Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

Abstract

Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3'-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA-DNA, LNA-LNA, LNA-RNA, RNA-DNA and RNA-RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA-DNA and LNA-RNA duplexes are found to be similar to regular RNA-DNA and RNA-RNA duplexes, whereas the LNA-LNA duplex is found to have its helix partly unwound and does not resemble RNA-RNA duplex in a number of properties. Duplexes with an LNA strand have on average longer interstrand phosphate distances compared to RNA-DNA and RNA-RNA duplexes. Furthermore, intrastrand phosphate distances in LNA strands are found to be shorter than in DNA and slightly shorter than in RNA. In case of induced sugar puckering, LNA is found to tune the sugar puckers in partner DNA strand toward C3'-endo conformations more efficiently than RNA. The LNA-LNA duplex has lesser backbone flexibility compared to the RNA-RNA duplex. Finally, LNA is less hydrated compared to DNA or RNA but is found to have a well-organized water structure.

Figure 1.

(A) Structural differences in the ribonucleotide units forming RNA and LNA. (B) Sequence of the bases present in nucleic acid strands A and B. In case of RNA, Thymine (T) bases are changed to Uracil (U) bases. The numbering starts from 1 to 9 beginning with the first base in the 5′ to 3′ direction in both the strands.

Figure 2.

Time evolution during the entire simulation of the root mean square deviation (rmsd) from the starting structures for all the heavy atoms of (a) LNA–DNA, (b) LNA–LNA, (c) LNA–RNA, (d) RNA–DNA and (e) RNA–RNA duplexes.

Figure 3.

Energy minimized structures of the last snapshots of duplexes studied with MD simulations in explicit solvent for 10 ns. Hydrogen atoms are omitted for clarity. Carbon atoms of Strand A are in cyan and that of Strand B in green for each duplex.

Figure 4.

Average ± SD interstrand phosphate distances in (a) LNA–DNA, (b) LNA–LNA, (c) LNA–RNA, (d) RNA–DNA and (e) RNA–RNA duplexes, calculated during the last 8 ns of the 10 ns MD trajectory.

Figure 5.

Average ± SD intrastrand phosphate distances in (a) LNA–DNA, (b) LNA–LNA, (c) LNA–RNA, (d) RNA–DNA and (e) RNA–RNA duplexes, calculated during the last 8 ns of the 10 ns MD trajectory.

Figure 6.

Root mean square fluctuations of the backbone atoms (P, O1P, O2P, O3′, C5′ and O5′) of (a) LNA(A)–DNA(B), (b) LNA(A)–LNA(B), (c) LNA(A)–RNA(B), (d) RNA(A)–DNA(B) and (e) RNA(A)–RNA(B) duplexes. All A strands are plotted in black and all B strands in red.

Figure 7.

A snapshot from the MD trajectory of LNA–LNA duplex depicting water-mediated hydrogen-bonding bridges formed by O1P of T5 in Strand A (carbon atoms in cyan) with other backbone oxygen atoms during the course of simulation resulting in a net occupancy of more than 100%. Similar hydrogen-bonding bridges have lower occupancies in both DNA and RNA strands. Hydrogen atoms are omitted and water oxygen atoms are shown as spheres. The water molecules were exchanged by other water molecules during the simulation.