The hepatitis B virus capsid or core protein (p21.5) binds nucleic acid through a carboxy-terminal protamine region that contains nucleic acid-binding motifs organized into four repeats (I to MV). Using carboxy-terminally truncated proteins expressed in Escherichia coli, we detected both RNAand DNA-binding activities within the repeats. RNA-binding and packaging activity, assessed by resolving purified E. coli capsids on agarose gels and disclosing their RNA content with ethidium bromide, required only the proximal repeat I (RRRDRGRS). Strikingly, a mutant in which four Arg residues replaced repeat I was competent to package RNA, demonstrating that Arg residues drive RNA binding. In contrast, probing immobilized core proteins with 32P-nucleic acid revealed an activity which (i) required more of the protamine region (repeats I and II), (ii) appeared to bind DNA better than RNA, and (iii) was apparently modulated by phosphorylation in p21.5 derived from Xenopus oocytes. Deletion analysis suggested that this activity may depend on an SPXX-type DNA-binding motif in repeat II. Similar motifs found in repeats III and IV may also function to bind DNA. On * Corresponding author. p21.5 appear to be specifically configured for a role in HBV replication. MATERIALS AND METHODS Reagents. Homogeneous preparations of recombinant capsids from Escherichia coli and from Saccharomyces cerevisiae were kindly provided by Chiron, Emeryville, Calif., and Merck, West Point, Pa., respectively. All chemical and biochemical reagents were of fine reagent grade. Restriction enzymes and T4 DNA ligase were obtained from Boehringer Mannheim; radiochemicals were obtained from NEN. Oligonucleotides were synthesized on a Milligen Biosearch 8700 synthesizer. DNA sequencing was performed with an Applied Biosystems 373A DNA sequencer. Standard protocols were used for molecular biology procedures. Construction of mutants and expression plasmids. HBV DNA of subtype adw (34) was used for all constructs. For expression in E. coli, the 185-amino-acid p21.5 coding region was mobilized by the polymerase chain reaction from plasmid 64-C (29) to the expression vector pAR3040 (31). The 5'