Nuclear DNA helicase II (NDH II) has been purified to near-homogeneity by exploiting its high affinity to poly[(rI).(rC)]-agarose. The purified enzyme was obtained as two catalytically active forms of 130- and 100-kDa molecular mass, respectively. After treatment with cyanogen bromide, the separated polypeptides displayed very similar digestion patterns. Thus, the 100-kDa form most likely is a proteolytic product of the 130-kDa polypeptide. For DNA unwinding, NDH II could use any of the four rNTPs or dNTPs with Km values between 20 and 100 microM. DNA unwinding was stimulated up to 20-fold by substrates that contained single-stranded 3'-tails. NDH II-catalyzed DNA unwinding was strongly inhibited by RNA, but was little affected by DNA. The strongest RNA inhibitor, poly[(rI).(rC)], was also the strongest effector of the NTPase activity of NDH II. The binding constant for poly[(rI).(rC)] binding was about 2 x 10(7) M-1; the minimal binding site size was determined as 16 nucleotides. In agreement with its high affinity to RNA, NDH II unwound double-stranded RNA. RNA unwinding required the presence of a nucleoside triphosphate and a divalent cation (Mg2+). Thus, like the prototypic replicative helicase large T antigen of simian virus 40, NDH II may function in both DNA and RNA unwinding.