Check these sites to see how many nucleotides to add to the 5’ end of restriction sites
http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/cleavage_linearized_vector.asp
http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/cleavage_olignucleotides.asp
USE NEAREST NEIGHBOR MELTING TEMPERATURES (TmNN) FROM
http://www.basic.northwestern.edu/biotools/oligocalc.html
USUALLY AIM FOR TmNN >= 50C