The effect of microwave irradiation on DNA hybridization

The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach

The impact of microwave (MW) irradiation on protein folding, potentially inciting misfolding, was investigated by employing molecular dynamics (MD) simulations. Twenty-nine proteins were subjected to MD simulations under equilibrium (300 K) and MW conditions, where the rotational temperature was elevated to 700 K. The utilized replacement model captures the microwave effects of δ- and γ-relaxation processes (frequency range of ∼300 MHz to ∼20 GHz). The results disclosed that MW heating incited a shift toward more compact protein conformations, as indicated by decreased root-mean-square deviations, root-mean-square fluctuations, head-to-tail distances, and radii of gyration. This compaction was attributed to the intensification of intramolecular electrostatic interactions and hydrogen bonds within the protein caused by MW-destabilized hydrogen bonds between the protein and solvent. The solvent-accessible surface area (SASA), particularly that of polar amino-acid residues, shrank under MW conditions, corresponding to a reduced polarity of the water solvent. However, MW irradiation produced no significant alterations in protein secondary structures; hence, MW heating was observed to primarily affect the protein tertiary structures.

Driving DNA Origami Assembly with a Terahertz Wave

Terahertz (THz) waves show nontrivial interactions with living systems, but the underlying molecular mechanisms have yet to be explored. Here, we employ DNA origami as a model system to study the interactions between THz waves and DNA structures. We find that a 3-min THz illumination (35.2 THz) can drive the unwinding of DNA duplexes at ∼10 °C below their melting point. Computational study reveals that the THz wave can resonate with the vibration of DNA bases, provoking the hydrogen bond breaking. The cooperation of thermal and nonthermal effects allows the unfolding of undesired secondary structures and the THz illumination can generate diverse DNA origami assemblies with the yield (>80%) ∼ 4-fold higher than that by the contact heating at similar temperatures. We also demonstrate the in situ assembly of DNA origami in cell lysate. This method enables remotely controllable assembly of intact biomacromolecules, providing new insight into the bioeffects of THz waves.

Recent advances in constructing high-order DNA structures

Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.

Could Microwave Irradiation Cause Misfolding of Peptides?

Microwaves have been experimentally shown to affect the folding dynamics of peptides and proteins. Using molecular dynamics, we performed all-atom simulations of a model β-peptide in aqueous solution where individual degrees of freedom of solvent molecules were decoupled to allow for investigation at non-equilibrium microwave-irradiated conditions. An elevated rotational temperature of the water medium was found to significantly affect the conformation of the peptide due to the weakened hydrogen-bonding interactions with the surrounding solvent molecules. Cluster analysis revealed that microwave irradiation can indeed act as a promoter in the formation of new misfolded peptide structures of the hairpin type, which are generally associated with the onset of several neurodegenerative disorders such as Alzheimer’s, Parkinson’s, Huntington’s, and Creutzfeldt–Jakob diseases as well as certain cancer types such as amyloidosis.

Microwave-accelerated diastereoselective catalyst-free one-pot four-component synthesis of 2-(N-carbamoylacetamide)-substituted 2,3-dihydrothiophenes in glycerol

In the current study, glycerol was successfully employed as a nonvolatile, non-toxic, non-flammable, biodegradable, very cheap, easily accessible, and efficient reaction medium for the microwave-enhanced diastereoselective synthesis of 2-(N-carbamoylacetamide)-substituted 2,3-dihydrothiophenes via a catalyst-free one-pot four-component reaction. A versatile range of starting materials were used, and diverse products were obtained in good to excellent yields and very short reaction times. Moreover, the reaction medium was recovered and reused several times without any loss of the efficiency.

