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Xylonucleic acid: synthesis, structure, and orthogonal pairing properties.

Maiti M, Maiti M, Knies C, Dumbre S, Lescrinier E, Rosemeyer H, Ceulemans A, Herdewijn P - Nucleic Acids Res. (2015)

Bottom Line: A detailed investigation of pairing and structural properties of XyloNAs in comparison to DNA/RNA has been performed by thermal UV-melting, CD, and solution state NMR spectroscopic studies.XyloNA has been shown to be an orthogonal self-pairing system which adopts a slightly right-handed extended helical geometry.Our study on one hand, provides understanding for superior structure-function (-pairing) properties of DNA/RNA over XyloNA for selection as an informational polymer in the prebiotic context, while on the other hand, finds potential of XyloNA as an orthogonal genetic system for application in synthetic biology.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.

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Top: Circular dichroism (CD) spectra of XyloNA and dXyloNA duplexes in water (12 μM, pH 7.0) at 10°C. For comparison, the CD spectra of the right-handed B-DNA, A-RNA and the left-handed Z-DNA duplexes are shown and illustrated. Bottom: Temperature dependent CD spectra of the XyloNA duplex showing a typical cooperative melting profile.
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Figure 4: Top: Circular dichroism (CD) spectra of XyloNA and dXyloNA duplexes in water (12 μM, pH 7.0) at 10°C. For comparison, the CD spectra of the right-handed B-DNA, A-RNA and the left-handed Z-DNA duplexes are shown and illustrated. Bottom: Temperature dependent CD spectra of the XyloNA duplex showing a typical cooperative melting profile.

Mentions: To gain insights into the helical conformation and dynamics of double-stranded (ds) XyloNA (ON-1), we have performed circular dichroism (CD) studies. The CD spectra of XyloNA appear to be different from the known CD spectra of various helical nucleic acid structures i.e. A-, B- and Z-type helices, (1) as shown in Figure 4. However, the CD spectrum of XyloNA was found to be very similar to that of our previously studied analogous dXyloNA system in water (24). A characteristic positive Cotton (effect) band at 256 nm was observed in the CD spectrum, which showed a gradual melting effect with increasing temperature (Figure 4, bottom). These observations suggest that the XyloNA duplex has formed a slightly right-handed extended ladder-like structure, as characterized by NMR (described in the following section), and is in line with our previous observation for dXyloNA (24). The repeated appearance of this type of CD spectrum can be considered as a finger-print for the right-handed extended duplex structure (RE-type helix), and might facilitate in the future cataloging of non-natural nucleic acid conformation by CD spectroscopy. Unlike dXyloNA duplex (24), the CD spectra of XyloNA in saline buffer (Supplementary Figure S5) appeared to be identical with the spectra in pure water. This suggests that the presence of the 2′-hydroxyl group in the XyloNA backbone has resulted in a reduced conformational flexibility compared to the dXyloNA system. In our previous study, the latter has been identified to be conformationally malleable since it exists in two different helical conformations in saline aqueous/buffer solution (24).


Xylonucleic acid: synthesis, structure, and orthogonal pairing properties.

Maiti M, Maiti M, Knies C, Dumbre S, Lescrinier E, Rosemeyer H, Ceulemans A, Herdewijn P - Nucleic Acids Res. (2015)

Top: Circular dichroism (CD) spectra of XyloNA and dXyloNA duplexes in water (12 μM, pH 7.0) at 10°C. For comparison, the CD spectra of the right-handed B-DNA, A-RNA and the left-handed Z-DNA duplexes are shown and illustrated. Bottom: Temperature dependent CD spectra of the XyloNA duplex showing a typical cooperative melting profile.
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Related In: Results  -  Collection

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Figure 4: Top: Circular dichroism (CD) spectra of XyloNA and dXyloNA duplexes in water (12 μM, pH 7.0) at 10°C. For comparison, the CD spectra of the right-handed B-DNA, A-RNA and the left-handed Z-DNA duplexes are shown and illustrated. Bottom: Temperature dependent CD spectra of the XyloNA duplex showing a typical cooperative melting profile.
Mentions: To gain insights into the helical conformation and dynamics of double-stranded (ds) XyloNA (ON-1), we have performed circular dichroism (CD) studies. The CD spectra of XyloNA appear to be different from the known CD spectra of various helical nucleic acid structures i.e. A-, B- and Z-type helices, (1) as shown in Figure 4. However, the CD spectrum of XyloNA was found to be very similar to that of our previously studied analogous dXyloNA system in water (24). A characteristic positive Cotton (effect) band at 256 nm was observed in the CD spectrum, which showed a gradual melting effect with increasing temperature (Figure 4, bottom). These observations suggest that the XyloNA duplex has formed a slightly right-handed extended ladder-like structure, as characterized by NMR (described in the following section), and is in line with our previous observation for dXyloNA (24). The repeated appearance of this type of CD spectrum can be considered as a finger-print for the right-handed extended duplex structure (RE-type helix), and might facilitate in the future cataloging of non-natural nucleic acid conformation by CD spectroscopy. Unlike dXyloNA duplex (24), the CD spectra of XyloNA in saline buffer (Supplementary Figure S5) appeared to be identical with the spectra in pure water. This suggests that the presence of the 2′-hydroxyl group in the XyloNA backbone has resulted in a reduced conformational flexibility compared to the dXyloNA system. In our previous study, the latter has been identified to be conformationally malleable since it exists in two different helical conformations in saline aqueous/buffer solution (24).

Bottom Line: A detailed investigation of pairing and structural properties of XyloNAs in comparison to DNA/RNA has been performed by thermal UV-melting, CD, and solution state NMR spectroscopic studies.XyloNA has been shown to be an orthogonal self-pairing system which adopts a slightly right-handed extended helical geometry.Our study on one hand, provides understanding for superior structure-function (-pairing) properties of DNA/RNA over XyloNA for selection as an informational polymer in the prebiotic context, while on the other hand, finds potential of XyloNA as an orthogonal genetic system for application in synthetic biology.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.

Show MeSH