Research graph
References from Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Local targets link to admitted publications; unresolved targets remain external evidence.
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field
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10.1016/j.addr.2021.114081 · External reference
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10.1021/acsnano.0c04753
10.1021/acsnano.0c04753 · External reference
The application of light-assisted drying to the thermal stabilization of nucleic acid nanoparticles
10.1089/bio.2022.0035 · 2022 · External reference
10.1101/2022.07.28.501902
10.1101/2022.07.28.501902 · External reference
Anhydrous nucleic acid nanoparticles for storage and handling at broad range of temperatures
10.1002/smll.202104814 · 2022 · External reference
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10.1101/2022.05.17.492310 · External reference
10.1038/s41586-020-2933-1
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10.1038/nature22981
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The push-to-open mechanism of the tethered mechanosensitive ion channel NompC
2021 · External reference
10.1126/sciadv.abg4617
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10.1007/s11427-020-1752-1
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10.1016/j.biotechadv.2014.01.006
10.1016/j.biotechadv.2014.01.006 · External reference
Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids
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Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size
10.1186/2045-3701-4-30 · 2014 · External reference
10.1016/j.virol.2013.04.019
10.1016/j.virol.2013.04.019 · External reference
10.1021/acsnano.1c02973
10.1021/acsnano.1c02973 · External reference
10.1021/acsnano.8b08849
10.1021/acsnano.8b08849 · External reference
Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation
10.1007/s13238-020-00710-0 · 2020 · External reference
10.1073/pnas.2001324117
10.1073/pnas.2001324117 · External reference
The FtsK-like motor TraB is a DNA-dependent ATPase that forms higher-order assemblies
10.1074/jbc.ra119.007459 · 2019 · External reference
Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating
10.1073/pnas.0812407106 · 2009 · External reference
10.1021/jacs.1c09259
10.1021/jacs.1c09259 · External reference
Discrimination of RNA fiber structures using solid-state nanopores
10.1039/d1nr08002d · 2022 · External reference
Continuous stochastic detection of amino acid enantiomers with a protein nanopore
10.1002/anie.201205687 · 2012 · External reference
Channel from bacterial virus T7 DNA packaging motor for the differentiation of peptides composed of a mixture of acidic and basic amino acids
10.1016/j.biomaterials.2019.119222 · 2019 · External reference
10.1038/s41587-019-0345-2
10.1038/s41587-019-0345-2 · External reference
Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states
10.1016/j.biomaterials.2017.01.031 · 2017 · External reference
10.1038/nbt.2799
10.1038/nbt.2799 · External reference
Detection of single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of Phi29 DNA packaging motor
10.1016/j.biomaterials.2021.121022 · 2021 · External reference
Oriented single directional insertion of nanochannel of bacteriophage SPP1 DNA packaging motor into lipid bilayer via polar hydrophobicity
10.1016/j.biomaterials.2016.08.002 · 2016 · External reference
Insertion of channel of phi29 DNA packaging motor into polymer membrane for high-throughput sensing
10.1016/j.nano.2020.102170 · 2020 · External reference
10.1021/acs.nanolett.1c02371
10.1021/acs.nanolett.1c02371 · External reference
Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells
10.1039/d1bm01264a · 2021 · External reference
10.1021/jacs.1c11758
10.1021/jacs.1c11758 · External reference
Protein identification by nanopore peptide profiling
10.1038/s41467-021-26046-9 · 2021 · External reference
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10.1039/c8cs00457a · External reference
10.1021/acscatal.0c03426
10.1021/acscatal.0c03426 · External reference
Simultaneous enzyme mimicking and chemical reduction mechanisms for nanoceria as a bio-antioxidant: a catalytic model bridging computations and experiments for nanozymes
10.1039/c9nr03473k · 2019 · External reference
Accelerated discovery of superoxide-dismutase nanozymes via high-throughput computational screening
10.1038/s41467-021-27194-8 · 2021 · External reference
