Im going to digest a vector with the same restriction enzyme on both the ends (which has a sticky end), and ligate a Product by digesting with the same enzyme. I feel there could be chances of self ligation rather than the product ligation. The vector is amp resistant and no other selectable markers are present. could anyone suggest me to avoid self ligated colonies and the way to select the colonies which has the insert.
I completely agree with Paul. I would only add that there are also visual screens that also can help assess whether or not a plated colony contains a clone with an insert. For example, classic "blue-white screening" (see link).
Of course, in this case, one needs to be using a vector and a host strain that supports this technique...but most common cloning vectors and strains do. Its not as common when working with expression vectors/hosts.
http://en.wikipedia.org/wiki/Blue_white_screen
I also agree with Paul, colony PCR can tell you the answer about the ligation. In addition, you can do positive using primer for your target gene and negative colony PCR using primer for your template(if your do truncation from your previous construct)
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