Computational Resources and Strategies to Construct Single-Molecule Models of FISH

• Type: Chapter or Part of a Book
• Date: 2021-02-13

Authors

Beatriz T. Magalhães (Author) FEUP; Rita S. Santos (Author) FEUP; Nuno F. Azevedo (Author) FEUP; Anália Lourenço (Author) Other

Book

Title: Fluorescence In-Situ Hybridization (FISH) for Microbial Cells. Methods in Molecular Biology

Pages: 317-330

ISBN: 978-1-0716-1114-2

Electronic ISBN: 978-1-0716-1115-9

Publisher: Humana Press

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Pubmed / Medline

Other information

Authenticus ID: P-00T-MDV

DOI: 10.1007/978-1-0716-1115-9_21

Abstract (EN): Currently, the interactions occurring between oligonucleotides and the cellular envelope of bacteria are not fully resolved at the molecular level. Understanding these interactions is essential to gain insights on how to improve the internalization of the tagged oligonucleotides during fluorescence in situ hybridization (FISH). Agent-based modeling (ABM) is a promising in silico tool to dynamically simulate FISH and bring forward new knowledge on this process. Notably, it is important to simulate the whole bacterial cell, including the different layers of the cell envelope, given that the oligonucleotide must cross the envelope to reach its target in the cytosol. In addition, it is also important to characterize other molecules in the cell to best emulate the cell and represent molecular crowding. Here, we review the main information that should be compiled to construct an ABM on FISH and provide a practical example of an oligonucleotide targeting the 23S rRNA of Escherichia coli. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.

Language: English

Type (Professor's evaluation): Scientific