Folding DNA into origami nanostructures enhances resistance to ionizing radiation

Sala, Leo; Zerolová, Agnes; Rodríguez, Álvaro; Reimitz, Dan; Davídková, Marie; Ebel, Kenny; Bald, Ilko; Kočišek, Jaroslav

doi:10.1039/d1nr02013g

Cited by 18 publications

(33 citation statements)

References 38 publications

(47 reference statements)

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“…To identify possible effects of the surface pretreatment on the structural integrity of the DOTs, we also quantified the fractions of intact and damaged DOTs based on an established classification scheme [ 30 , 37 , 38 ]. In this scheme, the classification “damaged” applies to all DOTs whose shape clearly deviates from the original DOT design (see Ref.…”

Section: Resultsmentioning

confidence: 99%

“…The numbers of intact and damaged DOTs visible in the AFM images were counted manually and averaged over five to twelve AFM images recorded under equivalent conditions. The established AFM-based classification of DOTs into intact, broken, denatured, and deformed was applied [ 30 , 37 ]. However, because of the different RMS roughness values obtained after the different pretreatments, only severely deformed DOTs were considered damaged, while slightly deformed ones were treated as intact.…”

Section: Methodsmentioning

confidence: 99%

“…In such settings, an insufficient Mg 2+ concentration will result in either high mobility of the adsorbed DONs, which makes them susceptible to post-adsorption manipulation [ 25 , 26 ], or the retardation [ 27 ] or even complete suppression [ 28 ] of DON adsorption. To avoid these issues, previous studies have mixed the Mg 2+ -free samples with Mg 2+ -containing solutions right before immobilization on mica [ 24 , 29 , 30 ]. While this approach has proven useful for evaluating the structural integrity of the DONs after exposure to denaturing environments [ 24 , 29 ] or ionizing radiation [ 30 ], it is incompatible with the in situ investigation of biomolecular processes such as protein binding [ 31 , 32 ], enzymatic reactions [ 33 , 34 ], or conformational dynamics [ 35 , 36 ] under essentially Mg 2+ -free conditions.…”

Section: Introductionmentioning

confidence: 99%

“…To avoid these issues, previous studies have mixed the Mg 2+ -free samples with Mg 2+ -containing solutions right before immobilization on mica [ 24 , 29 , 30 ]. While this approach has proven useful for evaluating the structural integrity of the DONs after exposure to denaturing environments [ 24 , 29 ] or ionizing radiation [ 30 ], it is incompatible with the in situ investigation of biomolecular processes such as protein binding [ 31 , 32 ], enzymatic reactions [ 33 , 34 ], or conformational dynamics [ 35 , 36 ] under essentially Mg 2+ -free conditions. In this work, we thus explore alternative means for immobilizing DONs at mica surfaces that do not rely on the addition of Mg 2+ ions to the DON-containing solution (see Figure 1 b–d).…”

Section: Introductionmentioning

confidence: 99%

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Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

et al. 2021

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DNA origami nanostructures (DONs) are promising substrates for the single-molecule investigation of biomolecular reactions and dynamics by in situ atomic force microscopy (AFM). For this, they are typically immobilized on mica substrates by adding millimolar concentrations of Mg2+ ions to the sample solution, which enable the adsorption of the negatively charged DONs at the like-charged mica surface. These non-physiological Mg2+ concentrations, however, present a serious limitation in such experiments as they may interfere with the reactions and processes under investigation. Therefore, we here evaluate three approaches to efficiently immobilize DONs at mica surfaces under essentially Mg2+-free conditions. These approaches rely on the pre-adsorption of different multivalent cations, i.e., Ni2+, poly-l-lysine (PLL), and spermidine (Spdn). DON adsorption is studied in phosphate-buffered saline (PBS) and pure water. In general, Ni2+ shows the worst performance with heavily deformed DONs. For 2D DON triangles, adsorption at PLL- and in particular Spdn-modified mica may outperform even Mg2+-mediated adsorption in terms of surface coverage, depending on the employed solution. For 3D six-helix bundles, less pronounced differences between the individual strategies are observed. Our results provide some general guidance for the immobilization of DONs at mica surfaces under Mg2+-free conditions and may aid future in situ AFM studies.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

et al. 2021

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“…In previous work, absolute single strand break cross sections have been determined for homooligomers, 20 , 21 mixed sequences, 22 telomeric DNA, 23 and ssDNA sensitized with potential radiosensitizers. 24 − 26 In addition to LEE irradiation, also experiments with vacuum-UV radiation 21 as well as X-rays and γ rays 27 have been performed. However, so far only single strand break cross sections have been determined.…”

mentioning

confidence: 99%

Low-Energy (5–20 eV) Electron-Induced Single and Double Strand Breaks in Well-Defined DNA Sequences

Ebel

Bald

2022

J. Phys. Chem. Lett.

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Ionizing radiation is used in cancer radiation therapy to effectively damage the DNA of tumors. The main damage is due to generation of highly reactive secondary species such as low-energy electrons (LEEs). The accurate quantification of DNA radiation damage of well-defined DNA target sequences in terms of absolute cross sections for LEE-induced DNA strand breaks is possible by the DNA origami technique; however, to date, it is possible only for DNA single strands. In the present work DNA double strand breaks in the DNA sequence 5′-d(CAC) 4 /5′-d(GTG) 4 are compared with DNA single strand breaks in the oligonucleotides 5′-d(CAC) 4 and 5′-d(GTG) 4 upon irradiation with LEEs in the energy range from 5 to 20 eV. A maximum of strand break cross section was found around 7 and 10 eV independent of the DNA sequence, indicating that dissociative electron attachment is the underlying mechanism of strand breakage and confirming previous studies using plasmid DNA.

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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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Folding DNA into origami nanostructures enhances resistance to ionizing radiation

Abstract: The multi-row design of DNA origami structures holds their shape even after severe nicking due to ionizing radiation and their folded structure has a protective effect, i.e., reduced damage compared to free scaffold and similarly sized plasmid DNA.

Cited by 18 publications

References 38 publications

Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

Low-Energy (5–20 eV) Electron-Induced Single and Double Strand Breaks in Well-Defined DNA Sequences

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

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