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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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Structural representations of the XyloNA duplex as determined by NMR structural analysis, (A) a close view of the minimum energy closest-to-average structure showing base stacking interactions and the proximity of the diagonal anomeric protons as observed in the NOESY spectra, (B) view from the minor groove, (C) side view with highlighted backbone, (D) view from the major groove, and (E) an overlay of 20 refined structures representing convergence in the structure calculation.
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Figure 7: Structural representations of the XyloNA duplex as determined by NMR structural analysis, (A) a close view of the minimum energy closest-to-average structure showing base stacking interactions and the proximity of the diagonal anomeric protons as observed in the NOESY spectra, (B) view from the minor groove, (C) side view with highlighted backbone, (D) view from the major groove, and (E) an overlay of 20 refined structures representing convergence in the structure calculation.

Mentions: To examine the nature of the helical structure adopted by the dsXyloNA (ON-1), we have undertaken solution state NMR structural analysis. Appearance of a single set of resonances in the NMR spectra suggests the formation of a unique type of duplex conformation (Figure 5A and B). The duplex forms Watson–Crick type base-pairing with anti-parallel strand orientation as evidenced by the hydrogen-bonded imino-proton signals in the NMR spectrum recorded in H2O (Figure 5A and Supplementary Figure S6). All the xylose sugar rings are in N-type puckering as suggested by the appearance of singlet anomeric-proton peaks in the 1H NMR spectrum (Figure 5B). Unlike native DNA/RNA double helices, unique diagonal cross-strand (n+1 to n-1) NOE interactions between anomeric (H1′) protons were observed in XyloNA self-duplex, as depicted in Figure 5C. Although less pronounced, a classical NOE-walk (Figure 6) between aromatic and anomeric protons was observed, that is generally more prominent in the natural DNA/RNA helices. During simulations, the structures were converged (structure statistics in SI, Supplementary Table S2) to a family of structures (Figure 7B-D and E) with similar geometries and energies. The aforementioned diagonal NOE distance restraints were also reflected in the final structure as depicted in Figure 7A. Diagnostic helical parameters and backbone dihedral angles were calculated and compared (Table 2) with the natural DNA/RNA helices. Atomic coordinates for 20 refined structures, structural restraints, and assigned chemical shifts have been deposited in the RCSB Protein Data Bank with PDB ID 2N4J. Unlike the natural B-DNA and A-RNA helices, XyloNA duplex like dXyloNA (24) has adopted a slightly right-handed extended ladder-like structure (Figure 7B–D) with significantly impaired helicity. This has been reflected by the relatively low helical twist (10.7° versus 32.7°) and high base-pair rise (5.1 Ǻ versus 2.8 Ǻ). Both the major and minor grooves are widened to an extent that they are almost indistinguishable (Figure 7B and D). Nucleobases are highly inclined with respect to the backbone, as shown by a high inclination value (Table 2). Thus, it is predominantly forming a zipper like interstrand stacking interaction to provide duplex stabilization, in contrary to a dominant intrastrand stacking as found in native DNA/RNA helices. This interstrand interaction could be a cause for higher thermodynamic stability in XyloNA. High and dissimilar inclination together with largely reduced helicity of XyloNA compared with DNA/RNA might be the reasons for its inability in cross-pairing with the DNA/RNA complements (37). A comparison of the torsion angles (Table 2) between XyloNA and DNA/RNA suggests a cooperative adjustment in different dihedral angles across the sugar-phosphate backbone. The chiral inversion in the 3′-carbon center of the sugar ring in XyloNA with respect to DNA/RNA primarily changed the endo-cyclic torsion angle δ to synclinal− from gauche+ or anticlinal+. This leads to a chain of inversions in α, γ and ζ torsion angles from an almost mirror-image domain (opposite in sign and magnitude, shown in Table 2) while retaining both the torsion angles β and ϵ in the anti domain. These distinctive features allow a rationalization of the structural orthogonality of XyloNA in comparison with the natural DNA/RNA.


