Computational Design and Modeling of DNA Nanostructures and DNA Nanodevices

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (20 November 2021) | Viewed by 1955

Special Issue Editor


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Guest Editor
Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
Interests: molecular dynamics; DNA nanostructures; molecular modeling; bioinformatics and computational biology; molecular docking; computer programming

Special Issue Information

Dear Colleagues,

The unique self-recognition properties of DNA, ruled by the strict Watson–Crick base pairing rules, make this molecule an ideal material for the creation of self-assembling, predesigned nanostructures, and nanodevices. In the thriving area of DNA nanotechnology, the computational design, modeling, and simulation of such structures are still one of the most addressed topics in the field. In fact, modern computer simulation techniques are fundamental for the understanding and planning of artificial nanostructures. This Special Issue aims to cover works describing novel methods or molecular simulation approaches applied to DNA nanostructures and nanodevices, with the aim to provide a more reliable structural and dynamic description of this class of structures. The volume is open to innovative contributions involving aspects of the following topics:

Molecular simulation of natural and artificial DNA structures;

QM/molecular mechanical (MM) methods for the study of DNA nanostructures;

Novel approaches for the modeling of DNA nanostructures and nanodevices;

Enhanced sampling techniques applied to the study of DNA nanoswitches and nanodevices;

Design, optimization, and visualization of large DNA nanostructures;

Molecular simulations of DNA self-assembly;

Simulating the aggregation of DNA nanostructures with proteins.

Dr. Federico Iacovelli
Guest Editor

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Published Papers (1 paper)

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Research

12 pages, 2864 KiB  
Article
Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations
by Alice Romeo, Mattia Falconi, Alessandro Desideri and Federico Iacovelli
Appl. Sci. 2021, 11(9), 4052; https://0-doi-org.brum.beds.ac.uk/10.3390/app11094052 - 29 Apr 2021
Cited by 1 | Viewed by 1527
Abstract
The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the [...] Read more.
The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices. Full article
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