Formation of Highly Ordered Multimers in G-Quadruplexes

Abstract

G-Rich DNA and RNA have a higher propensity to form G-quadruplex structures, but the presence of G-runs alone is not sufficient to prove that such sequences can form stable G-quadruplexes. While G-rich sequences are essential for G-quadruplex formation, not all G-rich sequences have the propensity to form G-quadruplex structures. In addition, monovalent metal ions, dehydrating agents, and loop sequences connecting the G-runs also play important roles in the topology of G-quadruplex folding. To date, no quantitative analysis of the CD spectra of G-quadruplexes in confrontation with the electrophoretic results has been performed. Therefore, in this study, we use information gained through the analysis of a series of well-known G-quadruplex-forming sequences to evaluate other less-studied sets of aptameric sequences. A simple and cost-effective methodology that can verify the formation of G-quadruplex motifs from oligomeric DNA sequences and a technique to determine the molecularity of these structures are also described. This methodology could be of great use in the prediction of G-quadruplex assembly, and the basic principles of our techniques can be extrapolated for any G-rich DNA sequences. This study also presents a model that can predict the multimerization of G-quadruplexes; the predictions offered by this model are shown to match the results obtained using circular dichroism.

Homogeneous chemiluminescent DNA assay based on allosteric activation of peroxidase-mimicking DNAzyme

“…2). 20,21 The similar spectrum was recorded for the complex of the probe and TDNA (Fig. 2 (curve 1), the spectrum of the probe (in the presence of K + and Na + cations) has a positive signal at around 264 nm and a negative signal at 242 nm, which are characteristic of parallel G-quadruplexes.…”

Structure–activity relationship study for design of highly active covalent peroxidase-mimicking DNAzyme

“…3. 21,32 Moreover, we showed that CD spectra of PMDNAzyme(T 10 ) in the presence and in the absence of K + cations were practically identical, whereas CD spectra of NH 2 -T 10 -EAD2 changed (Fig. 21 The similar spectrum was measured for the aptamer NH 2 -T 10 -EAD2 itself.…”

Self‐Assembly of G‐Rich Oligonucleotides Incorporating a 3′–3′ Inversion of Polarity Site: A New Route Towards G‐Wire DNA Nanostructures

“…Depending on the topological arrangement of the G‐rich strands participating in their formation, G‐wires can be classified into two categories: i) interlocked G‐wires , characterized by the cooperative assembly of interlocked slipped strands (Figure B) and ii) stacked G‐wires , characterized by the multimerization of G‐quadruplex building blocks held together by end‐to‐end π–π stacking (Figure C). Besides the well‐known interlocked G‐wires and G‐wires containing both topological motifs, only a few examples of exclusively stacked G‐wires have been reported so far …”