Principle of chemical RNA Fragmentation

[Tobi84]

Hello everyone,

I'm Tobias, Research technician.

I did some research regarding the the topic "Chemical RNA Fragmentation" and couldn't find anything helpfull.

I mean, I'm facing problems with my NGS preparation regarding the fragment lenghts.
If i have a very low amount of RNA (< 1ng input), my target reads (viral RNA) are likely to be ~200bp.
Now I'm targeting Viral RNA within backround RNA of nearly 100ng and the fragmentation seems to be totally different.

So - Specific Questions:

- Does the ratio between MG2+ Ions and RNA fragments affect the fragmentation
- How does MG2+ Ions and heat work on the RNA? Does the MG bind to the negative backbone, weaken the O-C connection between the bases? Or does the MG bin to the RNA, relaxing the strand and the movement of the RNA created by the heat simply breaks the RNA?
- Does MG hate RNA and beat it up with tiny tiny baseball bats?

I'm really looking forward to receive any hints and will be thankfull to receive answers

With best regards

Tobias