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)

Structural representations of the XyloNA duplex as determined by NMR structural analysis, (A) a close view of the minimum energy closest-to-average structure showing base stacking interactions and the proximity of the diagonal anomeric protons as observed in the NOESY spectra, (B) view from the minor groove, (C) side view with highlighted backbone, (D) view from the major groove, and (E) an overlay of 20 refined structures representing convergence in the structure calculation.
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Related In: Results  -  Collection

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Show All Figures
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Figure 7: Structural representations of the XyloNA duplex as determined by NMR structural analysis, (A) a close view of the minimum energy closest-to-average structure showing base stacking interactions and the proximity of the diagonal anomeric protons as observed in the NOESY spectra, (B) view from the minor groove, (C) side view with highlighted backbone, (D) view from the major groove, and (E) an overlay of 20 refined structures representing convergence in the structure calculation.
Mentions: To examine the nature of the helical structure adopted by the dsXyloNA (ON-1), we have undertaken solution state NMR structural analysis. Appearance of a single set of resonances in the NMR spectra suggests the formation of a unique type of duplex conformation (Figure 5A and B). The duplex forms Watson–Crick type base-pairing with anti-parallel strand orientation as evidenced by the hydrogen-bonded imino-proton signals in the NMR spectrum recorded in H2O (Figure 5A and Supplementary Figure S6). All the xylose sugar rings are in N-type puckering as suggested by the appearance of singlet anomeric-proton peaks in the 1H NMR spectrum (Figure 5B). Unlike native DNA/RNA double helices, unique diagonal cross-strand (n+1 to n-1) NOE interactions between anomeric (H1′) protons were observed in XyloNA self-duplex, as depicted in Figure 5C. Although less pronounced, a classical NOE-walk (Figure 6) between aromatic and anomeric protons was observed, that is generally more prominent in the natural DNA/RNA helices. During simulations, the structures were converged (structure statistics in SI, Supplementary Table S2) to a family of structures (Figure 7B-D and E) with similar geometries and energies. The aforementioned diagonal NOE distance restraints were also reflected in the final structure as depicted in Figure 7A. Diagnostic helical parameters and backbone dihedral angles were calculated and compared (Table 2) with the natural DNA/RNA helices. Atomic coordinates for 20 refined structures, structural restraints, and assigned chemical shifts have been deposited in the RCSB Protein Data Bank with PDB ID 2N4J. Unlike the natural B-DNA and A-RNA helices, XyloNA duplex like dXyloNA (24) has adopted a slightly right-handed extended ladder-like structure (Figure 7B–D) with significantly impaired helicity. This has been reflected by the relatively low helical twist (10.7° versus 32.7°) and high base-pair rise (5.1 Ǻ versus 2.8 Ǻ). Both the major and minor grooves are widened to an extent that they are almost indistinguishable (Figure 7B and D). Nucleobases are highly inclined with respect to the backbone, as shown by a high inclination value (Table 2). Thus, it is predominantly forming a zipper like interstrand stacking interaction to provide duplex stabilization, in contrary to a dominant intrastrand stacking as found in native DNA/RNA helices. This interstrand interaction could be a cause for higher thermodynamic stability in XyloNA. High and dissimilar inclination together with largely reduced helicity of XyloNA compared with DNA/RNA might be the reasons for its inability in cross-pairing with the DNA/RNA complements (37). A comparison of the torsion angles (Table 2) between XyloNA and DNA/RNA suggests a cooperative adjustment in different dihedral angles across the sugar-phosphate backbone. The chiral inversion in the 3′-carbon center of the sugar ring in XyloNA with respect to DNA/RNA primarily changed the endo-cyclic torsion angle δ to synclinal− from gauche+ or anticlinal+. This leads to a chain of inversions in α, γ and ζ torsion angles from an almost mirror-image domain (opposite in sign and magnitude, shown in Table 2) while retaining both the torsion angles β and ϵ in the anti domain. These distinctive features allow a rationalization of the structural orthogonality of XyloNA in comparison with the natural DNA/RNA.

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
Related in: MedlinePlus