Hi Cheng, there are two good ways to do that.

(1) Cloning your gene or region of interest into a plasmid. You can use QIAGEN or Sigma cloning kits. Design primers for your gene, PCR and clone, then check the clone with the same primers to prove the insert is there. Make sure the sequence matches, so sequencing is necessary.

(2) Ordering a BAC clone containing that region, for instance, from BACPAC https://bacpacresources.org/. They have fingerprinted clones ready and can do more complex work, such as construct design, for you. This is even simpler.

The method you suggested is valid for mRNA, I do not know whether it works for your sequence of interest or you just get tons of unspecific signals. Use CoT DNA, especially if the region selected has many repeats/intronic DNA.

Anastasia Naumenko

Hi Anastasia, Thank you for your answer!

This 1kb region that I want to visualize is actually introduced into the genome by me. Therefore I cannot use a BAC clone to probe it.

If I just clone this 1kb region into the plasmid to make probes, will it be too short to be detected. The protocols I read recommend using plasmids containing 5k to 10k of insertion.

Hi Cheng,

As I recall BACPAC offers construct design.

Well, maybe PNA FISH would be the best option for you then? In general, peptide nucleic acid probes enhance the signal greatly. Check out this paper Article Fluorescent in situ hybridization (FISH) – The next generation