scholarly journals A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA

2021 ◽  
Vol 22 (8) ◽  
pp. 3813
Author(s):  
Thomas Carzaniga ◽  
Giuliano Zanchetta ◽  
Elisa Frezza ◽  
Luca Casiraghi ◽  
Luka Vanjur ◽  
...  
Keyword(s):  
Energy Gap ◽  
Consensus Sequence ◽  
Interaction Strength ◽  
Label Free ◽  
Nonspecific Binding ◽  
Potential Wells ◽  
Double Stranded Dna ◽  
Equilibrium And Kinetics ◽  
Nonspecific Interactions ◽  
Dynamics Simulations

Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding—equilibrium and kinetics—by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4–DNA interactions. We found a strong enthalpy–entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.

scholarly journals The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

2021 ◽  
Vol 7 (17) ◽  
pp. eabf6106
Author(s):  
Weiwei He ◽  
Yen-Lin Chen ◽  
Lois Pollack ◽  
Serdal Kirmizialtin
Keyword(s):  
Structural Diversity ◽  
Conformational Ensemble ◽  
Structural Variations ◽  
Dna And Rna ◽  
X Ray Scattering ◽  
Double Stranded Dna ◽  
Binding Partners ◽  
Rna Duplexes ◽  
Dynamics Simulations ◽  
Integrate Solution

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

scholarly journals APPLICATION OF THE LENNARD-JONES POTENTIAL IN MODELLING ROBOT MOTION

2019 ◽  
Vol 9 (4) ◽  
pp. 14-17
Author(s):  
Piotr Wójcicki ◽  
Tomasz Zientarski
Keyword(s):  
Interaction Strength ◽  
Robot Motion ◽  
Lennard Jones Potential ◽  
Ordered Group ◽  
Jones Potential ◽  
Lennard Jones ◽  
Optimal Value ◽  
Potential Impact ◽  
Moving Groups ◽  
Dynamics Simulations

The article proposes a method of controlling the movement of a group of robots with a model used to describe the interatomic interactions. Molecular dynamics simulations were carried out in a system consisting of a moving groups of robots and fixed obstacles. Both the obstacles and the group of robots consisted of uniform spherical objects. Interactions between the objects are described using the Lennard-Jones potential. During the simulation, an ordered group of robots was released at a constant initial velocity towards the obstacles. The objects’ mutual behaviour was modelled only by changing the value of the interaction strength of the potential. The computer simulations showed that it is possible to find the optimal value of the potential impact parameters that enable the implementation of the assumed robotic behaviour scenarios. Three possible variants of behaviour were obtained: stopping, dispersing and avoiding an obstacle by a group of robots.

scholarly journals How to copy and paste DNA microarrays

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefan D. Krämer ◽  
Johannes Wöhrle ◽  
Philipp A. Meyer ◽  
Gerald A. Urban ◽  
Günter Roth
Keyword(s):  
Real Time ◽  
Dna Microarray ◽  
Dna Microarrays ◽  
Label Free ◽  
Binding Assays ◽  
Single Stranded Dna ◽  
Whole Process ◽  
Double Stranded Dna ◽  
Cost Efficient ◽  
Copy And Paste

Abstract Analogous to a photocopier, we developed a DNA microarray copy technique and were able to copy patterned original DNA microarrays. With this process the appearance of the copied DNA microarray can also be altered compared to the original by producing copies of different resolutions. As a homage to the very first photocopy made by Chester Charlson and Otto Kornei, we performed a lookalike DNA microarray copy exactly 80 years later. Those copies were also used for label-free real-time kinetic binding assays of apo-dCas9 to double stranded DNA and of thrombin to single stranded DNA. Since each DNA microarray copy was made with only 5 µl of spPCR mix, the whole process is cost-efficient. Hence, our DNA microarray copier has a great potential for becoming a standard lab tool.

scholarly journals Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Nano Research ◽  
2020 ◽  
Vol 14 (1) ◽  
pp. 328-333 ◽  
Author(s):  
Andrea Spitaleri ◽  
Denis Garoli ◽  
Moritz Schütte ◽  
Hans Lehrach ◽  
Walter Rocchia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Molecule ◽  
Dynamic Range ◽  
Protein Sequencing ◽  
High Fidelity ◽  
Label Free ◽  
Therapeutic Approaches ◽  
Highly Sensitive ◽  
Dynamics Simulations ◽  
Structure Of Proteins

AbstractSingle molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches. However, its technological realization can only be envisioned, and huge challenges need to be overcome. Major difficulties are inherent to the structure of proteins, which are composed by several different amino-acids. Despite long standing efforts, only few complex techniques, such as Edman degradation, liquid chromatography and mass spectroscopy, make protein sequencing possible. Unfortunately, these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement. It is known that proteins can distinguish closely similar molecules. Moreover, several proteins can work as biological nanopores in order to perform single molecule detection and sequencing. Unfortunately, while DNA sequencing by means of nanopores is demonstrated, very few examples of nanopores able to perform reliable protein-sequencing have been reported so far. Here, we investigate, by means of molecular dynamics simulations, how a re-engineered protein, acting as biological nanopore, can be used to recognize the sequence of a translocating peptide by sensing the “shape” of individual amino-acids. In our simulations we demonstrate that it is possible to discriminate with high fidelity, 9 different amino-acids in a short peptide translocating through the engineered construct. The method, here shown for fluorescence-based sequencing, does not require any labelling of the peptidic analyte. These results can pave the way for a new and highly sensitive method of sequencing.

