I am ligating gene of interest between EcoRI and HindIII within pET28(b+) plasmid. What could be the best incubation temperature and time for the ligation to proceed?
Room temperature is best. Though it can help to chill your ligation mixture on ice for 5 mins before to help your overhangs to anneal. I usually let the ligation proceed for 2 hours.
The ideal temperature depends on your ligase and type of ends (blunt vs sticky) you are trying to ligate. EcoRI and HindIII are both sticky ends. Read the protocol sheet for your particular ligase to see what is suggested. Keep in mind that ligase buffer does expire so check the date on yours.