Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

Шишкин, Олег В.; Elstner, Marcus; Frauenheim, Thomas; Suhai, Sándor

doi:10.3390/i4100537

Cited by 21 publications

(17 citation statements)

References 31 publications

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“…This method has been augmented with an empirical treatment of the dispersion forces, to extend its ability to larger biomolecules [45,46]. It was tested for H-bonded complexes, small peptides, as well as DNA H-bonding interactions [47,48]. A still more extended and improved version of SCC-DFTB is the DFTB3 method [49].…”

Section: Dftb Methodsmentioning

confidence: 99%

Multi-level molecular modelling for plasma medicine

Bogaerts¹,

Khosravian²,

Paal³

et al. 2015

J. Phys. D: Appl. Phys.

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Modeling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modeling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and nonreactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e., proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modeling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma-biomolecule interactions. biological targets, will be presented in future papers. Furthermore, more information on the specifics of the methods used can also be found in specialized reviews, as indicated below.In section 2, we will give a brief explanation of each of these methods. Depending on the application and kind of information that is envisaged, one or the other method is more suitable. This will be illustrated in section 3, where each of these modeling approaches is applied to specific model systems, relevant for plasma medicine applications. We selected three different types of biomolecules, which are present in the human cell, i.e., proteins, DNA and phospholipids in the cell membrane.A plasma produces a cocktail of chemical species that may be important in plasma medicine, and depending on the type of plasma, also electric fields, ions or photons can play a role. Nevertheless, we focus here only on the interaction mechanisms of reactive oxygen species (ROS), which are known to play an important role in plasma therapy. More specifically, we focus on the interactions of OH radicals with these biomolecules, as well as the consequences of these interactions. We have indeed demonstrated before that other ROS, like O, HO 2 , O 3 and H 2 O 2 , react more or less in the same way but are somewhat less reactive (except for O) [2][3][4], and moreover, we demonstrated that OH radicals are able to penetrate through a liquid layer surrounding biomolecules, while the O atoms rapidly form OH radicals upon reaction with H 2 O molecules [5]. For this reason, the OH radicals are selected here as being representative for the ROS produced by the plasma.In general, ROS can react with the cell membrane components (i.e., lipids and membrane proteins), as well as with biomolecules in the cell (e.g., DNA and proteins). They are able to oxidize lipids, proteins and DNA, and consequently damage these biomolecules or induce mutations in their structure. However, the underlying reaction...

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Section: Dftb Methodsmentioning

confidence: 99%

Multi-level molecular modelling for plasma medicine

Bogaerts¹,

Khosravian²,

Paal³

et al. 2015

J. Phys. D: Appl. Phys.

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“…There is also the stacking interaction at the GH-KL interface in complex II with 20-bp DNA segments (Fig. 4a), although such an interaction can be weaker than that between DNA nucleotides 38,39 (due to imperfect matching of the GH and KL segments). This leads to an increase in the relative concentration of complex II; therefore, the equilibrium between complexes I and II in a solution containing multiple copies of the 20-bp DNA operator shifts towards an increase in the concentration of complex II (K N 1).…”

Section: Structure Solution and Analysismentioning

confidence: 96%

Crystal Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound with Its DNA Operator Reveals Detailed Mechanism of Arginine Repression

Cherney¹,

Cherney²,

Garen³

et al. 2010

Journal of Molecular Biology

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“…In the case of larger systems, these calculations are considerably time and resource consuming [16]. For this reason, often, interactions are studied at higher computational level (e.g., MP2) for geometry optimized at DFT level [18,19].…”

Section: Introductionmentioning

confidence: 99%

Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

2018

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Stacking interactions play an important role in stabilizing DNA and RNA secondary structure. To select a computational level to study the stacking interactions, both energy and geometric criteria, as well as the time necessary to optimize the system, should be taken into account. In this work, an attempt was made to find the most optimal level of theory describing the stacking interactions in adenine dimers. The obtained results have shown that for this purpose, wB97XD/6-311G(p,d), wB97XD/aug-cc-pvdz, or B97D3/aug-cc-pvdz should be used. What is more, geometry of the most preferable arrangements of molecules was also pointed out, ensuring an optimal starting system for further analyses.

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Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

Cited by 21 publications

References 31 publications

Multi-level molecular modelling for plasma medicine

Multi-level molecular modelling for plasma medicine

Crystal Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound with Its DNA Operator Reveals Detailed Mechanism of Arginine Repression

Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

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