Influence of the single‐strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano‐cage family

Iacovelli, Federico; Alves, Cássio; Falconi, Mattia; Oteri, Francesco; Oliveira, Cristiano L. P.; Desideri, Alessandro

doi:10.1002/bip.22475

Cited by 15 publications

(24 citation statements)

References 38 publications

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“…In a series of previous works, PCA based on MD trajectories were used to detect the functional dynamics of DNA nanocages, but those calculations were carried out using the backbone phosphorus atoms (P) [ 13 , 14 , 15 , 16 , 17 ]. In this section, PCA analysis has been revised and the ENM motion analysis has been performed based on three nodes.…”

Section: Resultsmentioning

confidence: 99%

“…In the last years, we have been involved in the use of molecular dynamics (MD) simulations of DNA nanocages to characterize their structures and dynamics [ 12 ]. In detail, we have investigated local and global structural and mechanical properties of a truncated octahedral DNA nanocage family [ 13 ], probed the roles of thymidine linkers in the stability of DNA nanocages [ 14 , 15 , 16 , 17 ], and investigated the temperature dependent encapsulation mechanism of a DNA nanostructure [ 10 ]. oxDNA, a coarse grain model considering DNA at the nucleotide level, has been proposed to study the self-assembly of DNA nanostructures [ 18 , 19 , 20 ], mainly to simulate large systems, such as DNA origami based assembly [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

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Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

Iacovelli

et al. 2017

Molecules

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DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

Iacovelli

et al. 2017

Molecules

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“…In recent years, MD atomistic simulations have been successfully used to characterize the structure and dynamics of Seeman DNA nanostructures , to probe the stability and the dynamic properties of DNA nanocircles , and to investigate the effects of duplex length, sequence, salt concentration and superhelical density on the conformation of DNA nanocircles . Exploration of the properties of a truncated octahedral DNA nanocage family has shown unusual curvature and stacking imposed by the nanostructure that have never been observed in simulations of short DNA strands (Fig. ).…”

Section: State Of the Art In Dna Simulationmentioning

confidence: 99%

Decoding the conformation‐linked functional properties of nucleic acids by the use of computational tools

Iacovelli

Falconi

2015

The FEBS Journal

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DNA and RNA are large and flexible polymers selected by nature to transmit information. The most common DNA three-dimensional structure is represented by the double helix, but this biopolymer is extremely flexible and polymorphic, and can easily change its conformation to adapt to different interactions and purposes. DNA can also adopt singular topologies, giving rise, for instance, to supercoils, formed because of the limited free rotation of the DNA domain flanking a replication or transcription complex. Our understanding of the importance of these unusual or transient structures is growing, as recent studies of DNA topology, supercoiling, knotting and linking have shown that the geometric changes can drive, or strongly influence, the interactions between protein and DNA, so altering its own metabolism. On the other hand, the unique self-recognition properties of DNA, determined by the strict Watson-Crick rules of base pairing, make this material ideal for the creation of self-assembling, predesigned nanostructures. The construction of such structures is one of the main focuses of the thriving area of DNA nanotechnology, where several assembly strategies have been employed to build increasingly complex DNA nanostructures. DNA nanodevices can have direct applications in biomedicine, but also in the materials science field, requiring the immersion of DNA in an environment far from the physiological one. Crucial help in the understanding and planning of natural and artificial nanostructures is given by modern computer simulation techniques, which are able to provide a reliable structural and dynamic description of nucleic acids.

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“…The geometry is highly stable and its conformational variability is modulated by the length of the single stranded linker, being larger for longer linkers. [26][27][28][29] Fig. 1.…”

Section: Nucleic Acid-based Nanoparticlesmentioning

confidence: 99%

The Potential of Nucleic Acid-Based Nanoparticles for Biomedical Application

Biocca

Desideri

2015

Nano LIFE

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The recent development of biomedical nanotechnology is providing the appropriate know-how to build novel nanocarriers/nanocapsules to be used in the pharmaceutical industry for delivery of drugs and/or therapeutic payloads to specific cells. DNA is an extremely suitable polymer for the\ud generation of nanocapsules being biocompatible, stable and chemically modifiable. Moreover, the simple four bases mechanism allows the auto-assembly of geometrically defined systems. In this review, we describe the general properties of DNA nanocarriers, how they can be functionalized\ud for di®erent tasks, their interaction with cellular systems and we provide an outlook of their use in a therapeutic perspective

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Influence of the single‐strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano‐cage family

Cited by 15 publications

References 38 publications

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

Decoding the conformation‐linked functional properties of nucleic acids by the use of computational tools

The Potential of Nucleic Acid-Based Nanoparticles for Biomedical Application

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