Dear community
I'm having issues during my cloning.
I have to clone an insert of 4.2kb in a plasmid of 4.3 kb.
During my first try i opened the plasmid using EcoRV a than I used CIP enzyme to dephosphorilate the blunts ends. The insert come from a 9.5kb plasmid cutted with two enzymes than the insert was filled using Klenow enzyme and eluited. The size of insert and the blunt ends has results in multiple failed trasformation(chemical).
After that i decided to change my strategy.
First of all I switched from chemical trasformation to electroporation to enhance my trasformation efficency(Now I have 10^8 efficency).
Than I decided to cut the insert and the backbone plasmid with different enzymes. This because now is a sticky/blunt ligation which should be easier and directional. The problem is that now the backbone is became 3.4 kb while the insert has become 5.5 kb.
I used takara ligase and made 1:1 and 1:3 ratio based on 50 ng of backbone( and calculate the molecular ratio aswell) and the two controls (just backbone with and without enzyme). I got 1 colony in the control plate and 1 colony in the 1:3 ratio plate. How can I enhance my efficency? I also have neb ligase.
May I lost too much dna during the salt precipitation before the electroporation? should I start with more DNA, like 150ng?
All suggestions would be highly appriciated and sorry if my english is not perfect I'm tring to improve it.