Nanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes

Stassi, Stefano; Marini, Monica; Allione, Marco; Lopatin, Sergei; Laurini, Erik; Pricl, Sabrina; Pirri, Candido; Ricciardi, Carlo; Fabrizio, Enzo M. Di

doi:10.1038/s41467-019-09612-0

Cited by 23 publications

(30 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The observed increase in γ upon drug intercalation is in accord with recent experimental studies. 23,24 In contrast, we find that the persistence length and the bending modulus κ of dsDNA decrease upon intercalation of daunomycin or ethidium. There results for the change in of DNA upon drug intercalations reported in various experimental studies disagree with each other, as discussed in Ref.…”

Section: Discussionmentioning

confidence: 59%

“…3,19,20 Some experimental works have demonstrated that intercalators increase DNA melting force. 19,21,22 Recent SMFS experiments suggest that intercalators increase the stretch (or Young's) modulus of DNA, 23,24 whereas the bending rigidity and persistence length of dsDNA remain unaffected upon drug intercalation. 25,26 Despite these experimental studies, there is still controversy about the modifications in elastic properties of dsDNA in the presence intercalators.…”

Section: Introductionmentioning

confidence: 99%

“…13 These experimental results have also not been studied by simulations, except in references. 22,23,27 In particular, little seems to be known about the details of the effects of small-molecule binding on the functions of dsDNA, such as its dissociation mechanics.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Sahoo

Bagchi

Maiti

2019

The Journal of Chemical Physics

View full text Add to dashboard Cite

Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here we probe, via all-atom molecular dynamics (MD) simulations, change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs-i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.

show abstract

Section: Discussionmentioning

confidence: 59%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Sahoo

Bagchi

Maiti

2019

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…To study such complex connections, interdisciplinary research is undoubtedly the only possible approach forward. Future biological questions, technical improvements, and implementation will increase growth in this field with the integration of spectroscopic approaches with, e.g., big bang tomography [ 187 , 188 ] and fast scanning AFM [ 94 ].…”

Section: Conclusion and Future Trendsmentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

Self Cite

View full text Add to dashboard Cite

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

show abstract

“…However, this technique is expensive [59]. The second method is based on non-covalently binding of the dye to the DNA complex: through electrostatic interaction (within the external DNA double helix) [62], by binding to the minor or major groove of the DNA, and by intercalation (between base pairs) [59,63,64]. The latter allows easy and fast [65] incorporation at lower costs compared to covalently bound complexes.…”

Section: Fluorescence-based Sensorsmentioning

confidence: 99%

DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors

et al. 2020

View full text Add to dashboard Cite

DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.

show abstract

Nanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes

Cited by 23 publications

References 54 publications

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

DNA Studies: Latest Spectroscopic and Structural Approaches

DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors

Contact Info

Product

Resources

About