Directional mechanical stability of Bacteriophage φ29 motor’s 3WJ-pRNA: Extraordinary robustness along portal axis

Xu, Zhonghe; Sun, Yongtao; Weber, Jeffrey K.; Cao, Yi; Wang, Wei; Jasinski, Daniel L.; Guo, Peixuan; Zhou, Ruhong; Li, Jinyuan

doi:10.1126/sciadv.1601684

Cited by 17 publications

(39 citation statements)

References 58 publications

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“…These findings support the claim that pRNA 3WJ assembly was governed more by entropy (Binzel et al 2014(Binzel et al , 2016a. Furthermore, this robust RNA 3WJ stays intact at ultralow concentration, is resistant to a high molar urea denaturation (Shu et al 2011), and also remains stable under high mechanical rupture forces (Xu et al 2017). In addition, substituting uridine and cytidine with their 2 ′ -fluoro-modified counterparts further increases nanoparticle stability and prevents digestion by RNases (Layzer et al 2004).…”

Section: Introductionsupporting

confidence: 76%

Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2′-F RNA, and LNA in the context of Phi29 pRNA 3WJ

Piao

Wang²,

Binzel³

et al. 2017

RNA

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The question of whether RNA is more stable or unstable compared to DNA or other nucleic acids has long been a subject of extensive scrutiny and public attention. Recently, thermodynamically stable and degradation-resistant RNA motifs have been utilized in RNA nanotechnology to build desired architectures and integrate multiple functional groups. Here we report the effects of phosphorothioate deoxyribonucleotides (PS-DNA), deoxyribonucleotides (DNA), ribonucleotides (RNA), 2'-F nucleotides (2'-F), and locked nucleic acids (LNA) on the thermal and in vivo stability of the three-way junction (3WJ) of bacteriophage phi29 motor packaging RNA. It was found that the thermal stability gradually increased following the order of PS-DNA/PS-DNA < DNA/DNA < DNA/RNA < RNA/RNA < RNA/2'-F RNA < 2'-F RNA/2'-F RNA < 2'-F RNA/LNA < LNA/LNA. This proposition is supported by studies on strand displacement and the melting of homogeneous and heterogeneous 3WJs. By simply mixing different chemically modified oligonucleotides, the thermal stability of phi29 pRNA 3WJ can be tuned to cover a wide range of melting temperatures from 21.2°C to over 95°C. The 3WJ was resistant to boiling temperature denaturation, urea denaturation, and 50% serum degradation. Intravenous injection of fluorescent LNA/2'-F hybrid 3WJs into mice revealed its exceptional in vivo stability and presence in urine. It is thus concluded that incorporation of LNA nucleotides, alone or in combination with 2'-F, into RNA nanoparticles derived from phi29 pRNA 3WJ can extend the half-life of the RNA nanoparticles in vivo and improve their pharmacokinetics profile.

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Section: Introductionsupporting

confidence: 76%

Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2′-F RNA, and LNA in the context of Phi29 pRNA 3WJ

Piao

Wang²,

Binzel³

et al. 2017

RNA

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“…The ZIKV xrRNA1 (PDB code: 5TPY) was used in our simulations 14 . RNA was subjected to equilibrium simulations in an isolated system, following the similar protocol in the previous study 6 . After 100 ns equilibrium simulations without any restraint, the equilibriumed RNA configuration along with the water in first hydration shell (the cutoff distance is 3.5 Å) was extracted to be used as a starting structure for subsequent simulations.…”

Section: Methodsmentioning

confidence: 99%

“…For many nucleic acids, mechanical anisotropy is an inherent property which mechanical behavior varies with the direction of applied forces and is of high biological significance. For instance, the three-way-junction (3WJ)-pRNA derived from φ29 DNA packaging motor has been shown to exhibit high mechanical anisotropy upon Mg 2+ binding, which relates to its capability to withstand the strain caused by DNA condensation 5 , 6 . The mechanical anisotropy of the human telomeric DNA G-quadruplex can be changed by ligand binding, corresponding to its regulation on replication or transcription 7 .…”

Section: Introductionmentioning

confidence: 99%

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Niu

Liu

et al. 2020

Nat Commun

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“…For core structure of HCV-IRES, the tetraloop receptor which acts as crystallization module was removed in our studies, to better characterize the mechanical properties of the ring-like structure. These RNAs were subjected to equilibrium simulations in an isolated system, following the similar protocol in the previous study 56 . After 100ns equilibrium simulations without any restraint, the equilibriumed RNA configuration along with the water in first hydration shell (the cutoff distance is 3.5 Å), was extracted to be used as a starting structure for subsequent simulations.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Niu

Liu

et al. 2020

Preprint

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Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg 2+ and the key tertiary interactions. The absence of Mg 2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structure in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations on ZIKV xrRNA1 and another two RNAs with ring structures, the HCV IRES and THF riboswitch. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.RNAs' diverse roles in many cellular processes are dictated by their propensities to fold into stable three-dimensional structures driven by numerous tertiary interactions 1, 2 . These tertiary interactions are important to RNAs' structure, stability, dynamics, and folding kinetics 3 . While RNA folds into stable structure as it is synthesized, it undergoes unfolding and refolding events during many cellular processes such as translation, replication, reverse transcription, etc., during which molecular motors exert forces on the RNA in a directional manner (i.e. ribosome proceeds along the RNA template in the 5'→3' direction) 4 . For many nucleic acids, mechanical anisotropy is an inherent property which mechanical behavior varies with the direction of applied forces and is of high biological significance. For instance, the three-wayjunction-pRNA derived from φ29 DNA packaging motor has been shown to exhibit high mechanical anisotropy upon Mg 2+ binding, which relates to its capability to withstand the strain caused by DNA condensation 5, 6 . The mechanical anisotropy of the human telomeric DNA G-quadruplex can be changed by ligand binding, corresponding to its regulation on replication or transcription 7 . Understanding how RNA responds to a mechanical stretching force and the molecular mechanisms defining its mechanical anisotropy is important for not only elucidating key principles governing various mechano-biological processes but developing novel RNA-based biomaterials with tailored mechanical properties and RNA-targeted therapeutics 8 , thus, has been an important research topic in the field of RNA mechanics 9 .Exoribonuclease-resistant RNAs (xrRNAs) are a group of RNA elements which are capable of resisting the degradation by exonuclease 10, 11 . The ability to resist Xrn1 is surprising as Xrn1 is capable of processively degrading highly structured RNAs 12 . Recent crystal structures of xrRNAs from Murray Valley encephalitis virus (MVE...

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Directional mechanical stability of Bacteriophage φ29 motor’s 3WJ-pRNA: Extraordinary robustness along portal axis

Abstract: φ29 motor’s three-way junction serves as an effective connecting rod through its superb rigidity in the coaxial direction.

Cited by 17 publications

References 58 publications

Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2′-F RNA, and LNA in the context of Phi29 pRNA 3WJ

Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2′-F RNA, and LNA in the context of Phi29 pRNA 3WJ

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

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