Hi, I'm a non-English-speaking student currently studying ASO and certain brain disorders in graduate school.

I do not speak English well.

I write is written with the help of a translation program. Please excuse any clumsiness and lack of logic due to my lack of knowledge.

I have studied some ASO papers on targeting mRNA and promotional materials of companies offering ASO synthesis services. I know that there are some points to consider in ASO design.

1. binding site of the target sequence (binding sequence)

2. self-dimerization of the Aso

3. the possibility of hairpin formation of the Aso

4. Cg content of Aso (40~60%)

5. possibility of guanine quadruplex formation

6. the secondary structure of the target mRNA

7. length of Aso

8. modification of Aso

I know that there are many other factors to consider. I know that some of the above are being tested for feasibility by simulation programs.

Currently, I have to find the binding site of ASO (in gapmer form) for a specific gene's MRNA (not pre-mRNA).

It also doesn't take into account the mismatch strategy.

When it comes to ASO design: Is it important to look for binding sequences?

And after prioritizing the considerations, can I choose the remaining sequnces?

My idea is to get a specific gene sequence through python, push back the sequence by a certain length (15-25) one sequence at a time, and among them, consider the GC content, eliminate sequences with more than 40-60% GC content, eliminate sequences with high C or certain sequences because they are likely to be guanine quadruplexes of ASOs, eliminate them again through self dimerization prediction tool, program

Blast to confirm the specificity of this sequence.

-- I don't have any knowledge of bioinformatics or python. If I use such a program, I will analyze it with gpt, gemini and googling.

I know that the prediction of the structure of proteins is possible and that it has a high degree of agreement with the reality (X-ray crystal, cryo-EM).

However, I know that the actual structure of RNA is difficult to determine, and I know that it is difficult to predict. And I know that programs and tools are limited by the fact that the prediction does not match reality. Therefore, I think that the specific sequence should be considered first with the above considerations.

I'm curious to know what approach you use to design Aso.