I am using degenerate primers to amplify a family of genes. My results in an agarose gel are 6 bands (862pb, 632pb, 408pb, 335pb and 226pb). The bands of interest are 408pb and 335pb. What ratio of insert:vector should I use to get the highest number of clones containing the 408pb and 335pb inserts?
3:1(molar ratio) insert to vector ratio is usually sufficient, you can optimize the amount of insert and vector to improve ligation efficiency in situations where the 3:1 ratio is not working or when doing more complicated cloning. While 3:1 is sufficient for average size genes and vectors, this ratio is really meant to refer to the molarity of DNA ends available for ligation. You can check online ligation calculators like http://nebiocalculator.neb.com/ or http://www.insilico.uni-duesseldorf.de/Lig_Input.html
Just enter the concentration, lengths of your insert and vector, and what ratio you want, and it will tell you exactly how much of each to use.
Good luck.
If you are asking what conditions are required to preferentially clone the 408 and 335 fragments (if using the whole PCR reaction mix to clone into the vector) over the others then you cannot. I would bulk up your PCR reaction, gel purify the individual fragments (advisable in any case, even if you only had one band) and then follow the directions given by Snigdha.
If I were you, I'd gel purify the bands you want. It's faster, cheaper, and easier to run an agarose gel and do a quick gel extraction than to screen dozens (or hundreds) of clones.
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