Using a synthetic 66 @entity377 RNA template containing a stable hairpin structure derived from the @entity2858 genome, six predominant RNA cleavage products are found during DNA synthesis catalyzed by @entity2858 @entity138 . These major RNA cleavage sites correlate well with the pause sites seen during primer elongation [Suo, Z., _ Johnson, K. A. (1997) Biochemistry (manuscript submitted for publication)]. Thus, the RNase H and polymerase activities of @entity138 are coupled as @entity138 reads through the RNA secondary structure. The distance between the two active sites of @entity2858 @entity138 is 19-20 base pairs of DNA/RNA heteroduplex when the next template base is not paired. The heteroduplex region was enlarged by 2-3 base pairs once @entity138 encounters the template hairpin. A model for this change is presented. At the pause sites, the burst amplitudes of RNA cleavage are larger than the corresponding reaction amplitudes of next @entity377 incorporation at the polymerase site. Measurement of the steady state rates of RNA cleavage confirms that all substrates dissociate slowly from @entity138 . These results suggest that while substrates are bound nonproductively at the polymerase site, they are still bound productively at the RNase H active site of @entity138 . Characterization of an RNase H-deficient @entity138 mutant ( @entity52890 ) shows that RNase H activity is not critical for @entity138 to read through the RNA secondary structure. @entity2858 nucleocapsid does not increase the processivity of @entity2858 @entity138 but inhibits DNA elongation by blocking the binding of @entity138 to DNA substrates.

Effect of RNA secondary structure on RNA cleavage catalyzed by XXXX reverse transcriptase.

@entity2858 :: ('11676', 'Species') :: ['HIV-1'] @entity377 :: ('CHEBI:36976', 'Chemical') :: ['nucleotide'] @entity52890 :: ('p|SUB|D|443|N', 'ProteinMutation') :: ['D443N'] @entity138 :: ('MESH:C563738', 'Disease') :: ['RT']
@entity2858 :: (11676,Species) :: ['HIV-1']
