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Zhang Q, Yang L, Wang K, Guo L, Ning H, Wang S, Gong Y. Terahertz waves regulate the mechanical unfolding of tau pre-mRNA hairpins. iScience 2023; 26:107572. [PMID: 37664616 PMCID: PMC10470126 DOI: 10.1016/j.isci.2023.107572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/14/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
Intermolecular interactions, including hydrogen bonds, dominate the pairing and unpairing of nucleic acid chains in the transfer process of genetic information. The energy of THz waves just matches with the weak interactions, so THz waves may interact with biomolecules. Here, the dynamic effects of THz electromagnetic (EM) waves on the mechanical unfolding process of RNA hairpins (WT-30nt and its mutants, rHP, SARS-CoV-2, and SRV-1 SF206) are investigated using steered molecular dynamics (SMD) simulations. The results show that THz waves can either promote the unfolding of the double helix of the RNA hairpin during the initial unfolding phase (4-21.8 THz) or significantly enhance (23.8 and 25.5 THz) or weaken (37.4 and 41.2 THz) its structural stability during unfolding. Our findings have important implications for applying THz waves to regulate dynamic deconvolution processes, such as gene replication, transcription, and translation.
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Affiliation(s)
- Qin Zhang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Lixia Yang
- School of Physics, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Kaicheng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Lianghao Guo
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Hui Ning
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Shaomeng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Yubin Gong
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
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Rissanou AN, Ouranidis A, Karatasos K. Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study. SOFT MATTER 2020; 16:6993-7005. [PMID: 32667026 DOI: 10.1039/d0sm00736f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Complexation of a lipid-based ionizable cationic molecule (referred to as DML: see main text) with RNA in an aqueous medium was examined in detail by means of fully atomistic molecular dynamics simulations. The different stages of the DML-RNA association process were explored, while the structural characteristics of the final complex were described. The self-assembly process of the DML molecules was examined in the absence and in the presence of nucleotide sequences of different lengths. The formed DML clusters were described in detail in terms of their size and composition and were found to share common features in all the examined systems. Different timescales related to their self-assembly and their association with RNA were identified. It was found that beyond a time period of a few tens of ns, a conformationally stable DML-RNA complex was formed, characterized by DML clusters covering the entire contour of RNA. In a system with a 642-nucleotide sequence, the average size of the complex in the longest dimension was found to be close to 40 nm. The DML clusters were characterized by a rather low surface charge, while a propensity for the formation of larger size clusters close to RNA was noted. Apart from hydrophobic and electrostatic interactions, hydrogen bonding was found to play a key-role in the DML-DML and in the DML-RNA association. The information obtained regarding the structural features of the final complex, the timescales and the driving forces associated with the complexation and the self-assembly processes provide new insight towards a rational design of optimized lipid-based ionizable cationic gene delivery vectors.
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Affiliation(s)
- Anastassia N Rissanou
- Department of Chemical Engineering, University of Thessaloniki, P.O. BOX 420, 54124 Thessaloniki, Greece.
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Bajrovic I, Schafer SC, Romanovicz DK, Croyle MA. Novel technology for storage and distribution of live vaccines and other biological medicines at ambient temperature. SCIENCE ADVANCES 2020; 6:eaau4819. [PMID: 32181330 PMCID: PMC7056310 DOI: 10.1126/sciadv.aau4819] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/11/2019] [Indexed: 05/10/2023]
Abstract
A novel, thin-film platform that preserves live viruses, bacteria, antibodies, and enzymes without refrigeration for extended periods of time is described. Studies with recombinant adenovirus in an optimized formulation that supports recovery of live virus through 16 freeze-thaw cycles revealed that production of an amorphous solid with a glass transition above room temperature and nitrogen-hydrogen bonding between virus and film components are critical determinants of stability. Administration of live influenza virus in the optimized film by the sublingual and buccal routes induced antibody-mediated immune responses as good as or better than those achieved by intramuscular injection. This work introduces the possibility of improving global access to a variety of medicines by offering a technology capable of reducing costs of production, distribution, and supply chain maintenance.
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MESH Headings
- Adenoviridae/genetics
- Adenoviridae/immunology
- Administration, Buccal
- Administration, Sublingual
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- HEK293 Cells
- Humans
- Immunization/methods
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Injections, Intramuscular
- Male
- Membranes, Artificial
- Mice
- Mice, Inbred BALB C
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/prevention & control
- Orthomyxoviridae Infections/virology
- Preservation, Biological/methods
- Temperature
- Vaccine Potency
- Vaccines, Attenuated/biosynthesis
- Vaccines, Attenuated/pharmacology
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Affiliation(s)
- Irnela Bajrovic
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen C. Schafer
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dwight K. Romanovicz
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Maria A. Croyle
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX 78712, USA
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Singh RP, Hidalgo T, Cazade PA, Darcy R, Cronin MF, Dorin I, O’Driscoll CM, Thompson D. Self-Assembled Cationic β-Cyclodextrin Nanostructures for siRNA Delivery. Mol Pharm 2019; 16:1358-1366. [DOI: 10.1021/acs.molpharmaceut.8b01307] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Tania Hidalgo
- School of Pharmacy, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
| | - Pierre-Andre Cazade
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Raphael Darcy
- School of Pharmacy, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
| | - Michael F. Cronin
- School of Pharmacy, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
| | - Irina Dorin
- Malvern Panalytical Ltd., Grovewood Road, Malvern, Worcestershire WR14 1XZ, U.K
| | | | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
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The Mechanism for siRNA Transmembrane Assisted by PMAL. Molecules 2018; 23:molecules23071586. [PMID: 29966273 PMCID: PMC6099945 DOI: 10.3390/molecules23071586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/10/2018] [Accepted: 06/19/2018] [Indexed: 11/29/2022] Open
Abstract
The capacity of silencing genes makes small interfering RNA (siRNA) appealing for curing fatal diseases. However, the naked siRNA is vulnerable to and degraded by endogenous enzymes and is too large and too negatively charged to cross cellular membranes. An effective siRNA carrier, PMAL (poly(maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine), has been demonstrated to be able to assist siRNA transmembrane by both experiments and molecular simulation. In the present work, the mechanism of siRNA transmembrane assisted by PMAL was studied using steered molecular dynamics simulations based on the martini coarse-grained model. Here two pulling rates, i.e., 10−6 and 10−5 nm·ps−1, were chosen to imitate the passive and active transport of siRNA, respectively. Potential of mean force (PMF) and interactions among siRNA, PMAL, and lipid bilayer membrane were calculated to describe the energy change during siRNA transmembrane processes at various conditions. It is shown that PMAL-assisted siRNA delivery is in the mode of passive transport. The PMAL can help siRNA insert into lipid bilayer membrane by lowering the energy barrier caused by siRNA and lipid bilayer membrane. PMAL prefers to remain in the lipid bilayer membrane and release siRNA. The above simulations establish a molecular insight of the interaction between siRNA and PMAL and are helpful for the design and applications of new carriers for siRNA delivery.
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