ArticleNucleic acids research2008
Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 70 citations in OpenAlex.
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- Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations.ACS nano · 2018Article
- LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures.Scientific reports · 2017Article
- The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.Journal of computational chemistry · 2017Article
- Pharmacomodulation of microRNA Expression in Neurocognitive Diseases: Obstacles and Future Opportunities.Current neuropharmacology · 2017Review
- Gold Nanoparticles for Diagnostics: Advances towards Points of Care.Diagnostics (Basel, Switzerland) · 2016Review
- Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).The journal of physical chemistry. B · 2014Article
- Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.PloS one · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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