10.1016/j.virol.2020.12.010
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10.1101/cshperspect.a032649
10.1101/cshperspect.a032649 · External reference
Conformational shannon entropy of mRNA structures from force spectroscopy measurements predicts the efficiency of -1 programmed ribosomal frameshift stimulation
10.1103/physrevlett.126.038102 · 2021 · External reference
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Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication
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Altering SARS coronavirus frameshift efficiency affects genomic and subgenomic RNA production
10.3390/v5010279 · 2013 · External reference
Ablation of programmed -1 ribosomal frameshifting in venezuelan equine encephalitis virus results in attenuated neuropathogenicity
10.1128/jvi.01766-16 · 2017 · External reference
10.1371/journal.pcbi.1008603
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10.1126/science.abf3546
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10.1073/pnas.2023051118 · External reference
10.1101/2021.08.06.455424
10.1101/2021.08.06.455424 · External reference
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10.1186/1471-2164-9-339 · 2008 · External reference
High-throughput interrogation of programmed ribosomal frameshifting in human cells
10.1038/s41467-020-16961-8 · 2020 · External reference
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10.1002/wrna.1373 · External reference
Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses
10.1038/s41422-020-0290-0 · 2020 · External reference
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
10.1261/rna.075341.120 · 2020 · External reference
10.1146/annurev-biophys-070816-033920
10.1146/annurev-biophys-070816-033920 · External reference
Ribosomal frameshifting viral RNAs
10.1099/0022-1317-76-8-1885 · 1995 · External reference
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
2016 · External reference
Solution structure of the HIV-1 frameshift inducing stem-loop RNA
10.1093/nar/gkg654 · 2003 · External reference
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10.1016/0092-8674(89)90124-4 · External reference
Ribosomal pausing during translation of an RNA pseudoknot
1993 · External reference
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10.1038/nature04735 · External reference
10.1073/pnas.1204114109
10.1073/pnas.1204114109 · External reference
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10.1021/ja410344b · External reference
10.1101/2020.09.15.298604
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10.1101/2020.07.10.197079 · External reference
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10.1101/2020.06.29.178343 · External reference
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10.1093/nar/gkaa1053 · External reference
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In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs
2021 · External reference
10.1101/2020.06.15.153197
10.1101/2020.06.15.153197 · External reference
Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid
10.1016/j.molcel.2020.11.041 · 2020 · External reference
10.1093/nargab/lqab043
10.1093/nargab/lqab043 · External reference
A comprehensive analysis of cis-acting RNA elements in the SARS-CoV-2 genome by a bioinformatics approach
10.3389/fgene.2020.572702 · 2020 · External reference
Peptidyl-transferase inhibitors have antiviral properties by altering programmed -1 ribosomal frameshifting efficiencies: development of model systems
10.1073/pnas.94.13.6606 · 1997 · External reference
New targets for antivirals: the ribosomal A-site and the factors that interact with it
10.1006/viro.2002.1567 · 2002 · External reference
Identification of RNA pseudoknot-binding ligand that inhibits the -1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening
10.1021/ja1098325 · 2011 · External reference
10.1074/jbc.ac120.013449
10.1074/jbc.ac120.013449 · External reference
10.1021/acscentsci.0c00984
10.1021/acscentsci.0c00984 · External reference
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element
10.1016/j.bpj.2020.10.012 · 2021 · External reference
10.1073/pnas.0806929106
10.1073/pnas.0806929106 · External reference
10.1038/nprot.2018.010
10.1038/nprot.2018.010 · External reference
10.1093/nar/gkaa1013
10.1093/nar/gkaa1013 · External reference
10.1261/rna.076141.120
10.1261/rna.076141.120 · External reference
10.1016/j.molcel.2020.11.004
