Complex between Human RNase HI and the phosphonate-DNA/RNA duplex: Molecular dynamics study

Abstract

Our 200ns MD simulations show that even fully modified oligonucleotides bearing the 3′-O-P-CH2-O-5′ (but not 3′-O-CH2-P-O-5′) phosphonate linkages can be successfully attached to the surface of Human RNase H. It enables to explain that oligonucleotides consisting of the alternating 3′-O-P-CH2-O-5′ phosphonate and phosphodiester linkages are capable to elicit the RNase H activity (while the 3′-O-CH2-P-O-5′ phosphonates are completely inactive). Stability of the binuclear active site of Human RNase H was achieved using the one-atom model for Mg2+ in conjunction with a polarized phosphate group of the scissile bond, which is wedged between both magnesium ions. The reference MD simulation (lasting for 1000ns), which was produced using a well-established seven-point (with dummy atoms) model for Mg2+ led to essentially the same results. The MD run (lasting for 500ns) produced for the Thermus thermophilus Argonaute enzyme shows the transferability of our approach for the stabilization of a binuclear active site. Glu512 was bound in the T. thermophilus Argonaute active site to the 2′-OH of the nucleotide adjacent to the scissile phosphate and one of the two active-site divalent metal ions in exactly the same way as Glu186 in Human RNase H. Glu512 thus completes the catalytic tetrad of Argonaute.