Abstract: The subject of the invention is the ribonuclease which cleaves RNA strand in DNA-RNA hybrids, wherein ribonuclease comprises fusion protein comprising catalytic domain of RNase HI (RNase HI) or derivative thereof with a zinc finger DNA-RNA hybrid binding domain, and wherein the zinc finger binding domain has the ability to bind to specific sequences in the DNA-RNA hybrid. The invention also relates to new methods for determination of the sequence preference of DNA-RNA hybrid binding protein(s) or its domain(s) and allows determining the sequence recognized by sequence specific binding protein in the DNA-RNA hybrid.