10.1016/j.molcel.2020.11.004 · External reference
10.1007/978-1-4419-6351-2
10.1007/978-1-4419-6351-2 · 2010 · External reference
Adventures with RNA graphs
10.1016/j.ymeth.2018.03.009 · 2018 · External reference
Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction
10.1093/nar/gkx045 · 2017 · External reference
RAG-Web: RNA structure prediction/design using RNA-As-Graphs
10.1093/bioinformatics/btz611 · 2020 · External reference
RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications Int
10.3390/ijms23169249 · 2022 · External reference
Graph, pseudoknot, and SARS-CoV-2 genomic RNA: A biophysical synthesis
10.1016/j.bpj.2021.01.030 · 2021 · External reference
10.1021/jacs.1c03003
10.1021/jacs.1c03003 · External reference
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression
10.1038/s41467-022-31353-w · 2022 · External reference
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning
10.1038/s41467-019-13395-9 · 2019 · External reference
10.1093/bioinformatics/btt509
10.1093/bioinformatics/btt509 · External reference
RNAcmap: A fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis
2021 · External reference
10.1093/bioinformatics/btab165
10.1093/bioinformatics/btab165 · External reference
10.1093/bioinformatics/btac421
10.1093/bioinformatics/btac421 · External reference
RNA backbone torsion and pseudotorsion angle prediction using dilated convolutional neural networks
10.1021/acs.jcim.1c00153 · 2021 · External reference
10.1093/bioinformatics/btaa652
10.1093/bioinformatics/btaa652 · External reference
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement
10.1038/s41467-021-23100-4 · 2021 · External reference
10.1126/science.abe5650
10.1126/science.abe5650 · External reference
10.1038/s41580-019-0136-0
10.1038/s41580-019-0136-0 · External reference
10.1038/s41565-019-0517-8
10.1038/s41565-019-0517-8 · External reference
10.1016/s1359-0278(96)00037-5
10.1016/s1359-0278(96)00037-5 · External reference
10.1038/s41579-018-0117-x
10.1038/s41579-018-0117-x · External reference
A modelling paradigm for RNA virus assembly
10.1016/j.coviro.2018.07.003 · 2018 · External reference
10.1146/annurev-biophys-052118-115611
10.1146/annurev-biophys-052118-115611 · External reference
10.1126/science.abg2822
10.1126/science.abg2822 · External reference
10.1016/j.virusres.2008.06.010
10.1016/j.virusres.2008.06.010 · External reference
Viral tRNAs and tRNA-like structures
10.1002/wrna.42 · 2010 · External reference
10.1126/science.abe8526
10.1126/science.abe8526 · External reference
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE
10.1021/ja043822v · 2005 · External reference
10.1101/2021.08.10.455819
10.1101/2021.08.10.455819 · External reference
10.1021/acs.jpcb.8b00575
10.1021/acs.jpcb.8b00575 · External reference
Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias
10.1021/acs.jpcb.0c11365 · 2021 · External reference
SHAPER: A web server for fast and accurate SHAPE reactivity prediction
10.3389/fmolb.2021.721955 · 2021 · External reference
10.1261/rna.1800210
10.1261/rna.1800210 · External reference
RNA 3D structure prediction using coarse-grained models
10.3389/fmolb.2021.720937 · 2021 · External reference
IsRNA: an iterative simulated reference state approach to modeling correlated interactions in RNA folding
10.1021/acs.jctc.7b01228 · 2018 · External reference
10.1021/acs.jctc.0c01148
10.1021/acs.jctc.0c01148 · External reference
10.1021/acs.jpcb.1c07288
10.1021/acs.jpcb.1c07288 · External reference
10.1016/j.jmb.2005.12.014
10.1016/j.jmb.2005.12.014 · External reference
10.1261/rna.026658.111
10.1261/rna.026658.111 · External reference
10.1021/jacs.5b07910
10.1021/jacs.5b07910 · External reference
Nanopore electric snapshots of an RNA tertiary folding pathway
10.1038/s41467-017-01588-z · 2017 · External reference
10.1021/acs.jpcb.8b04249
10.1021/acs.jpcb.8b04249 · External reference
Cotranscriptional folding kinetics of ribonucleic acid secondary structures
10.1063/1.3671644 · 2011 · External reference
RLDOCK: A New Method for Predicting RNA-Ligand Interactions
10.1021/acs.jctc.0c00798 · 2020 · External reference
10.1016/j.ymeth.2021.01.009
10.1016/j.ymeth.2021.01.009 · External reference
RNA-ligand molecular docking: Advances and challenges
2021 · External reference
Analytical modeling and deep learning approaches to estimating RNA SHAPE reactivity from 3D structure
10.4310/cis.2019.v19.n3.a4 · 2019 · External reference
