Profiling single-molecule reaction kinetics under nanopore confinement

The development of single-molecule reaction inside nanoconfinement is benefit to study the intrinsic molecular mechanism of a complex chemical reaction. However, the reaction kinetics model of single-molecule reaction inside confinement remains elusive. Herein we engineered the Aerolysin nanopore reactor to elaborate the single-molecule reaction kinetics inside nanoconfinement. By identifying bond forming and non-forming events directly, a four-state kinetics model is proposed for the first time. Our results demonstrated that the single-molecule reaction kinetics inside a nanopore depends on the voltage-dependent frequency of captured individual reactant and the fraction of effective collision inside nanopore confined space. This new insight will guide the design of nanoconfinement for resolving the single-molecule chemistry, and shed light on the mechanistic understanding of dynamic covalent chemistry in-side a nanopore

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Single Molecule Reaction Kinetics within Femtoliter Volume Containers

Biophysical Journal ◽

10.1016/j.bpj.2008.12.3176 ◽

2009 ◽

Vol 96 (3) ◽

pp. 602a

Author(s):

Ana Jofre ◽

Ben Faulk ◽

Shira Stav

Keyword(s):

Reaction Kinetics ◽

Single Molecule ◽

Molecule Reaction

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Towards a full quantitative description of single-molecule reaction kinetics in biological cells

Physical Chemistry Chemical Physics ◽

10.1039/c8cp02043d ◽

2018 ◽

Vol 20 (24) ◽

pp. 16393-16401 ◽

Cited By ~ 26

Author(s):

Denis S. Grebenkov ◽

Ralf Metzler ◽

Gleb Oshanin

Keyword(s):

Single Molecule ◽

First Passage Time ◽

Quantitative Description ◽

Threshold Value ◽

Mathematical Concept ◽

Passage Time ◽

Molecule Reaction ◽

Cylindrical Annulus ◽

The Moment ◽

First Time

The first-passage time (FPT), i.e., the moment when a stochastic process reaches a given threshold value for the first time, is a fundamental mathematical concept with immediate applications. We present a robust explicit approach for obtaining the full distribution of FPT to a partially reactive target in a cylindrical-annulus domain.

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Formation and Trapping of the Thermodynamically Unfavoured Inverted-Hemicucurbit[6]uril

10.26434/chemrxiv.7977566 ◽

2019 ◽

Author(s):

Elena Prigorchenko ◽

Sandra Kaabel ◽

Triin Narva ◽

Anastassia Baškir ◽

Maria Fomitšenko ◽

...

Keyword(s):

Complex Formation ◽

Combinatorial Chemistry ◽

Trifluoroacetic Acid ◽

Chloride Anion ◽

Binding Affinities ◽

Dynamic Covalent Chemistry ◽

Reaction Selectivity ◽

Low Concentration ◽

Dynamic Combinatorial Chemistry ◽

First Time

Amplification of a thermodynamically unfavoured macrocyclic product through the directed shift of the equilibrium between dynamic covalent chemistry library members is difficult to achieve. We show for the first time that during condensation of formaldehyde and cis-N,N'-cyclohexa-1,2-diylurea formation of inverted-cis-cyclohexanohemicucurbit[6]uril (i-cis-cycHC[6]) can be induced at the expense of thermodynamically favoured cis-cyclohexanohemicucurbit[6]uril (cis-cycHC[6]). The formation of i-cis-cycHC[6] is enhanced in low concentration of the templating chloride anion and suppressed in excess of this template. We found that reaction selectivity is governed by the solution-based template-aided dynamic combinatorial chemistry and continuous removal of the formed cycHC[6] macrocycles from the equilibrating solution by precipitation. Notably, the i-cis-cycHC[6] was isolated with 33% yield. Different binding affinities of three diastereomeric i-cis-, cis-cycHC[6] and their chiral isomer (R,R)-cycHC[6] for trifluoroacetic acid demonstrate the influence of macrocycle geometry on complex formation.

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Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽

10.3390/genes10060481 ◽

2019 ◽

Vol 10 (6) ◽

pp. 481 ◽

Cited By ~ 1

Author(s):

Chen ◽

Lin ◽

Xie ◽

Zhong ◽

Zhang ◽

...

