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G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold.

Marušič M, Veedu RN, Wengel J, Plavec J - Nucleic Acids Res. (2013)

Bottom Line: Both 5' with 3 nt and 3' with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology.Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex.Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.

View Article: PubMed Central - PubMed

Affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia, School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Brisbane, 4072 Australia, Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark, EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia and Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia.

ABSTRACT
The formation of a single G-quadruplex structure adopted by a promising 25 nt G-rich vascular endothelial growth factor aptamer in a K(+) rich environment was facilitated by locked nucleic acid modifications. An unprecedented all parallel-stranded monomeric G-quadruplex with three G-quartet planes exhibits several unique structural features. Five consecutive guanine residues are all involved in G-quartet formation and occupy positions in adjacent DNA strands, which are bridged with a no-residue propeller-type loop. A two-residue D-shaped loop facilitates inclusion of an isolated guanine residue into the vacant spot within the G-quartet. The remaining two G-rich tracts of three residues each adopt parallel orientation and are linked with edgewise and propeller loops. Both 5' with 3 nt and 3' with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology. Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex. Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.

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Related in: MedlinePlus

Close-up views of (a) stacking of T1-T3 on G4-G11-G14-G19 quartet and (b-c) two distinct conformations of A25 in the T22-A25 capping structure stacked over the G6-G8-G16-L21 quartet. Guanine, LNA, adenine, thymine and cytosine residues of loops are depicted in orange, yellow, red, blue and pink, respectively; G-quartet forming residues are shown in gray.
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gkt697-F7: Close-up views of (a) stacking of T1-T3 on G4-G11-G14-G19 quartet and (b-c) two distinct conformations of A25 in the T22-A25 capping structure stacked over the G6-G8-G16-L21 quartet. Guanine, LNA, adenine, thymine and cytosine residues of loops are depicted in orange, yellow, red, blue and pink, respectively; G-quartet forming residues are shown in gray.

Mentions: Residues of the T1-T3 and T22-A25 regions exhibit several inter-residual NOE contacts and are well defined in the calculated structures. The T1-T3 flanking region participates in continuous stacking of a G4-G6 strand of the G-quadruplex core (Figures 4b and 7a). T3 displays one of the highest numbers of NOE restraints per residue (Supplementary Figure S5), and its stacked position on G4-G11-G14-G19 quartet is very well defined. Although stacking interactions with T3 keep G2 in relatively restrained conformational space, T1 exhibits the greatest level of flexibility in the T1-T3 segment (Figure 4b).Figure 7.


G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold.

Marušič M, Veedu RN, Wengel J, Plavec J - Nucleic Acids Res. (2013)

Close-up views of (a) stacking of T1-T3 on G4-G11-G14-G19 quartet and (b-c) two distinct conformations of A25 in the T22-A25 capping structure stacked over the G6-G8-G16-L21 quartet. Guanine, LNA, adenine, thymine and cytosine residues of loops are depicted in orange, yellow, red, blue and pink, respectively; G-quartet forming residues are shown in gray.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814366&req=5

gkt697-F7: Close-up views of (a) stacking of T1-T3 on G4-G11-G14-G19 quartet and (b-c) two distinct conformations of A25 in the T22-A25 capping structure stacked over the G6-G8-G16-L21 quartet. Guanine, LNA, adenine, thymine and cytosine residues of loops are depicted in orange, yellow, red, blue and pink, respectively; G-quartet forming residues are shown in gray.
Mentions: Residues of the T1-T3 and T22-A25 regions exhibit several inter-residual NOE contacts and are well defined in the calculated structures. The T1-T3 flanking region participates in continuous stacking of a G4-G6 strand of the G-quadruplex core (Figures 4b and 7a). T3 displays one of the highest numbers of NOE restraints per residue (Supplementary Figure S5), and its stacked position on G4-G11-G14-G19 quartet is very well defined. Although stacking interactions with T3 keep G2 in relatively restrained conformational space, T1 exhibits the greatest level of flexibility in the T1-T3 segment (Figure 4b).Figure 7.

Bottom Line: Both 5' with 3 nt and 3' with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology.Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex.Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.

View Article: PubMed Central - PubMed

Affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia, School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Brisbane, 4072 Australia, Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark, EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia and Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia.

ABSTRACT
The formation of a single G-quadruplex structure adopted by a promising 25 nt G-rich vascular endothelial growth factor aptamer in a K(+) rich environment was facilitated by locked nucleic acid modifications. An unprecedented all parallel-stranded monomeric G-quadruplex with three G-quartet planes exhibits several unique structural features. Five consecutive guanine residues are all involved in G-quartet formation and occupy positions in adjacent DNA strands, which are bridged with a no-residue propeller-type loop. A two-residue D-shaped loop facilitates inclusion of an isolated guanine residue into the vacant spot within the G-quartet. The remaining two G-rich tracts of three residues each adopt parallel orientation and are linked with edgewise and propeller loops. Both 5' with 3 nt and 3' with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology. Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex. Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.

Show MeSH
Related in: MedlinePlus