Room-Temperature and Selective Triggering of Supramolecular DNA Assembly/Disassembly by Nonionizing Radiation

Recent observations have suggested that nonionizing radiation in the microwave and terahertz (THz; far-infrared) regimes could have an effect on double-stranded DNA (dsDNA). These observations are of significance owing to the omnipresence of microwave emitters in our daily lives (e.g., food preparation, telecommunication, and wireless Internet) and the increasing prevalence of THz emitters for imaging (e.g., concealed weapon detection in airports, skin cancer screenings) and communication technologies. By examining multiple DNA nanostructures as well as two plasmid DNAs, microwaves were shown to promote the repair and assembly of DNA nanostructures and single-stranded regions of plasmid DNA, while intense THz pulses had the opposite effect (in particular, for short dsDNA). Both effects occurred at room temperature within minutes, showed a DNA length dependence, and did not affect the chemical integrity of the DNA. Intriguingly, the function of six proteins (enzymes and antibodies) was not affected by exposure to either form of radiation under the conditions examined. This particular detail was exploited to assemble a fully functional hybrid DNA-protein nanostructure in a bottom-up manner. This study therefore provides entirely new perspectives for the effects, on the molecular level, of nonionizing radiation on biomolecules. Moreover, the proposed structure-activity relationships could be exploited in the field of DNA nanotechnology, which paves the way for designing a new range of functional DNA nanomaterials that are currently inaccessible to state-of-the-art assembly protocols.

Acceleration of DNA melting kinetics using alternating electric fields

We verify both theoretically and by simulation that an AC electric field, with a frequency much higher than the dissociation rate, can significantly accelerate the dissociation rate of biological molecules under isothermal conditions. The cumulative effect of the AC field is shown to break a key bottleneck by reducing the entropy (and increasing the free energy of the local minimum) via the alignment of the molecular dipole with the field. For frequencies below a resonant frequency which corresponds to the inverse Debye dipole relaxation time, the dissociation rate can be accelerated by a factor that scales as ω(ϵ'(ω)-1)E02 , where ω is the field frequency, E₀ is the field amplitude, and ϵ'(ω) is the frequency-dependent real permittivity of the molecule. At large amplitudes, we find that the accelerated melting rate becomes universal, independent of duplex size and sequence, which is in drastic contrast to Ohmic thermal melting. We confirm our theory with isothermal all-atomic molecular dynamics simulation of short DNA duplexes with known melting rates, demonstrating several orders in enhancement with realistic fields.

Microwave irradiation affects ion pairing in aqueous solutions of alkali halide salts

Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water's rotational motion on the ion pairing of ionic solutes in aqueous solutions. The situation with rotational temperature higher than the translational one, T_rot>T_trs, is mimicking the non-equilibrium effects of microwaves on model solutions of alkali halide salts. The simulations reveal that an increase in the rotational temperature at constant translational temperature exerts significant changes in the structure of the solution. The latter are reflected in increased pairing of the oppositely charged ions, which can be explained by the weaker ability of rotationally excited water to screen and separate the opposite charges. It seems that Collins' law of matching water affinities retains its validity also in the non-equilibrium situation where the rotational temperature exceeds the translational one. On the other hand, the equilibrium effect (i.e., an increase in the solution's overall temperature T≡T_rot = T_trs) favors the formation of small-small (NaCl), while it has a little effect on large-large (CsI) ion pairs. This is in accordance with water becoming less polar solvent upon a temperature increase. Furthermore, we investigated the effects of excited translational motion of water (and ions) on the ion pairing by increasing the translational temperature, while keeping the rotational one unchanged (i.e., T_trs>T_rot). Interestingly, in certain cases the faster translational motion causes an increase in correlations. The temperature variations in the like-ion association constants, K_as⁺⁺ and K_as^--, are also examined. Here the situation is more complex but, in most cases, a decrease in the ion pairing is observed.

Microwave non-thermal effect reduces ELISA timing to less than 5 minutes

Microwave-mediated ELISA, which occurs in less than 5 minutes, is due to a microwave non-thermal effect. We postulate that the microwave non-thermal effect is a microwave catalytic effect acting by lowering the activation energy of reactants.

