Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles

Kanayama, Naoki; Kishi, Satomi; Takarada, Tohru; Maeda, Mizuo

doi:10.1039/d0cc05085g

Cited by 12 publications

(10 citation statements)

References 43 publications

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“…3,6,12−16 For instance, Kanayama et al have developed a setup to induce blunt-end stacking through photo-switching. 17 Although the strength of DNA stacking interactions has been extensively studied for twist values close to B-form DNA, 2,11,18−20 the dependence on the relative orientation (twist) of stacking base pairs is much less explored, except for few cases. 21 In the case of blunt-end stacking, the twisting at the blunt-end step is much less restricted compared to regular dsDNA.…”

Section: ■ Introductionmentioning

confidence: 99%

“…However, frequently DNA molecules interact via blunt-end stacking, for example, produced by endonuclease cleavage, for example, as an intermediate in the CRISPR/Cas mechanism − or during repair of double-strand breaks upon DNA damage. Also, spontaneous assembly of long end-to-end aggregates of duplex DNA oligonucleotides has been observed, resulting in formation of long rod-like structures. , Blunt-end DNA stacking also influences DNA crystallization, fraying at DNA ends, and plays a major role in DNA origami nanotechnology. ,,− For instance, Kanayama et al have developed a setup to induce blunt-end stacking through photo-switching . Although the strength of DNA stacking interactions has been extensively studied for twist values close to B-form DNA, ,,− the dependence on the relative orientation (twist) of stacking base pairs is much less explored, except for few cases .…”

Section: Introductionmentioning

confidence: 99%

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Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations

2021

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DNA blunt ends can associate mediated by stacking interactions between the terminal base pairs that form blunt ends. The blunt end association plays a role in DNA repair and recombination processes and can also be of importance for the design of DNA-based nano-materials. Its function depends on the sequence and on the geometric arrangement that leads to stable interaction. For a stacked state, the relative orientation (twisting) of the base pairs is important. Molecular dynamics and advanced sampling simulations were used to calculate free energy change associated with twist changes of the stacked blunt-end base pairs. The calculations reproduce blunt stacking arrangements found in crystal structures of DNA oligonucleotides as free energy minima. To elucidate the physical origin of the stabilization of certain angular arrangements, the interactions between backbone atoms in the blunt-end stack were switched off in additional free energy calculations. It allows us to decipher the contributions to stacking stabilization due to the nucleobases and the backbone and to analyze the sequence dependence of the angular stacking preferences. Good qualitative agreement was also found for the comparison with quantum mechanical calculations. The results may help in the design of novel DNA-based materials.

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Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations

2021

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“…Finally, we wish to emphasize that the terminal-specific duplex–duplex interaction does not usually occur at the typical concentration of solution (μM-order) even under the high-salt conditions. , Surface-immobilized duplex strands have significantly restricted freedom in diffusional motion and conformation, and such a situation would be favorable to promote the terminal-specific interaction upon their approach to each other. We believe that such an effect is also responsible for the terminal sequence-specific noncrosslinking aggregation behavior of DNA-functionalized nanomaterials …”

Section: Resultsmentioning

confidence: 98%

“…We believe that such an effect is also responsible for the terminal sequence-specific noncrosslinking aggregation behavior of DNA-functionalized nanomaterials. 60…”

Section: Influence Of Cationmentioning

confidence: 99%

Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers

2021

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The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force−distance (F−D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3− 5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F−D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F−D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl 2 solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.

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“…A different strategy for the photo-responsive reversible assembly of gold nanoparticles was demonstrated by Kanayama and co-workers. 155 In their study, they functionalised dsDNA with an azobenzene derivative with a d -threoninol linker for the reversible assembly of gold nanoparticles via end-to-end stacking between blunt-ended DNA duplexes. This interaction did not involve hybridisation between complementary ssDNA, but originated from the π–π stacking between terminal nucleobases coming in close proximity under the appropriate ionic strength conditions.…”

Section: Cyclobutane Pyrimidine Dna Modificationsmentioning

confidence: 99%

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

et al. 2021

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Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles

Abstract: End-to-end intermolecular interaction between double-stranded DNAs grafted onto individual nanoparticles is regulated by terminal base pairing/unpairing triggered by the photo-isomerization of an azobenzene moiety inserted in the vicinity of the...

Cited by 12 publications

References 43 publications

Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations

Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations

Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

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