Abstract
The nucleolin-binding G-quadruplex AS1411 aptamer has been widely used for cancer therapy and diagnosis and linked to nanoparticles for its selective targeting activity. We applied a computational and experimental integrated approach to study the effect of engineering AS1411 aptamer on an octahedral truncated DNA nanocage to obtain a nanostructure able to combine selective cancer-targeting and anti-tumor activity. The nanocages functionalized with one aptamer molecule (Apt-NC) displayed high stability in serum, were rapidly and selectively internalized in cancer cells through an AS1411-dependent mechanism, and showed over 200-fold increase in anti-cancer activity when compared with the free aptamer. Comparison of Apt-NCs and free AS1411 intracellular distribution showed that they traffic differently inside cells: Apt-NCs distributed through the endo-lysosomal pathway and were never found in the nuclei, while the free AS1411 was mostly found in the perinuclear region and in nucleoli. Molecular dynamics simulations indicated that the aptamer, when linked to the nanocage, sampled a limited conformational space, more confined than in the free state, which is characterized by a large number of metastable conformations. A different intracellular trafficking of Apt-NCs compared with free aptamer and the confined aptamer conformations induced by the nanocage were likely correlated with the high cytotoxic enhancement, suggesting a structure–function relationship for the AS1411 aptamer activity.
Highlights
Aptamers are short single-stranded DNA or RNA oligonucleotides with stable threedimensional structures capable of binding with high affinity to a variety of molecular targets [1]
The 26-base G-rich AS1411 aptamer has been identified as an anti-cancer agent, which recognizes nucleolin on the cancer cell surface with high selectivity and affinity [5,6]
Molecular dynamics simulations of two 3D models of free AS1411 in comparison with the aptamer-functionalized nanocage indicated that the free aptamer sampled a large number of metastable conformations, while the conformations were more localized and confined into a low-energy conformational basin when linked to the nanocage. These results indicate that the nanocage constrains the aptamer in a more defined conformation, likely correlated to the different intracellular localization and higher therapeutic effect
Summary
Aptamers are short single-stranded DNA or RNA oligonucleotides with stable threedimensional structures capable of binding with high affinity to a variety of molecular targets [1]. A unique class of aptamers is constituted of G-rich sequences that, under physiological conditions, spontaneously fold into non-canonical four-stranded structures named G-quadruplexes. These are characterized by the stacking of two or more successive planes of four guanine residues arranged in a square planar array via Hoogsteen hydrogen bonding (a G-quartet). G-quadruplex structures are highly polymorphic, and a single sequence can fold into several different conformations, depending on the relative orientations of strands and types of loops [2,3,4]. As other G-quadruplex aptamers, AS1411 adopts a mixture of multiple structures in solution, and one of them has been solved through
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
