Anion-specific structure and stability of guanidinium-bound DNA origami

Hanke, Marcel; Dornbusch, Daniel; Hadlich, Christoph; Roßberg, André; Hansen, Niklas; Grundmeier, Guido; Tsushima, Satoru; Keller, Adrian; Fahmy, Karim

doi:10.1016/j.csbj.2022.05.037

Cited by 9 publications

(40 citation statements)

References 61 publications

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“…For investigating the time dependence of DNA origami denaturation in the different Gdm salts, we exposed DNA origami triangles [ 40 ] to comparably low Gdm salt concentrations of 2 M. The Rothemund triangle is one of the most studied DNA origami nanostructures, particularly with regard to its stability under various conditions [ 1 , 2 , 5 , 10 , 11 , 12 , 14 , 16 , 17 , 20 , 24 , 25 , 41 , 42 , 43 , 44 , 45 ], including the presence of molar concentrations of Gdm salts [ 28 , 29 , 30 ]. It is composed of three trapezoids of parallel double helices that are connected to each other via one scaffold crossover and four bridging staples.…”

Section: Resultsmentioning

confidence: 99%

“…It is composed of three trapezoids of parallel double helices that are connected to each other via one scaffold crossover and four bridging staples. For exposure to 2 M GdmCl, only low to moderate fractions of damaged DNA origami triangles have been observed in the temperature range between 23 and 42 °C [ 30 ]. However, in the current work, we extended the temperature range slightly and recorded AFM images of the DNA origami triangles after incubation at 25, 40, and 50 °C, in order to assess a broader dynamic range in the observable damage.…”

Section: Resultsmentioning

confidence: 99%

“…In our previous studies, we investigated the denaturation of DNA origami nanostructures by chaotropic guanidinium (Gdm) salts [ 28 , 29 , 30 ], which are widely used in biotechnology and biophysics as potent protein denaturants [ 31 ]. In general, the denaturation of a polypeptide chain is associated with a gain in conformational entropy, which is counteracted by an entropy loss of the surrounding water molecules resulting from the increase of solvent-excluded volume upon unfolding [ 32 ].…”

Section: Introductionmentioning

confidence: 99%

“…However, the molecular mechanisms involved in Gdm + –protein interactions are still a topic of intense research [ 34 , 35 ], and only few studies so far have attempted to elucidate its effects on dsDNA [ 36 , 37 ]. Our previous investigations revealed that Gdm + -induced DNA origami denaturation is governed by a complex interplay among the denaturing Gdm + ions, the environmental conditions such as temperature and Gdm + concentration [ 28 ], the counteranion species [ 30 ], and the presence of additional cations, which was found to induce more severe denaturation [ 29 ]. The counteranion species in particular was found to have a surprisingly strong influence on the denaturant activity of Gdm + .…”

Section: Introductionmentioning

confidence: 99%

“…The counteranion species in particular was found to have a surprisingly strong influence on the denaturant activity of Gdm + . Using a combination of in situ circular dichroism (CD) spectroscopy and ex situ AFM, a thermodynamic model of DNA origami denaturation by guanidinium chloride (GdmCl) and guanidinium sulfate (Gdm 2 SO 4 ) was derived on the basis of principle component analysis (PCA) and iterative target test factor analysis (ITTFA) [ 30 ]. The results showed that Gdm + -induced DNA origami denaturation proceeds via three successive state transitions involving an intermediate pre-melding state.…”

Section: Introductionmentioning

confidence: 99%

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Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate

Hanke

Hansen

Tomm

et al. 2022

IJMS

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Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm2SO4), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm2SO4 at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm2SO4 with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate

Hanke

Hansen

Tomm

et al. 2022

IJMS

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Effect of Ionic Strength on the Thermal Stability of DNA Origami Nanostructures

et al. 2023

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The stability of DNA origami nanostructures in aqueous media is closely tied to the presence of cations that screen electrostatic inter‐helix repulsion. Here, the thermal melting behavior of different DNA origami nanostructures is investigated in dependence on Mg2+ concentration and compared to calculated ensemble melting temperatures of the staple strands used in DNA origami folding. Strong deviations of the measured DNA origami melting temperatures from the calculated ones are observed, in particular at high ionic strength where the melting temperature saturates and becomes independent of ionic strength. The degree of deviation between the measured and calculated melting temperatures further depends on the superstructure and in particular the mechanical properties of the DNA origami nanostructures. This indicates that thermal stability of a given DNA origami design at high ionic strength is governed predominantly not by electrostatic inter‐helix repulsion but mostly by mechanical strain.

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Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions

Linko

Keller

2023

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Programmable, custom‐shaped, and nanometer‐precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular‐level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review – through its specific viewpoint – may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.

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Anion-specific structure and stability of guanidinium-bound DNA origami

Cited by 9 publications

References 61 publications

Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate

Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate

Effect of Ionic Strength on the Thermal Stability of DNA Origami Nanostructures

Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions

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