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Li J, Zhou Y, Chen SJ. Embracing exascale computing in nucleic acid simulations. Curr Opin Struct Biol 2024; 87:102847. [PMID: 38815519 PMCID: PMC11283969 DOI: 10.1016/j.sbi.2024.102847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/18/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
This mini-review reports the recent advances in biomolecular simulations, particularly for nucleic acids, and provides the potential effects of the emerging exascale computing on nucleic acid simulations, emphasizing the need for advanced computational strategies to fully exploit this technological frontier. Specifically, we introduce recent breakthroughs in computer architectures for large-scale biomolecular simulations and review the simulation protocols for nucleic acids regarding force fields, enhanced sampling methods, coarse-grained models, and interactions with ligands. We also explore the integration of machine learning methods into simulations, which promises to significantly enhance the predictive modeling of biomolecules and the analysis of complex data generated by the exascale simulations. Finally, we discuss the challenges and perspectives for biomolecular simulations as we enter the dawning exascale computing era.
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Affiliation(s)
- Jun Li
- Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, 223 Physics Bldg., Columbia, 65211, MO, USA
| | - Yuanzhe Zhou
- Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, 223 Physics Bldg., Columbia, 65211, MO, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, 223 Physics Bldg., Columbia, 65211, MO, USA.
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2
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Li S, Chu Y, Guo X, Mao C, Xiao SJ. Circular RNA oligonucleotides: enzymatic synthesis and scaffolding for nanoconstruction. NANOSCALE HORIZONS 2024. [PMID: 39042106 DOI: 10.1039/d4nh00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
We report the efficient synthesis of monomeric circular RNAs (circRNAs) in the size range of 16-44 nt with a novel DNA dumbbell splinting plus T4 DNA ligation strategy. Such a DNA dumbbell splinting strategy was developed by one group among ours recently for near-quantitative conversion of short linear DNAs into monomeric circular ones. Furthermore, using the 44 nt circRNA as scaffold strands, we constructed hybrid RNA:DNA and pure RNA:RNA double crossover tiles and their assemblies of nucleic acid nanotubes and flat arrays.
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Affiliation(s)
- Shijie Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yanxin Chu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xin Guo
- Bruker (Beijing) Scientific Technology Co. Ltd, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Shou-Jun Xiao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
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Elonen A, Wimbes L, Mohammed A, Orponen P. DNAforge: a design tool for nucleic acid wireframe nanostructures. Nucleic Acids Res 2024; 52:W13-W18. [PMID: 38747339 PMCID: PMC11223811 DOI: 10.1093/nar/gkae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 07/06/2024] Open
Abstract
DNAforge is an online tool that provides a unified, user-friendly interface to several recent design methods for DNA and RNA wireframe nanostructures, with the possibility of integrating additional methods into the same framework. Currently, DNAforge supports three design methods for DNA nanostructures and two for RNA nanostructures. The tool enables the design, visualisation and sequence generation for highly complex wireframe nanostructures with a simple fully automated process. DNAforge is freely accessible at https://dnaforge.org/.
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Affiliation(s)
- Antti Elonen
- Department of Computer Science, Aalto University, Finland
| | - Leon Wimbes
- Department of Computer Science, Aalto University, Finland
- Department of Mathematics and Computer Science, Philipps University of Marburg, Germany
| | | | - Pekka Orponen
- Department of Computer Science, Aalto University, Finland
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Sun J, Lu S, Xiao J, Xu N, Li Y, Xu J, Deng M, Xuanyuan H, Zhang Y, Wu F, Jin W, Liu K. Inhibition of SARS-CoV-2 Replication by Self-Assembled siRNA Nanoparticles Targeting Multiple Highly Conserved Viral Sequences. Viruses 2024; 16:1072. [PMID: 39066234 PMCID: PMC11281333 DOI: 10.3390/v16071072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 07/28/2024] Open
Abstract
Coronavirus infectious disease 2019 (COVID-19), caused by severe acute respiratory virus type 2 (SARS-CoV-2), has caused a global public health crisis. As an RNA virus, the high gene mutability of SARS-CoV-2 poses significant challenges to the development of broad-spectrum vaccines and antiviral therapeutics. There remains a lack of specific therapeutics directly targeting SARS-CoV-2. With the ability to efficiently inhibit the expression of target genes in a sequence-specific way, small interfering RNA (siRNA) therapy has exhibited significant potential in antiviral and other disease treatments. In this work, we presented a highly effective self-assembled siRNA nanoparticle targeting multiple highly conserved regions of SARS-CoV-2. The siRNA sequences targeting viral conserved regions were first screened and evaluated by their thermodynamic features, off-target effects, and secondary structure toxicities. RNA motifs including siRNA sequences were then designed and self-assembled into siRNA nanoparticles. These siRNA nanoparticles demonstrated remarkable uniformity and stability and efficiently entered cells directly through cellular endocytic pathways. Moreover, these nanoparticles effectively inhibited the replication of SARS-CoV-2, exhibiting a superior inhibitory effect compared to free siRNA. These results demonstrated that these self-assembled siRNA nanoparticles targeting highly conserved regions of SARS-CoV-2 represent highly effective antiviral candidates for the treatment of infections, and are promisingly effective against current and future viral variants.