Keyword(s):

Insecticide Resistance ◽

Single Molecule ◽

Functional Categories ◽

Genetic Studies ◽

Sequencing Technologies ◽

Clusters Of Orthologous Groups ◽

Long Read ◽

Main Gene ◽

First Time ◽

Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

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The synthesis of polymeric dyes based on waterborne polyurethane: a reaction kinetics study using UV absorption spectroscopy

New Journal of Chemistry ◽

10.1039/c9nj05490a ◽

2020 ◽

Vol 44 (7) ◽

pp. 2930-2940 ◽

Cited By ~ 1

Author(s):

Jun Zhu ◽

Jie Li ◽

Chao Sang ◽

Yunjun Luo

Keyword(s):

Reaction Kinetics ◽

Absorption Spectroscopy ◽

Waterborne Polyurethane ◽

Uv Absorption ◽

Kinetics Study ◽

Uv Absorption Spectroscopy ◽

First Time ◽

Polymeric Dyes

The preparation of waterborne polyurethane based polymeric dyes (DWPU) with anthraquinone chromophores was monitored by using UV absorption spectroscopy for the first time.

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BAX requires VDAC2 to mediate apoptosis and to limit tumor development

10.1101/266668 ◽

2018 ◽

Author(s):

Hui San Chin ◽

Mark F. van Delft ◽

Robert L. Ninnis ◽

Mark X. Li ◽

Iris K. L. Tan ◽

...

Keyword(s):

Tumor Development ◽

Anion Channel ◽

Tumor Formation ◽

Cytotoxic Action ◽

Voltage Dependent Anion Channel ◽

Genome Wide ◽

Anti Cancer ◽

Voltage Dependent ◽

Genetic Deletion ◽

First Time

AbstractIntrinsic apoptosis is critical for normal physiology including the prevention of tumor formation. BAX and BAK are essential for mediating this process and for the cytotoxic action of many anticancer drugs. BAX and BAK are thought to act in a functionally redundant manner and are considered to be regulated similarly. From an unbiased genome-wide CRISPR/Cas9 screen, we identified VDAC2 (voltage-dependent anion channel 2) as essential for BAX, but not BAK, to function. The genetic deletion of VDAC2 abrogated the association of BAX and BAK with mitochondrial complexes that contain VDAC1, VDAC2 and VDAC3. By disrupting its localization to mitochondria, BAX is rendered completely ineffective. Moreover, we defined an interface unique to VDAC2 that is required to drive BAX activity. Consequently, interfering with this interaction or deleting VDAC2 phenocopied the loss of BAX, including impairing the killing of tumor cells by anti-cancer agents such as the BCL-2 inhibitor venetoclax. Furthermore, the ability of BAX to prevent tumor formation was attenuated in the absence of VDAC2. Taken together, our studies show for the first time that BAX-mediated apoptosis, but not BAK-mediated apoptosis, is critically dependent on VDAC2, hence revealing the differential regulation of BAX and BAK.

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PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings

Frontiers in Genetics ◽

10.3389/fgene.2021.635043 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fiza Liaquat ◽

Muhammad Farooq Hussain Munis ◽

Samiah Arif ◽

Urooj Haroon ◽

Jianxin Shi ◽

...

Keyword(s):

Single Molecule ◽

Gene Annotation ◽

Treated Group ◽

Full Length ◽

Open Reading Frames ◽

Interacting Protein ◽

Schima Superba ◽

Long Read ◽

First Time ◽

Potential Tool

Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT), and Coding Non-Coding Index (CNCI) databases and observed 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba.

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Modelling reaction kinetics inside cells

Essays in Biochemistry ◽

10.1042/bse0450041 ◽

2008 ◽

Vol 45 ◽

pp. 41-56 ◽

Cited By ~ 56

Author(s):

Ramon Grima ◽

Santiago Schnell

Keyword(s):

Molecular Biology ◽

Reaction Kinetics ◽

Single Molecule ◽

Predictive Accuracy ◽

Reaction Pathway ◽

Imaging Techniques ◽

Deterministic Models ◽

Non Invasive ◽

The Past ◽

Fundamental Length

In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this chapter we review four distinct theoretical and simulation frameworks: (i) non-spatial and deterministic, (ii) spatial and deterministic, (iii) non-spatial and stochastic and (iv) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models.

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