10 research outputs found
Features of âAll LNAâ Duplexes Showing a New Type of Nucleic Acid Geometry
âLocked nucleic acidsâ (LNAs) belong to the backbone-modified nucleic acid family. The 2âČ-O,4âČ-C-methylene-ÎČ-D-ribofuranose nucleotides are used for single or multiple substitutions in RNA molecules and thereby introduce enhanced bio- and thermostability. This renders LNAs powerful tools for diagnostic and therapeutic applications. RNA molecules maintain the overall canonical A-type conformation upon substitution of single or multiple residues/nucleotides by LNA monomers. The structures of âallâ LNA homoduplexes, however, exhibit significant differences in their overall geometry, in particular a decreased twist, roll and propeller twist. This results in a widening of the major groove, a decrease in helical winding, and an enlarged helical pitch. Therefore, the LNA duplex structure can no longer be described as a canonical A-type RNA geometry but can rather be brought into proximity to other backbone-modified nucleic acids, like glycol nucleic acids or peptide nucleic acids. LNA-modified nucleic acids provide thus structural and functional features that may be successfully exploited for future application in biotechnology and drug discovery
The crystal structure of an âAll Lockedâ nucleic acid duplex
âLocked nucleic acidsâ (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 Ă
X-ray structure of an âall LNAâ duplex containing exclusively modified ÎČ-d-2âČ-O-4âČC-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
Diffraction techniques and vibrational spectroscopy opportunities to characterise bones
From a histological point of view, bones that allow body mobility and protection of internal organs consist not only of different organic and inorganic tissues but include vascular and nervous elements as well. Moreover, due to its ability to host different ions and cations, its mineral part represents an important reservoir, playing a key role in the metabolic activity of the organism. From a structural point of view, bones can be considered as a composite material displaying a hierarchical structure at different scales. At the nanometre scale, an organic part, i.e. collagen fibrils and an inorganic part, i.e. calcium phosphate nanocrystals are intimately mixed to assure particular mechanical properties
Comparative X-ray structure analyses of nucleic acids
Hochaufgelöste Strukturen von NukleinsĂ€uren geben Aufschluss ĂŒber die
Konformation, Hydratation und Ligandenbindung der MolekĂŒle. Als Modellsysteme
fĂŒr natĂŒrliche NukleinsĂ€uren wurden zwei tRNA-AkzeptorstĂ€mme und zum Vergleich
eine davon abgeleitete modifizierte âlockedâ NukleinsĂ€ure untersucht. Um eine
maximale Auflösung der Strukturen zu erzielen, wurden KristallisationsansÀtze
unter Mikrogravitationsbedingungen durchgefĂŒhrt und gleichzeitig die LĂ€nge der
untersuchten MolekĂŒle auf sieben Basenpaare begrenzt. Anhand der Struktur des
tRNAArg-Akzeptorstammes konnte beispielhaft die Bindung von kleinen MolekĂŒlen
an einfache NukleinsÀurefaltungsmotive gezeigt werden. Die Ergebnisse stehen
im Einklang mit Untersuchungen zur basen-spezifischen Bindung von kleinen
MolekĂŒlen an Aptamere und Riboswitches. Die Struktur des tRNASer-
Akzeptorstammes weist durch ihre hohe Auflösung von 1,2 Ă
eine nahezu
vollstÀndige Hydratation aller Basenpaare auf. Da der Akzeptorstamm von tRNAs
wesentliche IdentitĂ€tsmerkmale fĂŒr die Erkennung durch die korrespondierenden
Aminoacyl-tRNA-Synthetasen trÀgt, konnte durch einen Vergleich mit einem
Isoakzeptor der Einfluss des Wassernetzwerkes auf die Interaktion mit
natĂŒrlichen Bindungspartnern untersucht werden. Dies wurde durch eine
Superpositionierung der beiden Isoakzeptoren mit der Seryl-tRNA-Synthetase
bestÀtigt und ausgeweitet. Die Sequenz und Struktur des tRNASer-
Akzeptorstammes stellten die Grundlage fĂŒr die Untersuchung der davon
abgeleiteten Struktur einer âlockedâ NukleinsĂ€ure hinsichtlich Konformation,
Hydratation und Ligandenbindung dar. Dies ermöglichte einen
sequenzunabhÀngigen Vergleich der LNA mit der korrespondierenden RNA. Dabei
zeigte sich, dass die LNA eine vorher nicht beschriebene Doppelhelixstruktur
einnimmt, aus der heraus GrĂŒnde fĂŒr die hohe thermische StabilitĂ€t dieser
NukleinsÀureklasse abgeleitet werden konnten. Die Duplex ist im Vergleich zur
RNA durch eine Streckung bei gleichzeitiger Ăffnung charakterisiert, was
konformationell eher anderen modifizierten als der natĂŒrlichen NukleinsĂ€ure
Ă€hnelt. Trotz der strukturellen Unterschiede gleichen das Hydratationsmuster
und das Ligandenbindungsverhalten in weiten Bereichen dem der natĂŒrlichen
NukleinsÀure.High-resolution X-ray crystallography of nucleic acids is a powerful method to
investigate conformation, hydration and ligand-binding of these molecules. Two
tRNA-acceptorstem-microhelices where employed as model systems for natural
nucleic acids and compared to a modified âlockedâ nucleic acid, which sequence
was derived from one of those acceptorstems. Oligonucleotides were restricted
to a length of seven base pairs and crystallization was even performed under
microgravity conditions to maximize resolution of the structures. The
structure of the tRNAArg acceptorstem can be seen as a model for the binding
of small molecules to simple structural motifs of nucleic acids. The results
are consistent with investigations on base-specific interactions of small
molecules with aptamers and riboswitches. Due to its high resolution of 1.2 Ă
,
the structure of the tRNASer acceptorstem reveals a nearly complete hydration
of all base pairs. Since tRNA acceptorstems carry important identity elements
for the interaction with the cognate aminoacyl-tRNA-synthetase, a comparison
with an isoacceptor yielded insight into the impact of the hydration network
for the interaction of tRNAs with other molecules. These findings were
confirmed and extended by a superposition of the two isoacceptors with the
seryl-tRNA-synthetase. The highly-resolved structure of the tRNASer
acceptorstem was the fundament for the investigation of a âlockedâ nucleic
acid. The sequence of the LNA was derived from the acceptorstem. This allowed
a sequence independent comparison of the modified nucleic acid with its
corresponding natural counterpart. The structure was investigated with focus
on conformation, hydration and ligand-binding. It could be demonstrated, that
the LNA shows a double helix geometry, which differs significantly from
natural nucleic acids and can be rather brought in vicinity to other modified
nucleic acids. The structure of the LNA duplex can be described as a stretched
helix with an enlarged helical pitch. Despite these structural differences the
hydration and ligand-binding ability of the modified nucleic acid are similar
to those observed in RNA
Crystallization and X-ray diffraction analysis of an âall-lockedâ nucleic acid duplex derived from a tRNASer microhelix
A completely âall-lockedâ nucleic acid duplex was designed from an E. coli tRNASer microhelix. The helix consists exclusively of LNA building blocks and was crystallized. The crystals diffracted to 1.9â
Ă
resolution
Escherichia coli tRNAArg acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis
Various E. coli tRNAArg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis
Crystallization and preliminary X-ray diffraction data of an LNA 7-mer duplex derived from a ricin aptamer
An all-LNA duplex was designed from the stem region of an RNA aptamer which has been generated against ricin. The LNA duplex was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 2.8â
Ă