Suction Energy for Double-Stranded DNA Inside Single-Walled Carbon Nanotubes

2017 ◽  
Vol 70 (4) ◽  
pp. 387-400 ◽  
Author(s):  
Mansoor H Alshehri ◽  
James M Hill
Keyword(s):  
Carbon Nanotubes ◽  
Mathematical Modelling ◽  
Molecular Electronics ◽  
Continuum Approximation ◽  
Suction Force ◽  
Dsdna Molecule ◽  
Double Stranded Dna ◽  
Modelling Techniques ◽  
Dynamics Simulations ◽  
Walled Carbon Nanotubes

Summary Deoxyribonucleic acid (DNA) and carbon nanotubes (CNTs) constitute hybrid materials with the potential to provide new components with many applications in various technology areas, such as molecular electronics, field devices and medical applications. Using classical applied mathematical modelling, we investigate the suction force experienced by a double-stranded DNA (dsDNA) molecule which is assumed to be located on the axis near an open end of a semi-infinite single-walled CNT. We employ both the 6-12 Lennard-Jones potential and the continuum approximation, which assumes that a discrete atomic structure can be replaced by a surface with constant average atomic density. While most research in the area is dominated by molecular dynamics simulations, here we use elementary mechanical principles and classical applied mathematical modelling techniques to formulate explicit analytical criteria and ideal model behaviour. We observe that the suction behaviour depends on the radius of the CNT, and we predict that it is less likely for a dsDNA molecule to be accepted into the CNT when the value of the tube radius is ${<}12.9$ Å. The dsDNA molecule will be accepted into the CNT for radii lager than 13 Å, and we show that the optimal single-walled CNT necessary to fully enclose the DNA molecule has a radius of 13.56 Å, which approximately corresponds to the chiral vector numbers (20, 20). This means that the ideal single-walled CNT to be used to encapsulate a dsDNA is (20, 20) which has the required radius of 13.56 Å.

scholarly journals A Conserved Residue in the Yeast Bem1p SH3 Domain Maintains the High Level of Binding Specificity Required for Function

2011 ◽  
Vol 286 (22) ◽  
pp. 19470-19477 ◽  
Author(s):  
Maryna Gorelik ◽  
Karen Stanger ◽  
Alan R. Davidson
Keyword(s):  
Sequence Similarity ◽  
Consensus Sequence ◽  
Binding Specificity ◽  
Biologically Relevant ◽  
Protein Protein Interaction ◽  
Nonspecific Interactions ◽  
High Level ◽  
Conserved Residue

The yeast Bem1p SH3b and Nbp2p SH3 domains are unusual because they bind to peptides containing the same consensus sequence, yet they perform different functions and display low sequence similarity. In this work, by analyzing the interactions of these domains with six biologically relevant peptides containing the consensus sequence, they are shown to possess finely tuned and distinct binding specificities. We also identify a residue in the Bem1p SH3b domain that inhibits binding, yet is highly conserved for the purpose of preventing nonspecific interactions. Substitution of this residue results in a marked reduction of in vivo function that is caused by titration of the domain away from its proper targets through nonspecific interactions with other proteins. This work provides a clear illustration of the importance of intrinsic binding specificity for the function of protein-protein interaction modules, and the key role of “negative” interactions in determining the specificity of a domain.

Label-Free Aptamer Fluorescence Determination of Trace Pb2+ Using AuPd Nanoalloy Probe as Catalyst

2013 ◽  
Vol 631-632 ◽  
pp. 18-21 ◽  
Author(s):  
Zhi Liang Jiang ◽  
Mei Ling Tang ◽  
Qing Ye Liu ◽  
Ai Hui Liang
Keyword(s):  
Detection Limit ◽  
Fluorescence Quenching ◽  
Fluorescence Intensity ◽  
Water Samples ◽  
Catalytic Effect ◽  
Rhodamine 6G ◽  
Label Free ◽  
Double Stranded Dna ◽  
Fluorescence Determination

In the condition of 1.24 mmol/L EDTANa2, 16.7 mmol/L NaCl and 0.17 mmol/L Tris, the substrate chain of double-stranded DNA (dsDNA) could be cracked by Pb2+ to release single-stranded DNA (ssDNA) that adsorb onto AuPd nanoparticle (AuPdNP) and form stable AuPdNP-ssDNA, but the dsDNA can not protect AuPdNP that were aggregated to big AuPdNP aggregations (AuPdNPA) under the action of NaCl. The AuPdNP-ssDNA and AuPdNPA could be separated by centrifugation. With the concentration of Pb2+ increased, the released ssDNA increased, the AuPdNP-ssDNA in centrifugation solution increased and the catalytic effect enhanced on the fluorescence quenching reaction of Rhodamine 6G (Rh6G) and NaH2PO2, which led the fluorescence intensity at 552nm to decrease. The decreased fluorescence intensity (ΔF552nm) was linear to the concentration of Pb2+ in the range of 0.33-8.00 nmol/L, a detection limit of 0.21 nmol/L. The proposed method was applied to detect Pb2+ in water samples, with satisfactory results.

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