ARTICLE | doi:10.20944/preprints202309.1896.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: biochips; Digital Microfluidic Biochips; deep reinforcement learning; optimization
Online: 27 September 2023 (11:24:50 CEST)
Digital Microfluidic Biochips (DMFBs), used in various kinds of fields like DNA analysis, clinical diagnosis, and PCR testing, have made biochemical experiments more compact, efficient, and user-friendly than previous ways. However, their reliability is often compromised by their inability to adapt to all kinds of errors. All errors in biochips can be categorized into two types: known errors and unknown errors. Known errors are detectable before the start of the routing process through sensors or cameras. Unknown errors, in contrast, become apparent only during the routing process and remain undetected by sensors or cameras, which is the biggest issue to unexpectedly stop the routing process and diminishes the reliability of biochips. This paper introduces a deep reinforcement learning-based routing algorithm designed to manage not only known errors but also unknown errors. Our experiments demonstrate that our algorithm outperforms previous ones in terms of the success rate of the routing in the scenario including both known errors and unknown errors. Additionally, our algorithm contributes to detecting unknown errors during the routing process and identifying the most efficient routing path with high probability.
ARTICLE | doi:10.20944/preprints202305.1428.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: Angiotensin converting enzyme II; Polystyrene; Molecular dynamics simulation; Adsorption behaviors; Biochips
Online: 19 May 2023 (10:20:13 CEST)
The adsorption of proteins on polymer is widely used in biosensors. Here, molecular dynamics (MD) simulation was used to study the immobilization of angiotensin converting enzyme II (ACE2) with six initial orientations proposed on polystyrene (PS) at the ambient conditions of pH (4.5, 6, 7, 8, 9.5) and NaCl (0.01, 0.05, 0.1, 0.15, 0.2, 0.25 M). ACE2 immobilization under favorable ambient conditions was characterized by minimum distance (short), settlement time (fast), interaction energy (substantial) and protein configuration (stable). ACE2 orientations proposed in 0.15M NaCl were respectively preferable to (90, 0, 0), (0, 0, 0) and (0, 270, 0), (180, 0, 0) and (0, 90, 0), (90, 0, 0) at pH 4.5, 6, 7, 9.5. ACE2 immobilization was further evaluated at pH 7 by optimizing NaCl concentration. Its proposed orientations of (i) (0, 270, 0), (ii) (0, 0, 0) and (90, 0, 0), and (iii) (0, 90, 0) and (90, 0, 0) were preferable in 0.05, 0.1 and 0.2 M NaCl, respectively. The great significance of cubic-orientation settlement mode provides tangible improvement for the microfabrication of biochips for rapid diagnosis of severe acute respiratory syndrome coronavirus II (SARS-CoV-2).
ARTICLE | doi:10.20944/preprints201904.0205.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: antibody coating; proximity-enhanced reaction; immunoglobulins; IgG; protein A; protein G; bio-interaction; immunoprecipitation; pull-down assay; immunocapture; stabilization; yield; regeneration; nanoparticles; microparticles; biochips; immunosensor; photochemical crosslinker; click chemistry; herceptin; trastuzumab
Online: 18 April 2019 (07:55:11 CEST)
Crosslinking of proteins for their irreversible immobilization on surfaces is a proven and popular method. However, many protocols lead to random orientation and the formation of undefined or even inactive by-products. Most concepts to obtain a more targeted conjugation or immobilization requires the recombinant modification of at least one binding partner, which is often impractical or prohibitively expensive. Here a novel method is presented, which is based on the chemical preactivation of Protein A or G with selected conventional crosslinkers. In a second step, the antibody is added, which is subsequently crosslinked in the Fc part. This leads to an oriented and covalent immobilization of the immunoglobulin with a very high yield. Protocols for Protein A and Protein G with murine and human IgG are presented. This method may be useful for the preparation of columns for affinity chromatography, immunoprecipitation, antibodies conjugated to magnetic particles, permanent and oriented immobilization of antibodies in biosensor systems, microarrays, microtitration plates or any other system, where the loss of antibodies needs to be avoided, and maximum binding capacity is desired. This method is directly applicable even to antibodies in crude cell culture supernatants, raw sera or protein-stabilized antibody preparations without any purification nor enrichment of the IgG. This new method delivered much higher signals as a traditional method and, hence, seems to be preferable in many applications.