Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

DNA origami nanostructures are a versatile tool that can be used to arrange functionalities with high local control to study molecular processes at a single-molecule level. Here, we demonstrate that DNA origami substrates can be used to suppress the formation of specific guanine (G) quadruplex structures from telomeric DNA. The folding of telomeres into G-quadruplex structures in the presence of monovalent cations (e.g. Na(+) and K(+)) is currently used for the detection of K(+) ions, however, with insufficient selectivity towards Na(+). By means of FRET between two suitable dyes attached to the 3'- and 5'-ends of telomeric DNA we demonstrate that the formation of G-quadruplexes on DNA origami templates in the presence of sodium ions is suppressed due to steric hindrance. Hence, telomeric DNA attached to DNA origami structures represents a highly sensitive and selective detection tool for potassium ions even in the presence of high concentrations of sodium ions.

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“…[7] Telomeres are located at the ends of eukaryotic chromosomes, and stabilize and protect the genome.…”

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confidence: 99%

Ion‐Selective Formation of a Guanine Quadruplex on DNA Origami Structures

2014

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“…A G-rich sequence with only three G-tracts may form a G-triplex with stacked G-triads, in which a central guanine connects with two other guanines by Hoogsteen-like hydrogen-bonds (Figure 1)78910. The formation of these G-triplexes has been hypothesized111213, and experiments have suggested that they might be intermediates during folding or unfolding of G-quadruplexes91314151617. Recently, Limongelli et al demonstrated the formation of G-triplexes in the G-rich sequence, 5'-GGTTGGTGTGG-3', using nuclear magnetic resonance (NMR) experiment in a dilute solution78.…”

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confidence: 99%

Divalent cations and molecular crowding buffers stabilize G-triplex at physiologically relevant temperatures

Jiang

Cui

Zhao

et al. 2015

Sci Rep

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G-triplexes are non-canonical DNA structures formed by G-rich sequences with three G-tracts. Putative G-triplex-forming sequences are expected to be more prevalent than putative G-quadruplex-forming sequences. However, the research on G-triplexes is rare. In this work, the effects of molecular crowding and several physiologically important metal ions on the formation and stability of G-triplexes were examined using a combination of circular dichroism, thermodynamics, optical tweezers and calorimetry techniques. We determined that molecular crowding conditions and cations, such as Na+, K+, Mg2+ and Ca2+, promote the formation of G-triplexes and stabilize these structures. Of these four metal cations, Ca2+ has the strongest stabilizing effect, followed by K+, Mg2+, and Na+ in a decreasing order. The binding of K+ to G-triplexes is accompanied by exothermic heats, and the binding of Ca2+ with G-triplexes is characterized by endothermic heats. G-triplexes formed from two G-triad layers are not stable at physiological temperatures; however, G-triplexes formed from three G-triads exhibit melting temperatures higher than 37°C, especially under the molecular crowding conditions and in the presence of K+ or Ca2+. These observations imply that stable G-triplexes may be formed under physiological conditions.

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“…HS-AFM imaging of DNA origami locators presenting G-quadruplex--forming domains captured molecular phenomena associated with this process, such as protein sliding, 3D hopping between DNA strands, G-quadruplex formation, and protein dissociation. In fact, the power of DNA origami locators as imaging probes for AFM is best illustrated by the observation of key in-pathway intermediates in G-quadruplex formation, such as G hairpins and G triplexes (Figure 1 c ) (37). The direct observation of these intermediates had, until then, proved elusive by any known experimental technique.…”

Section: In Vitro Imaging Of Biomoleculesmentioning

confidence: 99%

“…( c ) Visualization of G-quadruplex formation by two G-rich sequences positioned proximally. Panel c modified from Reference 37 with permission.…”

Section: Figurementioning

confidence: 99%

Nucleic Acid–Based Nanodevices in Biological Imaging

Chakraborty

Veetil

Jaffrey

et al. 2016

Annu. Rev. Biochem.

129

109

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The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid--based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid--based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

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Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

Cited by 110 publications

References 39 publications

Ion‐Selective Formation of a Guanine Quadruplex on DNA Origami Structures

Ion‐Selective Formation of a Guanine Quadruplex on DNA Origami Structures

Divalent cations and molecular crowding buffers stabilize G-triplex at physiologically relevant temperatures

Nucleic Acid–Based Nanodevices in Biological Imaging

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