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

Area of Science:

• Microbiology
• Computational Biology
• Molecular Biology

Background:

• Oligonucleotide interactions with bacterial cell envelopes are not fully understood at the molecular level.
• Improved understanding is crucial for enhancing oligonucleotide internalization in fluorescence in situ hybridization (FISH).

Purpose of the Study:

• To review essential information for constructing agent-based models (ABMs) of FISH.
• To provide a practical example of an ABM for targeting 23S rRNA in Escherichia coli.

Main Methods:

• Agent-based modeling (ABM) as an in silico tool to simulate FISH dynamics.
• Detailed consideration of bacterial cell envelope layers and intracellular molecular crowding in ABM.

Main Results:

• Identification of key data requirements for building accurate ABMs of FISH.
• Demonstration of ABM applicability with a specific Escherichia coli 23S rRNA target.

Conclusions:

• ABM is a promising approach to elucidate oligonucleotide-bacterial interactions during FISH.
• Simulating the complete bacterial cell, including its envelope and molecular environment, is vital for accurate FISH modeling.