Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme


Bacillus halodurans (Bh) ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids. Long timescale molecular dynamics simulations have been performed on the BhRNase H-DNA-RNA hybrid complex and the respective monomers to understand the recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation. Several structural and energetic analyses were performed and significant structural changes are observed in enzyme and hybrid duplex during complex formation. Hybrid molecule binding to RNase H enzyme leads to conformational changes in the DNA strand. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids and the characteristic minor groove widthseem to be crucial for efficient binding. Sugar moieties in certain positions interacting with the protein structure undergo notable conformational transitions. The water coordination and arrangement around the metal ions in active site region are quite stable, suggesting their important role in enzymatic catalysis. Details of key interactions found at the interface of enzyme-nucleic acid complex that are responsible for its stability are discussed.

Molecular dynamics simulation results have shown that the DNA nucleotides of DNA-RNA hybrid that are interacting with ribonuclease H enzyme show interesting conformational changes upon binding.

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We thank AICTE, and Department of Atomic Energy-BRNS (37(2)/14/05/2015/BRNS/20046) for financial assistance. GS thanks Council of Scientific and Industrial Research (CSIR), India for senior research fellowship.

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Correspondence to U DEVA PRIYAKUMAR.

Additional information

Supplementary Information

This includes methods to calculate hydration numbers and hydrogen bonds (Supplementary methods), RMSD and radius of gyration (figure S1; table S1), Ramachandran plot (figure S2), hydrogen bond distances (figure S3), helical parameters (figures S4–S5), backbone angles (figure S6), buried surface area (figure S7), hydrogen bond distances (figure S8), pseudorotation angles (table S2), stacking interactions (table S3), hydration numbers and sasa (table S4), and statistics of hydrogen bonds (tables S5, S6, S7). Supplementary Information is available at

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SURESH, G., PRIYAKUMAR, U.D. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme. J Chem Sci 127, 1701–1713 (2015).

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  • HIV-1 reverse transcriptase
  • MD simulations
  • ribonuclease H activity
  • retroviral therapy
  • conformational transition
  • protein-nucleic acid interactions.