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. 2005 Apr 14;33(7):2166–2175. doi: 10.1093/nar/gki510

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© The Author 2005. Published by Oxford University Press. All rights reserved

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Model of interaction of RNase H1 with RNA–DNA hybrid. Interaction of E.coli RNase HI with HIV-1 PPT RNA–DNA hybrid is shown (a and b). The model was constructed as described in Materials and Methods. The RNA strand is in red and the DNA strand in blue. 5′-DNA and 3′-RNA mark the position of the ends of the hybrid. The right side of the figure (c and d) is the model for two molecules of mouse RNase H1 interacting with ∼12 bp of the PPT. The yellow RNase H domain (HD) is in the same orientation as the E.coli RNase HI protein on the left side of the figure and is connected to the green dsRHbd (ds) by the gray connection domain c. The second RNase H1 molecule is in dark green and is in the opposite orientation, making it unable to cleave the hybrid. The lower portion of the figure (b and d) are an end-on views of structures (a and c) with the hybrid in (d) surrounded by the two RNase H1 molecules.