Design of a protein-targeted DNA aptamer using atomistic simulation

Author(s):  
Loan Huynh ◽  
Alan Chen
2003 ◽  
Vol 775 ◽  
Author(s):  
Byeongchan Lee ◽  
Kyeongjae Cho

AbstractWe investigate the surface kinetics of Pt using the extended embedded-atom method, an extension of the embedded-atom method with additional degrees of freedom to include the nonbulk data from lower-coordinated systems as well as the bulk properties. The surface energies of the clean Pt (111) and Pt (100) surfaces are found to be 0.13 eV and 0.147 eV respectively, in excellent agreement with experiment. The Pt on Pt (111) adatom diffusion barrier is found to be 0.38 eV and predicted to be strongly strain-dependent, indicating that, in the compressive domain, adatoms are unstable and the diffusion barrier is lower; the nucleation occurs in the tensile domain. In addition, the dissociation barrier from the dimer configuration is found to be 0.82 eV. Therefore, we expect that atoms, once coalesced, are unlikely to dissociate into single adatoms. This essentially tells that by changing the applied strain, we can control the patterning of nanostructures on the metal surface.


Author(s):  
Van-Trang Nguyen ◽  
Minh-Quy Le

We study through molecular dynamics finite element method with Stillinger-Weber potential the uniaxial compression of (0, 24) armchair and (31, 0) zigzag black phosphorene nanotubes with approximately equal diameters. Young's modulus, critical stress and critical strain are estimated with various tube lengths. It is found that under uniaxial compression the (0, 24) armchair black phosphorene nanotube buckles, whereas the failure of the (31, 0) zigzag one is caused by local bond breaking near the boundary.


2019 ◽  
Author(s):  
Matthew Healey ◽  
Muttuswamy Sivakumaran ◽  
Mark Platt

<p>Prion diseases are a group of fatal transmissible neurological conditions caused by the change in conformation of the normal intrinsic cellular prion protein (PrP<sup>C</sup>) in to the highly ordered insoluble amyloid state conformer (PrP<sup>SC</sup>). We present a rapid assay using Aptamers and Resistive Pulse Sensing, RPS, to extract and quantify proteins from complex sample matrices, demonstrate with the quantification of PrP<sup>c</sup>. We functionalise the surface of superparamagnetic beads, SPBs, with a DNA aptamer. First SPB’s termed P-Beads, are used to pre-concentrate the analyte from a large sample volume. The PrP<sup>c</sup> protein is then eluted from the P-Beads before aptamer modified sensing beads, S-Beads, are added. The velocity of the S-Beads through the nanopore reveals the concentration of the PrP<sup>c</sup> protein. The process is done in under an hour and allows the detection of picomol’s of protein. The technique could be easily adopted to the mutated version of the protein and integrated into clinical workflows for the screening of blood donations and transfusions. </p>


2016 ◽  
Vol 8 (1) ◽  
pp. 01028-1-01028-8 ◽  
Author(s):  
A. V. Khomenko ◽  
◽  
D. V. Boyko ◽  
M. V. Zakharov ◽  
K. P. Khomenko ◽  
...  

2013 ◽  
Vol 85 (17) ◽  
pp. 8391-8396 ◽  
Author(s):  
Jing Pan ◽  
Hanyu Zhang ◽  
Tae-Gon Cha ◽  
Haorong Chen ◽  
Jong Hyun Choi

Author(s):  
Xing Luo ◽  
Zhibo Zhang ◽  
Yongnan Xiong ◽  
Yao Shu ◽  
Jiazhen He ◽  
...  
Keyword(s):  

2021 ◽  
Vol 22 (5) ◽  
pp. 2409
Author(s):  
Anastasia A. Bizyaeva ◽  
Dmitry A. Bunin ◽  
Valeria L. Moiseenko ◽  
Alexandra S. Gambaryan ◽  
Sonja Balk ◽  
...  

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.


Langmuir ◽  
2021 ◽  
Vol 37 (17) ◽  
pp. 5213-5221
Author(s):  
Alexander Shaver ◽  
Nandini Kundu ◽  
Brian E. Young ◽  
Philip A. Vieira ◽  
Jonathan T. Sczepanski ◽  
...  

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