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Generate a semi-permanent ssDNA bubble within a plasmid or similar?

MarioS
in Biochemistry and Molecular Biology

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Hi fellow wage slaves,

for a HTS experiment i would need a permanent open "ssDNA bubble" similar to a transcription bubble (>13 nucleotides). I am not sure if that's even possible, but the following criteria are important:

1. Open ssDNA bubble within replicable (in E. coli) genetic element.

2. No proteins, nucleic acids, or other toxic chemicals supporting the bubble. Can help during nucleation, but bubble has to be accessible for protein interaction.

3. Stable in bioorthogonal conditions. Physiological pH, salt, 37 °C, etc.

 

I am truly at a loss here, but maybe one of you has the sparking idea. I will put your name on the paper if this works ❤️

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