Real Time SPR Assessment of the Structural Changes of Adaptive Dynamic Constitutional Frameworks as a New Route for Sensing

Cross linked gold-dynamic constitutional frameworks (DCFs) are functional materials of potential relevance for biosensing applications, given their adaptivity and high responsivity against various external stimuli (such as pH, temperature) or specific interactions with biomolecules (enzymes or DNA) via internal constitutional dynamics. However, characterization and assessment of their dynamic conformational changes in response to external stimuli has never been reported. This study proves the capability of Surface Plasmon Resonance (SPR) assays to analyse the adaptive structural modulation of a functional matrix encompassing 3D gold-dynamic constitutional frameworks (Au-DCFs) when exposed to pH variations, as external stimuli. We analyse Au-DCFs formed from Au nanoparticles, (AuNP) connected through constitutionally dynamic polymers, dynamers, with multiple functionalities. For increased generality of this proof-of-concept assay, Au-DCFs, involving DCFs designed from 1,3,5-benzene-tricarbaldehyde (BTA) connecting centres and polyethylene glycol (PEG) connectors, are covalently attached to standard SPR sensing chips (Au nanolayers, carboxyl terminated or with carboxymethyl dextran, CMD top-layer) and analysed using state-of-the art SPR instrumentation. The SPR effects of the distance from the Au-DCFs matrix to the Au nanolayer of the sensing chip, as well as of Au-DCFs thickness were investigated. This study reveals the SPR response, augmented by the AuNP, to the conformational change, i.e., shrinkage, of the dynamer and AuNP matrix when decreasing the pH, and provides an unexplored insight into the sensing applicability of SPR real-time analysis of adaptive functional materials.

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Real-time analysis of RAG complex activity in V(D)J recombination

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1606721113 ◽

2016 ◽

Vol 113 (42) ◽

pp. 11853-11858 ◽

Cited By ~ 9

Author(s):

Jennifer Zagelbaum ◽

Noriko Shimazaki ◽

Zitadel Anne Esguerra ◽

Go Watanabe ◽

Michael R. Lieber ◽

...

Keyword(s):

Real Time ◽

Single Molecule ◽

Conformational Changes ◽

Signal Sequence ◽

High Mobility ◽

Time Analysis ◽

Complex Activity ◽

Synaptic Complex ◽

Single Molecule Fret ◽

Real Time Analysis

Single-molecule FRET (smFRET) and single-molecule colocalization (smCL) assays have allowed us to observe the recombination-activating gene (RAG) complex reaction mechanism in real time. Our smFRET data have revealed distinct bending modes at recombination signal sequence (RSS)-conserved regions before nicking and synapsis. We show that high mobility group box 1 (HMGB1) acts as a cofactor in stabilizing conformational changes at the 12RSS heptamer and increasing RAG1/2 binding affinity for 23RSS. Using smCL analysis, we have quantitatively measured RAG1/2 dwell time on 12RSS, 23RSS, and non-RSS DNA, confirming a strict RSS molecular specificity that was enhanced in the presence of a partner RSS in solution. Our studies also provide single-molecule determination of rate constants that were previously only possible by indirect methods, allowing us to conclude that RAG binding, bending, and synapsis precede catalysis. Our real-time analysis offers insight into the requirements for RSS–RSS pairing, architecture of the synaptic complex, and dynamics of the paired RSS substrates. We show that the synaptic complex is extremely stable and that heptamer regions of the 12RSS and 23RSS substrates in the synaptic complex are closely associated in a stable conformational state, whereas nonamer regions are perpendicular. Our data provide an enhanced and comprehensive mechanistic description of the structural dynamics and associated enzyme kinetics of variable, diversity, and joining [V(D)J] recombination.

