Accelerating chemical reactions by molecular sledding

Zhang, Lei; Zheng, Lifei; Meng, Zhuojun; Balinin, Konstantin; Loznik, Mark; Herrmann, Andreas

doi:10.1039/c7cc02500a

Cited by 6 publications

(5 citation statements)

References 32 publications

(10 reference statements)

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“…At the highest ratio of 3,200, the sliders bind to different tracks, yet the reaction rate still shows a 100-fold increase, thus strongly indicating that sliders can hop between tracks, because diffusion along the tracks alone should lead to a decrease in the reaction rate. Taken together, these results demonstrate the principle of diffusive binding, and its potential of reducing the dimensionality of the system and hence increasing the effective molarity of reactants [29][30][31] .…”

Section: Catalytic Transport Of Molecular Cargo Using Diffusive Bindi...supporting

confidence: 53%

“…Figure 3a shows an example of 200 ns trajectories of slider 2 diffusing on a pArg track (for other combinations, see Supplementary Figs. [31][32][33]. The sliders indeed form the expected ion pairs between the negatively charged carboxylate/phosphate residues on the sliders, and positively charged guanidinium/ammonium groups on the polymer tracks (Fig.…”

Section: Molecular Dynamic Simulations Of Sliders On Polycationic Tracksmentioning

confidence: 75%

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Catalytic transport of molecular cargo using diffusive binding along a polymer track

et al. 2019

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Article 25fa pilot End User AgreementThis publication is distributed under the terms of Article 25fa of the Dutch Copyright Act (Auteurswet) with explicit consent by the author. Dutch law entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work.This publication is distributed under The Association of Universities in the Netherlands (VSNU) 'Article 25fa implementation' pilot project. In this pilot research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication.You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited.If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website.

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Section: Catalytic Transport Of Molecular Cargo Using Diffusive Bindi...supporting

confidence: 53%

Section: Molecular Dynamic Simulations Of Sliders On Polycationic Tracksmentioning

confidence: 75%

Catalytic transport of molecular cargo using diffusive binding along a polymer track

et al. 2019

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“…These are preceded by helix-breaking residue or separated by several residues. Molecular sleds, which have been shown to slide along DNA ( Zhang et al, 2017a ) and may influence interactions with it, consist of spans of arginines or lysines or combinations of these. The inclusion of NLS sequences in the CPP would be beneficial if the peptide and its associated cargo must reach the nucleus.…”

Section: Introductionmentioning

confidence: 99%

Cell-Penetrating Peptides Predicted From CASC3, AKIP1, and AHRR Proteins

et al. 2021

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Peptides can be used as research tools and for diagnostic or therapeutic applications. Peptides, alongside small molecules and antibodies, are used and are gaining further interest as protein-protein interaction (PPI) modulators. Peptides have high target specificity and high affinity, but, unlike small molecule modulators, they are not able to cross the cell membranes to reach their intracellular targets. To overcome this limitation, the special property of the cell-penetrating peptides (CPPs) could benefit their cause. CPPs are a class of peptides that can enter the cells and with them also deliver the attached cargoes. Today, with the advancement of in silico prediction tools and the availability of protein databases, designing new and multifunctional peptides that are able to reach intracellular targets and inhibit certain cellular processes in a very specific manner is reachable. Although there are several efficient CPP sequences already known, the discovery of new CPPs is crucial for the development of efficient delivery methods for both biotechnological and therapeutic applications. In this work, we chose 10 human nuclear proteins from which we predicted new potential CPP sequences by using three different CPP predictors: cell-penetrating peptide prediction tool, CellPPD, and SkipCPP-Pred. From each protein, one predicted CPP sequence was synthesized and its internalization into cells was assessed. Out of the tested sequences, three peptides displayed features characteristic to CPPs. These peptides and also the predicted peptide sequences could be used to design and modify new CPPs. In this work, we show that we can use protein sequences as input for generating new peptides with cell internalization properties. Three new CPPs, AHRR8-24, CASC3251-264, and AKIP127-37, can be further used for the delivery of other cargoes or designed into multifunctional peptides with capability of internalizing cells.

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“…It is now known that many proteins involved in gene regulation, nucleic acid metabolism, and other processes are capable of sliding on DNA 2 3 4 5 6 7 8 9 . Furthermore, recent studies reported that even small peptides can bind to and slide on DNA, with the ability to carry a cargo; for example, a protein molecule or PCR primer, along DNA 10 11 12 13 14 .…”

Section: Introductionmentioning

confidence: 99%

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Xiong

Blainey

2017

JoVE

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We describe a simple, robust and high throughput single molecule flow-stretching assay for studying 1D diffusion of molecules along DNA. In this assay, glass coverslips are functionalized in a one-step reaction with silane-PEG-biotin. Flow cells are constructed by sandwiching an adhesive tape with pre-cut channels between a functionalized coverslip and a PDMS slab containing inlet and outlet holes. Multiple channels are integrated into one flow cell and the flow of reagents into each channel can be fully automated, which significantly increases the assay throughput and reduces hands-on time per assay. Inside each channel, biotin-λ-DNAs are immobilized on the surface and a laminar flow is applied to flow-stretch the DNAs. The DNA molecules are stretched to >80% of their contour length and serve as spatially extended templates for studying the binding and transport activity of fluorescently labeled molecules. The trajectories of single molecules are tracked by time-lapse Total Internal Reflection Fluorescence (TIRF) imaging. Raw images are analyzed using streamlined custom single particle tracking software to automatically identify trajectories of single molecules diffusing along DNA and estimate their 1D diffusion constants.

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Accelerating chemical reactions by molecular sledding

Cited by 6 publications

References 32 publications

Catalytic transport of molecular cargo using diffusive binding along a polymer track

Catalytic transport of molecular cargo using diffusive binding along a polymer track

Cell-Penetrating Peptides Predicted From CASC3, AKIP1, and AHRR Proteins

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

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