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Affiliation(s)
- Jianan Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Siya Lu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Jizhen Xiao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Nuo Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yingbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Jinfeng Xu
- College of Life Sciences & Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Maohua Deng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Hanlu Xuanyuan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yushi Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Fangli Wu
- College of Life Sciences & Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weibo Jin
- College of Life Sciences & Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Kuancheng Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
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Suess B. Synthetic RNA biology. RNA Biol 2024; 21:1-2. [PMID: 38616320 PMCID: PMC11018018 DOI: 10.1080/15476286.2024.2335746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology, Synthetic RNA Biology, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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Kanarskaya MA, Pyshnyi DV, Lomzov AA. Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines. Molecules 2023; 29:10. [PMID: 38202593 PMCID: PMC10779776 DOI: 10.3390/molecules29010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations. We have demonstrated the spontaneous formation of various self-limited and concatemer complexes. The linear concatemer complex is formed by a pair of oligomers without a linker in at least one of them. Longer linkers resulted in the formation of circular complexes. The self-limited complexes formation was confirmed using the toehold strand displacement. The MD simulations indicate the reliability of the complexes' structure and demonstrate their dynamics, which increase with the rise of complex size. The linearization of 2D circular complexes into 1D structures and a reverse cyclization process were demonstrated using a toehold-mediated approach. The approach proposed here for the construction and directed modification of the molecularity and shape of complexes will be a valuable tool in RNA nanotechnology, especially for the rational design of therapeutic nucleic acids with high target specificity and the programmable response of the immune system of organisms.
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Affiliation(s)
| | | | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (M.A.K.); (D.V.P.)
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Mentis AFA, Papavassiliou KA, Papavassiliou AG. DNA origami: a tool to evaluate and harness transcription factors. J Mol Med (Berl) 2023; 101:1493-1498. [PMID: 37813986 DOI: 10.1007/s00109-023-02380-x] [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: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
Alongside other players, such as CpG methylation and the "histone code," transcription factors (TFs) represent a key feature of gene regulation. TFs are implicated in critical cellular processes, ranging from cell death, growth, and differentiation, up to intranuclear signaling of steroid and other hormones, physical entities, and hypoxia regulation. Notwithstanding an extensive body of research in this field, several questions and therapeutic options remain unanswered and unexplored, respectively. Of note, many of these TFs represent therapeutic targets, which are either difficult to be pharmacologically tackled or are still not drugged via traditional approaches, such as small-molecule inhibition. Upon providing a brief overview of TFs, we focus herein on how synthetic biology/medicine could assist in their study as well as their therapeutic targeting. Specifically, we contend that DNA origami, i.e., a novel synthetic DNA nanotechnological approach, represents an excellent synthetic biology/medicine tool to accomplish the above goals, since it can harness several vital characteristics of DNA: DNA polymerization, DNA complementarity, DNA "programmability," and DNA "editability." In doing so, DNA origami can be applied to study TF dynamics during DNA transcription, to elucidate xeno-nucleic acids with distinct scaffolds and unconventional base pairs, and to use TFs as competitors of oncogene-engaged promoters. Overall, because of their potential for high-throughput design and their favorable pharmacodynamic and pharmacokinetic properties, DNA origami can be a novel armory for TF-related drug design. Last, we discuss future trends in the field, such as RNA origami and innovative DNA origami-based therapeutic delivery approaches.
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Affiliation(s)
| | - Kostas A Papavassiliou
- First University Department of Respiratory Medicine, Sotiria' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece.
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