Vibrational characteristics of DNA nanostructures obtained through a mass-weighted chemical elastic network model

Jo, Soojin; Son, Jae Sung; Lee, Byung Ho; Dugasani, Sreekantha Reddy; Park, Sungha; Kim, Moon Ki

doi:10.1039/c7ra06125k

Cited by 15 publications

(15 citation statements)

References 21 publications

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“…In an elastic network model (ENM), representative atoms are modeled as unit point masses, and connectivity between atoms is represented as a unit spring constant that varies depending on the cutoff distance, which is usually 12 Å in a C α coarse-grained protein model [ 34 , 35 , 36 , 37 , 38 ]. ENM methodology has been mainly used to analyze intrinsic mode shapes of proteins, but recently, it has also been used to analyze intrinsic vibrational features of DNA/RNA structures because of its advantages (i.e., low computational cost and large conformational change prediction) compared to the traditional full-atom molecular dynamics (MD) simulations [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. In comparison with a traditional ENM, the MWCENM is a more precise modeling method because it considers both the inertia effect and the chemical bond information of the target system.…”

Section: Methodsmentioning

confidence: 99%

“…Normal mode analysis (NMA) has been widely used to analyze intrinsic modes of biomolecules due to its wide adaptability and relatively low cost. Collective motions of biomolecules have a significant influence on their structural characteristics [ 18 , 19 , 20 , 21 ]. There have been considerable efforts to analyze vibrational characteristics based on NMA for various DNA/RNA native structures [ 22 , 23 , 24 , 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

“…There have been considerable efforts to analyze vibrational characteristics based on NMA for various DNA/RNA native structures [ 22 , 23 , 24 , 25 , 26 ]. Although dynamic analysis for some fabricated nanostructures has also been performed by NMA [ 20 , 21 , 27 , 28 , 29 , 30 , 31 ], finite-size nanostructures that have more complex geometries, as well as larger molecular weights, have rarely been studied.…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we introduced two representative finite-size DNA nanostructures, i.e., 2D rings and 3D buckyballs, and performed computational analysis on them using NMA based on a mass-weighted chemical elastic network model (MWCENM) and a symmetry-constrained elastic network model (SCENM) [ 21 , 32 ]. Intrinsic vibrations of the DNA 2D ring and 3D buckyball structures can be determined precisely and efficiently because MWCENM considers both molecular weights and chemical bonds, and SCENM uses the information of a repeated unit and connectivity between adjacent units.…”

Section: Introductionmentioning

confidence: 99%

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Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

Kim

Lee

et al. 2018

IJMS

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In order to incorporate functionalization into synthesized DNA nanostructures, enhance their production yield, and utilize them in various applications, it is necessary to study their physical stabilities and dynamic characteristics. Although simulation-based analysis used for DNA nanostructures provides important clues to explain their self-assembly mechanism, structural function, and intrinsic dynamic characteristics, few studies have focused on the simulation of DNA supramolecular structures due to the structural complexity and high computational cost. Here, we demonstrated the feasibility of using normal mode analysis for relatively complex DNA structures with larger molecular weights, i.e., finite-size DNA 2D rings and 3D buckyball structures. The normal mode analysis was carried out using the mass-weighted chemical elastic network model (MWCENM) and the symmetry-constrained elastic network model (SCENM), both of which are precise and efficient modeling methodologies. MWCENM considers both the weight of the nucleotides and the chemical bonds between atoms, and SCENM can obtain mode shapes of a whole structure by using only a repeated unit and its connectivity with neighboring units. Our results show the intrinsic vibrational features of DNA ring structures, which experience inner/outer circle and bridge motions, as well as DNA buckyball structures having overall breathing and local breathing motions. These could be used as the fundamental basis for designing and constructing more complicated DNA nanostructures.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

Kim

Lee

et al. 2018

IJMS

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“…This peak, however, is difficult to observe in the whole spore spectrum. [19][20][21] We also marked the phenylalanine peak, a major structural component of the spore, with the Raman peak at 1001 cm −1 . Overall, the peaks observed using our LTRS is consistent with what is found in the literature using similar approaches.…”

Section: Mapping Vibration Peaks Of the Spores Using Laser Tweezers Rmentioning

confidence: 99%

Disinfection chemicals mode of action on the bacterial spore structure and their Raman spectra

Malyshev

Dahlberg

Wiklund

et al. 2020

Preprint

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Contamination of toxic spore-forming bacteria is problematic since spores can survive a plethora of disinfection chemicals. It is also problematic to rapidly detect if the disinfection chemical was active, leaving spores dead. Robust decontamination strategies, as well as reliable detection methods to identify dead from viable spores, are thus critical. Vibrational detection methods such as Raman spectroscopy has been suggested for rapid diagnostics and differentiation of live and dead spores. We investigate in this work, using laser tweezers Raman spectroscopy, the changes in Raman spectra of Bacillus thuringiensis spores treated with sporicidal agents such as chlorine dioxide, peracetic acid, and sodium hypochlorite. We also imaged treated spores using SEM and TEM to verify if any changes to the spore structure can be correlated to the Raman spectra. We found that chlorine dioxide did not change the Raman spectrum or the spore structure; peracetic acid shows a time-dependent decrease in the characteristic DNA/DPA peaks and ∼20 % of the spores were degraded and collapsed; spores treated with sodium hypochlorite show an abrupt drop in DNA and DPA peaks within 20 minutes all though the spore structure was overall intact, however, the exosporium layer was reduced. Structural changes appeared over several minutes, compared to the inactivation time of the spores, which is less than a minute. We conclude that vibrational spectroscopy provides powerful means to detect changes in spores but it might be problematic to identify if spores are live or dead after a decontamination procedure.

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Vibration spectra of DNA and RNA segments

Jalilvand,

Mousavi

2024

Eur Biophys J

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Vibrational characteristics of DNA nanostructures obtained through a mass-weighted chemical elastic network model

Abstract: The proposed frequency analysis method is a feasible method for understanding DNA nanostructure's vibration characteristics, including both frequencies and mode shapes in atomic detail, adding to the molecular fingerprint provided by the conventional Raman spectrum.

Cited by 15 publications

References 21 publications

Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

Disinfection chemicals mode of action on the bacterial spore structure and their Raman spectra

Vibration spectra of DNA and RNA segments

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