sesame HD-ZIP proteins were identified, based on their protein sequence homology with Arabidopsis and protein domain(s) architecture prediction, followed by their phylogenetic, conserved domain(s) motifs and gene structure analyses to classify them into four classes (HD-ZIP Class I-IV). HD-ZIP Class I was also subdivided into four subgroups: α (SiHZ25, SiHZ43, SiHZ9 and SiHZ16), β1 (SiHZ10, SiHZ30, SiHZ32 and SiHZ26), β2 (SiHZ42 and SiHZ45) and γ (SiHZ17, SiHZ7 and SiHZ35) by a comparative phylogenetic analysis of sesame with Arabidopsis and maize. Afterwards, twenty-one days old sesame seedlings were exposed to drought stress by withholding water for 7 days (when soil moisture content reduced to ~16%) and gene expression of HD-ZIP Class I (13 members) was performed in well- watered (control) and drought stressed seedlings. The gene expression analysis showed that the expressions of SiHZ7 (6.8 fold) and SiHZ35 (2.6 fold) from γ subgroup were significantly high in drought seedlings. CONCLUSIONS This study is useful in demonstrating the role of SiHD-ZIP Class I in sesame drought responses at early seedling stage and to develop its novel drought tolerant varieties.
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Affiliation(s)
- Maryam Mehmood
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Muhammad Jadoon Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Nadeem Akhtar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Fizza Mughal
- Illinois Informatics Institute, University of Illinois, Urbana-Champaign, USA
| | - Syed Tahir Abbas Shah
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | | | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan.
| | - Irfan Sadiq
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan.
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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Zakrevsky P, Calkins E, Kao YL, Singh G, Keleshian VL, Baudrey S, Jaeger L. In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules. Nucleic Acids Res 2021; 49:2289-2305. [PMID: 33524109 PMCID: PMC7913685 DOI: 10.1093/nar/gkab021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/05/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022] Open
Abstract
GNRA tetraloop-binding receptor interactions are key components in the macromolecular assembly of a variety of functional RNAs. In nature, there is an apparent bias for GAAA/11nt receptor and GYRA/helix interactions, with the former interaction being thermodynamically more stable than the latter. While past in vitro selections allowed isolation of novel GGAA and GUGA receptors, we report herein an in vitro selection that revealed several novel classes of specific GUAA receptors with binding affinities comparable to those from natural GAAA/11nt interactions. These GUAA receptors have structural homology with double-locked bulge RNA modules naturally occurring in ribosomal RNAs. They display mutational robustness that enables exploration of the sequence/phenotypic space associated to GNRA/receptor interactions through epistasis. Their thermodynamic self-assembly fitness landscape is characterized by a rugged neutral network with possible evolutionary trajectories toward natural GNRA/receptor interactions. High throughput sequencing analysis revealed synergetic mutations located away from the tertiary interactions that positively contribute to assembly fitness. Our study suggests that the repertoire of GNRA/receptor interactions is much larger than initially thought from the analysis of natural stable RNA molecules and also provides clues for their evolution towards natural GNRA/receptors.
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Affiliation(s)
- Paul Zakrevsky
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Erin Calkins
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Yi-Ling Kao
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Gurkeerat Singh
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Vasken L Keleshian
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Stephanie Baudrey
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
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Translation of the long-term fundamental studies on viral DNA packaging motors into nanotechnology and nanomedicine. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1103-1129. [DOI: 10.1007/s11427-020-1752-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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Zhao J, Kennedy SD, Berger KD, Turner DH. Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:1968-1984. [PMID: 31904966 DOI: 10.1021/acs.jctc.9b00912] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA and DNA are rapidly emerging as targets for therapeutics and as potential frameworks for nanotechnology. Accurate methods for predicting and designing structures and dynamics of nucleic acids would accelerate progress in these and other applications. Suitable approximations for modeling nucleic acids are being developed but require validation against disparate experimental observations. Here, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations with AMBER force fields OL3 and ROC-RNA for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented. The results reflect recent progress in approximations and reveal remaining challenges.
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Affiliation(s)
- Jianbo Zhao
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Kyle D Berger
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
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Chen S, Hermann T. RNA-DNA hybrid nanoshapes that self-assemble dependent on ligand binding. NANOSCALE 2020; 12:3302-3307. [PMID: 31971536 DOI: 10.1039/c9nr09706f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Self-assembly of nucleic acid nanostructures is driven by selective association of oligonucleotide modules through base pairing between complementary sequences. Herein, we report the development of RNA-DNA hybrid nanoshapes that conditionally assemble under the control of an adenosine ligand. The design concept for the nanoshapes relies on ligand-dependent stabilization of DNA aptamers that serve as connectors between marginally stable RNA corner modules. Ligand-dependent RNA-DNA nanoshapes self-assemble in an all-or-nothing process by coupling adenosine binding to the formation of circularly closed structures which are stabilized through continuous base stacking in the resulting polygons. By screening combinations of various DNA aptamer constructs with RNA corner modules for the formation of stable complexes, we identified adenosine-dependent nanosquares whose shape was confirmed by atomic force microscopy. As a proof-of-concept for sensor applications, adenosine-responsive FRET-active nanosquares were obtained by dye conjugation of the DNA aptamer components.
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Affiliation(s)
- Shi Chen
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA. and Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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