The crystal structure of an ‘All Locked’ nucleic acid duplex

Abstract

‘Locked nucleic acids’ (LNAs) are known to introduce enhanced bio- and thermostability into natural nucleic acids rendering them powerful tools for diagnostic and therapeutic applications. We present the 1.9 Å X-ray structure of an ‘all LNA’ duplex containing exclusively modified β-d-2′-O-4′C-methylene ribofuranose nucleotides. The helix illustrates a new type of nucleic acid geometry that contributes to the understanding of the enhanced thermostability of LNA duplexes. A notable decrease of several local and overall helical parameters like twist, roll and propeller twist influence the structure of the LNA helix and result in a widening of the major groove, a decrease in helical winding and an enlarged helical pitch. A detailed structural comparison to the previously solved RNA crystal structure with the corresponding base pair sequence underlines the differences in conformation. The surrounding water network of the RNA and the LNA helix shows a similar hydration pattern.

Properties of an ‘LNA’-modified ricin RNA aptamer

“…Surprisingly, the shift in thermostability is far lower than expected, since the T m value of the LNA-RNA aptamer is lower than the T m of the 'all LNA' 7mer duplex. It is conceivable that this is due to the special structural arrangement in a mixed type RNA/LNA helix, as the RNA part resembles the structure of an A-type nucleic acid helix, whereas the LNA duplex has a totally different structural arrangement with a stronger hydrophobic interaction between the base pairs, resembling rather the structure of a 'ribbon' than of that of a helix [17]. There should be a transition of these different structural types in a mixed RNA/LNA helix.…”

“…The structure of an LNA helix visualizes a picture of a stretched helical ladder with altered local and overall geometric parameters [17]. This geometry can rather be placed in vicinity to the structure of glycol nucleic acids (GNAs) [19], peptide nucleic acids (PNAs) [20,21] or homo DNAs [22].…”

Atomistic Investigation of the Effect of Incremental Modification of Deoxyribose Sugars by Locked Nucleic Acid (β-d-LNA and α-l-LNA) Moieties on the Structures and Thermodynamics of DNA–RNA Hybrid Duplexes

“…However, a recent study showed that the structure of fully modified β-LNA duplex differs significantly compared to pure RNA duplex. 39 The full β-LNA modification results in decreasing twist and roll and narrowing minor groove compared to pure RNA duplex.…”

Photoinduzierter reduktiver Elektronentransfer in LNA:DNA‐Hybriden: Kompromiss aus Konformation und Basenstapelung

“…[20] Zusätzliche Modifikationen führen zu einer noch schwächeren helicalen Verdrehung bei unverändertem Basenabstand. [21] LNA:DNA-Hybride sind strukturell den DNA:RNA-Hybriden bezüglich ihrer Basenstapelung sehr ähnlich, ihre Flexibilität ist jedoch reduziert. Insbesondere wegen der Methylenbrücke ist das Phosphatrückgrat der LNA sehr steif.…”

“…Demnach müssen diese Unterschiede den Schlüsseleigen-schaften der A-Helix zugeschrieben werden, welche der geringere Basenabstand und helicale Verdrehung darstellen, [31] die zusammen eine bessere Basenstapelung ergeben. [20,21,32] Diese Eigenschaft übt in solchen Doppelhelices, die 50 % LNA-Einheiten enthalten, offensichtlich einen stärkeren Einfluss aus als der negative Effekt der gefestigten Zuckerkonformation, was letztlich zu besseren ET-Effizienzen als in reiner DNA des B-Typs führt.…”