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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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Representative structure and detailed views of four different fragments connecting G-rich strands in the G-quadruplex core. Guanine, LNA, adenine, thymine and cytosine residues are colored orange, yellow, red, blue and purple, respectively. Guanine residues of the G-quadruplex core are shown in light orange in the views of loop fragments.
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gkt697-F5: Representative structure and detailed views of four different fragments connecting G-rich strands in the G-quadruplex core. Guanine, LNA, adenine, thymine and cytosine residues are colored orange, yellow, red, blue and purple, respectively. Guanine residues of the G-quadruplex core are shown in light orange in the views of loop fragments.

Mentions: Structure calculation was based on a large number of NOE distance and other types of restraints (Table 1). We have refrained from using ambiguous NOE restraints in structural calculations. As a consequence, only 248 NOE distance restraints were used of ∼360 assigned NOE cross-peaks in 2D NOESY spectra. Ambiguous NOE restraints were, however, used in the evaluation process, and structures not in agreement with the observed NOEs were discarded. Superimposition of the 10 lowest energy structures with the lowest number of restraint violations is presented in Figure 4b, and representative structure in Figure 5.Figure 5.


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)

Representative structure and detailed views of four different fragments connecting G-rich strands in the G-quadruplex core. Guanine, LNA, adenine, thymine and cytosine residues are colored orange, yellow, red, blue and purple, respectively. Guanine residues of the G-quadruplex core are shown in light orange in the views of loop fragments.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkt697-F5: Representative structure and detailed views of four different fragments connecting G-rich strands in the G-quadruplex core. Guanine, LNA, adenine, thymine and cytosine residues are colored orange, yellow, red, blue and purple, respectively. Guanine residues of the G-quadruplex core are shown in light orange in the views of loop fragments.
Mentions: Structure calculation was based on a large number of NOE distance and other types of restraints (Table 1). We have refrained from using ambiguous NOE restraints in structural calculations. As a consequence, only 248 NOE distance restraints were used of ∼360 assigned NOE cross-peaks in 2D NOESY spectra. Ambiguous NOE restraints were, however, used in the evaluation process, and structures not in agreement with the observed NOEs were discarded. Superimposition of the 10 lowest energy structures with the lowest number of restraint violations is presented in Figure 4b, and representative structure in Figure 5.Figure 5.

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