Development of rapid microwave-mediated and low-temperature bacterial transformations

The introduction of exogenous DNA into Escherichia coli is a cornerstone of molecular biology. Herein, we investigate two new mechanisms for bacterial transformation involving either the use of microwave irradiation or a freeze-thaw protocol in liquid nitrogen. Ultimately, both methods afforded successful transfer of plasmid DNA into bacterial cells, with the freeze-thaw technique yielding efficiencies of ~10(5). More importantly, both techniques effectively eliminated the need for the preparation of competent cells.

The toxic effects of mobile phone radiofrequency (940 MHz) on the structure of calf thymus DNA

Currently, the biological effects of nonionizing electromagnetic fields (EMFs) including radiofrequency (RF) radiation have been the subject of numerous experimental and theoretical studies. The aim of this study is to evaluate the possible biological effects of mobile phone RF (940 MHz, 15 V/m and SAR=40 mW/kg) on the structure of calf thymus DNA (ct DNA) immediately after exposure and 2 h after 45 min exposure via diverse range of spectroscopic instruments. The UV-vis and circular dichroism (CD) experiments depict that mobile phone EMFs can remarkably cause disturbance on ct DNA structure. In addition, the DNA samples, immediately after exposure and 2 h after 45 min exposure, are relatively thermally unstable compared to the DNA solution, which was placed in a small shielded box (unexposed ct DNA). Furthermore, the exposed DNA samples (the DNA samples that were exposed to 940 MHz EMF) have more fluorescence emission when compared with the unexposed DNA, which may have occurred attributable to expansion of the exposed DNA structure. The results of dynamic light scattering (DLS) and zeta potential experiments demonstrate that RF-EMFs lead to increment in the surface charge and size of DNA. The structure of DNA immediately after exposure is not significantly different from the DNA sample 2 h after 45 min exposure. In other words, the EMF-induced conformational changes are irreversible. Collectively, our results reveal that 940 MHz can alter the structure of DNA. The displacement of electrons in DNA by EMFs may lead to conformational changes of DNA and DNA disaggregation. Results from this study could have an important implication on the health effects of RF-EMFs exposure. In addition, this finding could proffer a novel strategy for the development of next generation of mobile phone.

Individual degrees of freedom and the solvation properties of water

Using molecular dynamics simulations in conjunction with home-developed Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures. Elevated rotational temperature of the water medium is found to severely hinder hydration of polar molecules, to affect hydration of ionic species in a nonmonotonous way and to somewhat improve hydration of nonpolar species. As proteins consist of charged, polar, and nonpolar amino-acid residues, the developed methodology is also applied to critically evaluate the hypothesis that the overall decrease in protein hydration and the change in the subtle balance between hydration of various types of amino-acid residues provide a plausible physical mechanism through which microwaves enhance aberrant protein folding and aggregation.

Microwave-assisted synthesis of carbon nanodots through an eggshell membrane and their fluorescent application

Carbon nanodots (C-Dots) as a new form of carbonaceous nanomaterials have aroused much interest and intensive research due to their inspiring properties. Compared to traditional semiconductor quantum dots, these newly emergent nanodots possess a number of advantageous characteristics, among which low-toxicity is particularly fascinating. More and more research into C-Dots have focused on synthesis methods and biology-related applications. Microwave-assisted approaches have attracted attention because microwave treatment can provide intensive and efficient energy, and as a consequence shorten the reaction time. In this article, we designed a "green", rapid, eco-friendly and waste-reused approach to synthesize fluorescent and water-soluble C-Dots from eggshell membrane (ESM) ashes according to a microwave-assisted process. ESM selected as the carbon source was a common protein-rich waste in daily life and can be obtained easily and cheaply. The C-Dots from our method showed the maximal fluorescence emission peak at 450 nm and the fluorescence quantum yield was about 14%. We further designed a sensitive probe for glutathione based on the fluorescence turn off and on of the C-Dots-Cu(2+) system, which showed a linear range of 0.5-80 μmol L(-1) and detection limit of 0.48 μmol L(-1). In general, the C-Dots prepared briefly and inexpensively from ESM revealed excellent fluorescent property with promising potential for applications such as sample detection and biotechnology.