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Classification Connection of Twitter Data using K-Means Clustering

International Journal of Innovative Technology and Exploring Engineering - Special Issue ◽

10.35940/ijitee.f1004.0486s419 ◽

2019 ◽

Vol 8 (6S4) ◽

pp. 14-22

Keyword(s):

Social Media ◽

Real Time ◽

Clustering Methods ◽

Time Analysis ◽

Data Set ◽

Dynamic Data ◽

Real Time Analysis ◽

Twitter Data ◽

Social Media Platforms ◽

Insight Into

The rise of social media platforms like Twitter and the increasing adoption by people in order to stay connected provide a large source of data to perform analysis based on the various trends, events and even various personalities. Such analysis also provides insight into a person’s likes and inclinations in real time independent of the data size. Several techniques have been created to retrieve such data however the most efficient technique is clustering. This paper provides an overview of the algorithms of the various clustering methods as well as looking at their efficiency in determining trending information. The clustered data may be further classified by topics for real time analysis on a large dynamic data set. In this paper, data classification is performed and analyzed for flaws followed by another classification on the same data set.

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Flexible sample cell for real-time GISAXS, GIWAXS and XRR: design and construction

Journal of Synchrotron Radiation ◽

10.1107/s1600577518013218 ◽

2018 ◽

Vol 25 (6) ◽

pp. 1664-1672 ◽

Cited By ~ 4

Author(s):

M. Berlinghof ◽

C. Bär ◽

D. Haas ◽

F. Bertram ◽

S. Langner ◽

...

Keyword(s):

Thin Films ◽

Real Time ◽

Structural Changes ◽

Functional Materials ◽

Grazing Incidence ◽

Ex Situ ◽

Sample Cell ◽

Solvent Vapor ◽

Vapor Annealing ◽

Solvent Vapor Annealing

Since the properties of functional materials are highly dependent on their specific structure, and since the structural changes, for example during crystallization, induced by coating and annealing processes are significant, the study of structure and its formation is of interest for fundamental and applied science. However, structure analysis is often limited to ex situ determination of final states due to the lack of specialized sample cells that enable real-time investigations. The lack of such cells is mainly due to their fairly complex design and geometrical restrictions defined by the beamline setups. To overcome this obstacle, an advanced sample cell has been designed and constructed; it combines automated doctor blading, solvent vapor annealing and sample hydration with real-time grazing-incidence wide- and small-angle scattering (GIWAXS/GISAXS) and X-ray reflectivity (XRR). The sample cell has limited spatial requirements and is therefore widely usable at beamlines and laboratory-scale instruments. The cell is fully automatized and remains portable, including the necessary electronics. In addition, the cell can be used by interested scientists in cooperation with the Institute for Crystallography and Structural Physics and is expandable with regard to optical secondary probes. Exemplary research studies are presented, in the form of coating of P3HT:PC61PM thin films, solvent vapor annealing of DRCN5T:PC71BM thin films, and hydration of supported phospholipid multilayers, to demonstrate the capabilities of the in situ cell.

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Perovskite processing for photovoltaics: a spectro-thermal evaluation

Journal of Materials Chemistry A ◽

10.1039/c4ta04725g ◽

2014 ◽

Vol 2 (45) ◽

pp. 19338-19346 ◽

Cited By ~ 70

Author(s):

Alice E. Williams ◽

Peter J. Holliman ◽

Matthew J. Carnie ◽

Matthew L. Davies ◽

David A. Worsley ◽

...

Keyword(s):

Real Time ◽

Chemical Species ◽

Material Composition ◽

Time Analysis ◽

Real Time Analysis ◽

Solvent Retention ◽

Insight Into

A real-time analysis by STA-FTIR of changes occurring and volatiles evolved during processing of perovskites for PV technology. Solvent retention, presence of chemical species and decomposition of materials can be evaluated to gain insight into material composition.

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Real-time analysis of Pd2(dba)3 activation by phosphine ligands

Chemical Communications ◽

10.1039/c6cc08824d ◽

2017 ◽

Vol 53 (5) ◽

pp. 854-856 ◽

Cited By ~ 19

Author(s):

Eric Janusson ◽

Harmen S. Zijlstra ◽

Peter P. T. Nguyen ◽

Landon MacGillivray ◽

Julio Martelino ◽

...

Keyword(s):

Real Time ◽

Active Species ◽

Phosphine Ligands ◽

Time Analysis ◽

Esi Ms ◽

Real Time Analysis ◽

Insight Into

Real-time UV-Vis/ESI-MS monitoring of Pd2(dba)3 activation provides insight into active species and the effect of activation protocol on their formation.

