Okasaki fragment - (Feb/28/2008 )

The "flap" endonuclease recognizes the junction between the RNA & DNA near the 5' end of an Okasaki fragment. Name two structural features that might be recognized by the enzyme? Briefly explain

I dont quite understand this question..Any help would be appreciated

The Okasaki fragment is produced on the lagging strand of DNA during replication. Because DNA can only be produced in the 5'-3' direction, the lagging strand must be made of pieces that are cut and pasted back together. These pieces are made up of a RNA primer that the DNA polymerase extends but the product needs to be processed so that the RNA primer is removed, filled in with DNA and ligated back together to create one strand. The question is asking what potential structural features could the enzme that cuts out the RNA recognize in this fragment. First, do you know why these endonucleases are called "flap"? Look it up on wikipedia and you'll get your first answer. I'm not exactly sure of what your instructor is looking for as a second structural feature but I do know that RNA often takes on secondary structure (hairpins, loops) which are commonly used for enzyme recognition. The RNA primer could easily have a secondary structure specifically recognized by this enzyme.