A rapid and quantitative nitroceUulose filter-binding assay is described for the detection of nuclear factor I, aI HpLa ceUl sequence-specific DNA-binding protein required for the initiation of adenovirus DNA replication.In this apsay, the abundant nonspecific DNA-binding activity present in unfractionated HeLa nuclear extracts was greatly reduced by preincubation of these extracts with a homopolyrneric competitor DNA. Subsequently, specific DNA-binding activity was detected as the preferential retention of a labeled 48-base-pair DNA fragment contiinig a functionl nuclear factor I binding te compared with a control DNA fragment to which nuclear factor I-dd not bind specificaly. This specifi.c DNA-binding activity was shown to be both quantitative and time dependent. Furthermore, the conditions of this assay alowed footprinting of nuclear factor I in unfractionated HeLa nuclear extracts and quantitative detection of the protein during purification. Using unfrozen HeLa cells an4 reagents known to limit endogenous proteolysis, nuclear factor I was purified to near homogeneity from HeLa nuclear extracts by a combination of standard chromatography and specific DNA affinity chromatography. Over a 400-fold purification of nuclear factor I, on the basis of the specific activity of both sequence-specific DNA bipding and complementation of adenovirus DNA replication in vitro, was affected by this purification. The most highly purified fraction was greatly enriched for a polypeptide of 160 kilodaltons on silver-stained sodium dodecyl sulfate-polyacrylamide gels. Furthermore, this protein cosedimented with specific DNA-binding activity on glycerol gradients. That tihis fraction indeed contained nuclear factor I was demonstrated by both DNase I footprinting and its functiop in the initiation of adenovirus DNA replication.Finally, the stoichiometry of specific DNA binding by nuclear factor I is shown to be most consistent with 2 mol of the 160-kilodalton polypeptide binding per mol Qf nuclear factor I-binding site.The efficient replication of adenovirus DNA can be accomplished in vitro by five purified proteins in the presence of the appropriate cofactors (for ,a review, see reference 43). Three of these proteins, adenovirus DNA polymerase (26, 45), DNA-binding protein (DBP) (13,22,38,46), and terminal protein precursor (pTP) (6,8,11,27,44,48), are viral encoded. The two remaining proteins required to fully reconstitute adenovirus replic4tion in vitro are the HeLa cell proteins nuclear factors I (NFI) and II.Nuclear factor II appears to be required for the completion but not the initiation of DNA replication in vitro because, in the absence of nuclear factor II, DNA replication initiates normally but terminates randonily, approximately one-third the way into the genome. Purified preparations of nuclear factor II contain topoisomerase I activity. Furthermore, topoisomerase I purified from either HeLa cells or calf thymus can completely substitute for factor II. Thus, it seems likely that factor II is a type I topoisomerase (33...