During RNA FISH, the fluorescent probes are hybridized with target RNAs with 20-24bp base pairing.
But how strong this interaction is with only several hydogen bonds?
How much salt or fomamide are needed for break this interaction?
The strength of the interaction between target RNA and hybridized probes depends on factors such as base pairing complementarity and binding conditions. Strong interactions are characterized by precise base pairing, leading to stable duplex formation, while weaker interactions may result from mismatches or suboptimal binding conditions, influencing overall stability.
You can check NUPACK to calculate your exact break solution concentration. Moreover you can just use DNaseI to remove the probes or use high concentration formamide(about ~60%)
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