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Vibrational Study on Structure and Bioactivity of Protein Fibers Grafted with Phosphorylated Methacrylates

Molecules ◽

10.3390/molecules26216487 ◽

2021 ◽

Vol 26 (21) ◽

pp. 6487

Author(s):

Michele Di Di Foggia ◽

Masuhiro Tsukada ◽

Paola Taddei

Keyword(s):

Conformational Changes ◽

Structural Changes ◽

Raman Band ◽

Functional Materials ◽

Fold Increase ◽

Oxidation Products ◽

Cysteic Acid ◽

Silk Fibers ◽

Phosphate Phase ◽

Wool Keratin

In the last decades, silk fibroin and wool keratin have been considered functional materials for biomedical applications. In this study, fabrics containing silk fibers from Bombyx mori and Tussah silk fibers from Antheraea pernyi, as well as wool keratin fabrics, were grafted with phosmer CL and phosmer M (commercial names, i.e., methacrylate monomers containing phosphate groups in the molecular side chain) with different weight gains. Both phosmers were recently proposed as flame retarding agents, and their chemical composition suggested a possible application in bone tissue engineering. IR and Raman spectroscopy were used to disclose the possible structural changes induced by grafting and identify the most reactive amino acids towards the phosmers. The same techniques were used to investigate the nucleation of a calcium phosphate phase on the surface of the samples (i.e., bioactivity) after ageing in simulated body fluid (SBF). The phosmers were found to polymerize onto the biopolymers efficiently, and tyrosine and serine underwent phosphorylation (monitored through the strengthening of the Raman band at 1600 cm−1 and the weakening of the Raman band at 1400 cm−1, respectively). In grafted wool keratin, cysteic acid and other oxidation products of disulphide bridges were detected together with sulphated residues. Only slight conformational changes were observed upon grafting, generally towards an enrichment in ordered domains, suggesting that the amorphous regions were more prone to react (and, sometimes, degrade). All samples were shown to be bioactive, with a weight gain of up to 8%. The most bioactive samples contained the highest phosmers amounts, i.e., the highest amounts of phosphate nucleating sites. The sulphate/sulphonate groups present in grafted wool samples appeared to increase bioactivity, as shown by the five-fold increase of the IR phosphate band at 1040 cm−1.

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An Interactive Minicomputer Program for the Indexing and Simulation of Electron Diffraction Patterns

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100092670 ◽

1976 ◽

Vol 34 ◽

pp. 542-543

Author(s):

R.P. Goehner ◽

W.T. Hatfield ◽

Prakash Rao

Keyword(s):

Electron Diffraction ◽

Real Time ◽

Pattern Analysis ◽

Flow Diagram ◽

Hard Copy ◽

Time Analysis ◽

Real Time Analysis ◽

Transmission Electron ◽

One Step ◽

Diffraction Patterns

Computer programs are now available in various laboratories for the indexing and simulation of transmission electron diffraction patterns. Although these programs address themselves to the solution of various aspects of the indexing and simulation process, the ultimate goal is to perform real time diffraction pattern analysis directly off of the imaging screen of the transmission electron microscope. The program to be described in this paper represents one step prior to real time analysis. It involves the combination of two programs, described in an earlier paper(l), into a single program for use on an interactive basis with a minicomputer. In our case, the minicomputer is an INTERDATA 70 equipped with a Tektronix 4010-1 graphical display terminal and hard copy unit.A simplified flow diagram of the combined program, written in Fortran IV, is shown in Figure 1. It consists of two programs INDEX and TEDP which index and simulate electron diffraction patterns respectively. The user has the option of choosing either the indexing or simulating aspects of the combined program.

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Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100128833 ◽

1987 ◽

Vol 45 ◽

pp. 910-911

Author(s):

M. Boublik ◽

V. Mandiyan ◽

J.F. Hainfeld ◽

J.S. Wall

Keyword(s):

16S Rrna ◽

Conformational Changes ◽

Ribosomal Proteins ◽

Structural Changes ◽

Ribosomal Subunit ◽

Compact Structure ◽

E Coli ◽

Freeze Dried ◽

16S Rna ◽

30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

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