Gene-PROBER

Gene-PROBER designs polynucleotide probes for fluorescence in situ hybridization (FISH) to enable targeted detection and visualization of microbial genes and genomic regions at the single-cell level.

Key Features:

• Polynucleotide mixture design: Generates polynucleotide mixtures tailored to target specific genes or genomic regions within bacteria, archaea, and viruses to maximize hybridization specificity and efficiency.
• Workflow flexibility: Provides four distinct workflows selectable based on the availability of non-target sequences and the chosen probe synthesis approach (chemical synthesis or PCR-based methods).
• Melting temperature optimization: Distributes designed polynucleotides along the target sequence and harmonizes their melting properties to allow use of a single probe mixture in one hybridization reaction.
• Cross-reactivity minimization: Selects probe sequences to minimize cross-reactivity with non-target sequences by evaluating sequence specificity.
• Synthesis feasibility assessment: Assesses probes for synthesis feasibility with respect to the chosen synthesis method.

Scientific Applications:

• geneFISH: Enables targeted detection and visualization of specific genes within individual microbial cells for gene localization and expression studies.
• phageFISH: Supports detection of viral (phage) genetic material within microbial hosts at the single-cell level.
• Microbial ecology, pathogenesis and evolutionary biology studies: Facilitates analysis of microbial communities, host–pathogen interactions, and evolutionary distribution of genes within complex samples.

Methodology:

Selects polynucleotide sequences that align to target genes or regions while minimizing cross-reactivity, distributes probes along targets to achieve uniform melting temperature, evaluates sequence specificity and melting temperature uniformity, assesses synthesis feasibility, and offers four workflow options based on availability of non-target sequences and chosen synthesis method.