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10.1002/wrna.1349 · External reference
10.3390/nano9050681
10.3390/nano9050681 · External reference
10.1021/acs.chemrev.7b00427
10.1021/acs.chemrev.7b00427 · External reference
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions
10.1016/j.str.2010.10.006 · 2011 · External reference
Atomic-resolution structural information from scattering experiments on macromolecules in solution
10.1103/physreve.87.052712 · 2013 · External reference
10.1016/j.bpj.2014.06.006
10.1016/j.bpj.2014.06.006 · External reference
Exploring RNA structure and dynamics through enhanced sampling simulations
10.1016/j.sbi.2018.01.004 · 2018 · External reference
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10.1093/nar/gkab459 · External reference
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10.1107/s1600576719002450 · External reference
Using the maximum entropy principle to combine simulations and solution experiments
10.3390/computation6010015 · 2018 · External reference
10.1126/sciadv.abf6106
10.1126/sciadv.abf6106 · External reference
10.1016/j.sbi.2019.12.016
10.1016/j.sbi.2019.12.016 · External reference
10.1021/acs.chemrev.7b00427
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RNA dynamics: it is about time
10.1016/j.sbi.2008.04.004 · 2008 · External reference
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Force-extension formula for the worm-like chain model from a variational principle
10.1016/j.jtbi.2009.10.009 · 2010 · External reference
10.1016/j.addr.2022.114316
10.1016/j.addr.2022.114316 · External reference
Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser
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Intercellular and systemic spread of RNA and RNAi in plants
10.1002/wrna.1160 · 2013 · External reference
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Conformation of an RNA pseudoknot
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Induced fit in RNA-protein recognition
10.1038/79575 · 2000 · External reference
10.1146/annurev-genom-120219-073756
10.1146/annurev-genom-120219-073756 · External reference
The determination of RNA folding nearest neighbor parameters
10.1007/978-1-62703-709-9_3 · 2014 · External reference
10.1101/cshperspect.a003608
10.1101/cshperspect.a003608 · External reference
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10.1038/nnano.2010.231 · External reference
Locking and unlocking thrombin function using immunoquiescent nucleic acid nanoparticles with regulated retention in vivo
10.1021/acs.nanolett.2c02019 · 2022 · External reference
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10.1016/j.jsb.2019.06.005 · External reference
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10.1093/nar/gkt801 · External reference
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10.1021/acssynbio.1c00336 · External reference
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Simultaneous silencing of lysophosphatidylcholine acyltransferases 1–4 by nucleic acid nanoparticles (NANPs) improves radiation response of melanoma cells
10.1016/j.nano.2021.102418 · 2021 · External reference
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10.3390/molecules26030652 · External reference
Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles
10.1038/s41596-020-0393-6 · 2020 · External reference
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10.1093/nar/gkaa908 · External reference
10.1093/nar/gky1215
10.1093/nar/gky1215 · External reference
RNA fibers as optimized nanoscaffolds for siRNA coordination and reduced immunological recognition
10.1002/adfm.201805959 · 2018 · External reference
Functionally-interdependent shape-switching nanoparticles with controllable properties
2017 · External reference
Programmable nucleic acid based polygons with controlled neuroimmunomodulatory properties for predictive QSAR modeling
10.1002/smll.201701255 · 2017 · External reference
Expanding structural space for immunomodulatory nucleic acid nanoparticles via spatial arrangement of their therapeutic moieties
10.1002/adfm.202205581 · 2022 · External reference
Programmable DNA-augmented hydrogels for controlled activation of human lymphocytes
2021 · External reference
10.1021/acsami.1c09230
10.1021/acsami.1c09230 · External reference
Toll-like receptor-mediated recognition of nucleic acid nanoparticles (NANPs) in human primary blood cells
10.3390/molecules24061094 · 2019 · External reference