Can electromagnetic fields influence the structure and enzymatic digest of proteins? A critical evaluation of microwave-assisted proteomics protocols

This study reevaluates the putative advantages of microwave-assisted tryptic digests compared to conventionally heated protocols performed at the same temperature. An initial investigation of enzyme stability in a temperature range of 37-80 °C demonstrated that trypsin activity declines sharply at temperatures above 60 °C, regardless if microwave dielectric heating or conventional heating is employed. Tryptic digests of three proteins of different size (bovine serum albumin, cytochrome c and β-casein) were thus performed at 37 °C and 50 °C using both microwave and conventional heating applying accurate internal fiber-optic probe reaction temperature measurements. The impact of the heating method on protein degradation and peptide fragment generation was analyzed by SDS-PAGE and MALDI-TOF-MS. Time-dependent tryptic digestion of the three proteins and subsequent analysis of the corresponding cleavage products by MALDI-TOF provided virtually identical results for both microwave and conventional heating. In addition, the impact of electromagnetic field strength on the tertiary structure of trypsin and BSA was evaluated by molecular mechanics calculations. These simulations revealed that the applied field in a typical laboratory microwave reactor is 3-4 orders of magnitude too low to induce conformational changes in proteins or enzymes.

Non-thermal effects of terahertz radiation on gene expression in mouse stem cells

In recent years, terahertz radiation sources are increasingly being exploited in military and civil applications. However, only a few studies have so far been conducted to examine the biological effects associated with terahertz radiation. In this study, we evaluated the cellular response of mesenchymal mouse stem cells exposed to THz radiation. We apply low-power radiation from both a pulsed broad-band (centered at 10 THz) source and from a CW laser (2.52 THz) source. Modeling, empirical characterization, and monitoring techniques were applied to minimize the impact of radiation-induced increases in temperature. qRT-PCR was used to evaluate changes in the transcriptional activity of selected hyperthermic genes. We found that temperature increases were minimal, and that the differential expression of the investigated heat shock proteins (HSP105, HSP90, and CPR) was unaffected, while the expression of certain other genes (Adiponectin, GLUT4, and PPARG) showed clear effects of the THz irradiation after prolonged, broad-band exposure.

Microwave catalysis revisited: an analytical solution

In our previous work [Bren, U., et al. J. Phys. Chem. A 2008, 112, 166] we proposed a novel physical mechanism for microwave catalysis based on rotationally hot reactive species and verified its validity through a Monte Carlo simulation of a realistic chemical reaction: neutral ester hydrolysis. This article represents a continuation of our ongoing effort toward quantitative understanding of the microwave catalytic effect. It provides a derivation of an analytical solution for the microwave catalysis. The obtained expression is compared with the results of the Monte Carlo simulation and is applied to reproduce the microwave catalytic effect experimentally observed in the polyethylene terephthalate solvolysis. Implications for the interactions of microwaves with living organisms in the context of widespread mobile telephony are also discussed.

Understanding microwave heating effects in single mode type cavities-theory and experiment

This paper explains the phenomena which occur in commercially available laboratory microwave equipment, and highlights several situations where experimental observations are often misinterpreted as a 'microwave effect'. Electromagnetic simulations and heating experiments were used to show the quantitative effects of solvent type, solvent volume, vessel material, vessel internals and stirring rate on the distribution of the electric field, the power density and the rate of heating. The simulations and experiments show how significant temperature gradients can exist within the heated materials, and that very different results can be obtained depending on the method used to measure temperature. The overall energy balance is shown for a number of different solvents, and the interpretation and implications of using the results from commercially available microwave equipment are discussed.