RNase H, lead or alkaline hydrolysis.

RNase H (Ribonuclease H ) is an endoribonuclease that specifically hydrolyzes the phosphodiester bonds of RNA which is hybridized to DNA. This enzyme does not digest single or double-stranded DNA.

it supllied by NEB

RNase H. People also use this to remove the mRNA from the first strand cDNA synthesized (mRNA/cDNA hybrid) when you construct cDNA.

Thank you for your response. I am afraid that RnaseH will not do the job out of two reasons - 

1. I do not have an hybrid between dna and rna but rather a single strand that start with rna and continue with dna. 

2. I understood that even in hybrids the RNAseH enzyme does not cut the bond between rna and dna.

Does anyone know the condition for alakaline treatment?

Oh, I see. You just want to remove the short RNA primer 'linked' to the DNA fragment (Okazaki fragment), which is in front of the Okazaki fragment.

I found this paper, kind of old (1994). In this paper, it describes that calf RNase HI can be used to remove the primer RNA from the rest of Okazaki DNA fragment. I hope this will help.

"Structure-specific Cleavage of the RNA Primer from Okazaki Fragments by  Calf Thymus RNase HI* "

And right,  the RNase H hydrolyzes/digests only the RNA phosphodiester bonds of the RNA/DNA hybrids (see attached picture). RNA molecules and DNA molecules hybridize to each other through 'hydrogen bonding'. [Note: the picture is small and may need to download to computer and blow it up to see it well]