How do you extract your nucleic acids ?

Edit : usually, nucleic extraction is easier in immature fruits : there is plenty of  polysaccharides/polyphenols/poly[whatever sheaty stuff] in ripe fruits inhibiting nucleic extraction and enzymatic following steps.

I don't know cactus biology but if it's like fig (Ficus carica), perhaps you're facing an excess of latex or something similar which is absent from your ripe fruits.

I think extracting DNA or RNA from the fruit skin or epidermis of the fruit skin will give better quality of DNA or RNA. I work with Aloe species and I have done DNA extraction using the epidermis of the leaf. I have scratched all the gel and wiped the leaf properly until I was left with the thin layer of the leaf. This reduced contamination with polysaccharides and polyphenols.

Hi Amna,

concerning RNA extraction the results you expect depends what you are looking for. If you look for specific mRNA for example  present (expressed) in mature and absent in immature fruits the results obtained will be different. About DNA extraction I agree with Thomas and Devine. Good luck!

I want to check the presence of expressed genes at different conditions. and while mature fruit was available I've used pulpy part (between peel and seeds). As you people suggest, Now I can go with DNA extraction with unripe fruit and RNA with ripe fruit. 

Hope to get same results of DNA in both ripe and unripe fruit.

I guess yes you can, Follow the link below,

http://www.academicjournals.org/article/article1380016067_Brasil%20et%20al.pdf

I hope this helps you. All the best.

http://www.academicjournals.org/article/article1380016067_Brasil%20et%20al.pdf