Single DNA Electron Spin Resonance Spectroscopy in Aqueous Solutions
Fazhan Shi, Fei Kong, Pengju Zhao, Xiaojun Zhang, Ming Chen, Sanyou Chen, Qi Zhang, Mengqi Wang, Xiangyu Ye, Zhecheng Wang, Zhuoyang Qin, Xing Rong, Jihu Su, Pe… 展开作者
Fazhan Shi, Fei Kong, Pengju Zhao, Xiaojun Zhang, Ming Chen, Sanyou Chen, Qi Zhang, Mengqi Wang, Xiangyu Ye, Zhecheng Wang, Zhuoyang Qin, Xing Rong, Jihu Su, Pengfei Wang, Peter Z. Qin, Jiangfeng Du
Magnetic resonance spectroscopy of single biomolecules under near-physiological conditions may substantially advance understanding of biological function, yet remains very challenging. Here we use nitrogen-vacancy centers in diamonds to detect electron spin resonance spectra of individual, tethered DNA duplexes labeled with a nitroxide spin label in aqueous buffer solutions at ambient temperatures. This paves the way for magnetic resonance studies on single biomolecules and their inter-molecular interactions in a native-like environment.
The effect of magnesium ion Mg2+ on the dielectric relaxation of semidilute DNA aqueous solutions has been studied by means of dielectric spectroscopy in the 100 Hz-100 MHz frequency range. De Gennes-Pfeuty-Dobrynin semidilute solution correlation length is the pertinent fundamental length scale for sufficiently low concentration of added salt, describing the collective properties of Mg-DNA solutions. No relaxation fingerprint of the DNA denaturation bubbles, leading to exposed hydrophobic core scaling, was detected at low DNA concentrations, thus indicating an increased stability of the doubl…
The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration vary from 0 to 2 M. The conductivity of solutions without DNA but with the same concentration of KCl salt are also performed. The results show that in case of salt free solution of DNA the melting process of the double helix is observed, while in case of DNA solution with added salt the macromolecule denaturation is not featured. For salt concentrations lower …
We present a development of a high precision, tunable far-infrared (terahertz) frequency-domain dielectric spectrometer for studying the dynamics of biomolecules in aqueous solutions in the gigahertz-to-terahertz frequency. As a first application we report on the measurement of the absorption and refractive index for liquid water in the frequency range from 5 GHz to 1.12 THz (0.17 to 37.36 cm-1 or 0.268 to 60 mm). The system provides a coherent radiation source with a power up to 20 mW in the gigahertz-to-terahertz region. The power signal-to-noise ratio of our instrument reaches 1015 and the …
We study the interaction of berberine and sanguinarine (plant alkaloids) with DNA in aqueous solutions, by using optical spectroscopy methods (absorption and fluorescence). The dependencies of alkaloid spectral characteristics on the concentration ratio N/c between the DNA base pairs and alkaloid molecules in the solutions are considered, and the manifestations of the alkaloid-DNA binding are revealed. The character of binding is found to depend on N/c. The parameters of the binding of berberine and sanguinarine with DNA are determined, by using the modified Scatchard and McGhee-von Hippel equ…
Single strand breaks are induced in DNA plasmids, pBR322 and pUC19, in aqueous media by intense ultrashort laser pulses (820 nm wavelength, 45 fs pulse duration, 1 kHz repetition rate) at intensities of 1-12 TW cm$^{-2}$. The intense laser radiation generates, {\it in situ}, electrons that induce transformation of supercoiled DNA into relaxed DNA. The extent of electron-mediated relaxation of DNA structure is quantified. Introduction of electron and radical scavengers inhibits DNA damage.
Single strand breaks are induced in DNA plasmids, pBR322 and pUC19, in aqueous media exposed to strong fields generated using ultrashort laser pulses (820 nm wavelength, 45 fs pulse duration, 1 kHz repetition rate) at intensities of 1-12 TW cm$^{-2}$. The strong fields generate, {\it in situ}, electrons and radicals that induce transformation of supercoiled DNA into relaxed DNA, the extent of which is quantified. Introduction of electron and radical scavengers inhibits DNA damage; results indicate that OH radicals are the primary (but not sole) cause of DNA damage.
Effects of the size and concentration of depleting agents on the stabilization of the double-helix structure and DNA condensation: a single molecule force spectroscopy study
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in…
In solution, UV-vis spectroscopy is often used to investigate structural changes in biomolecules (i.e., nucleic acids), owing to changes in the environment of their chromophores (i.e., the nucleobases). Here we address whether action spectroscopy could achieve the same for gas-phase ions, while taking the advantage of additional spectrometric separation of complex mixtures. We therefore systematically studied the action spectroscopy of homo-base 6-mer DNA strands (dG6, dA6, dC6, dT6) and discuss the results in light of gas-phase structures validated by ion mobility spectrometry and infrared io…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA pro…
DNA and proteins are chiral: their three-dimensional structure cannot be superimposed with its mirror image. Circular dichroism spectroscopy is widely used to characterize chiral compounds, but data interpretation is difficult in the case of mixtures. We recorded for the first time the electronic circular dichroism spectra of DNA helices separated in a mass spectrometer. We electrosprayed guanine-rich strands having various secondary structures as negative ions, irradiated them with a laser, and measured the difference in electron photodetachment efficiency between left and right circularly po…
Knowledge of the mechanisms of interaction between self-aggregating peptides and nucleic acids or other polyanions is key to the understanding of many aggregation processes underlying several human diseases (e.g. Alzheimer's and Parkinson's diseases). Determining the affinity and kinetic steps of such interactions is challenging due to the competition between hydrophobic self-aggregating forces and electrostatic binding forces. Kahalalide F (KF) is an anticancer hydrophobic peptide which contains a single positive charge that confers strong aggregative properties with polyanions. This makes KF…
$TiO_{2}$ nanoparticles (NPs) are widely used in the environmental engineering, medicine, chemical and food industries due to their unique photocatalytic and biocidal properties. NPs may generate reactive oxygen species and, hence, have the toxic effect on the living cells via oxidative stress. An external UV irradiation may magnify the photocatalytic properties of $TiO_{2}$ NPs. In this regard, we have analyzed the influence of $TiO_{2}$ NPs on the conformation and thermal stability of native DNA in a buffer solution without and under UV irradiation exploiting absorption spectroscopy with DNA…
Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far, single base detection might be possible in more drastic cleanliness conditions such as ultra high vacuum. Here, we report on high resolution imaging and pulling attempts at low temperature (5K) of a single strand DNA (ssDNA) molecules composed of 20 cytosine bases adsorbed on Au(111) by scanning probe microscopy and numerical calculations. Using electrospray…
Real time laser induced fluorescence spectroscopy usage for microanalysis of DNA double helix defects is shown. The method is based on Forster resonance energy transfer (FRET) in intercalator-donor pair (acridine orange as a donor and ethidium bromide as an acceptor). Transition metal ions such as Cu(II), Cu(I), Ag(I), silver nanoparticles (AgNPs), photo- and thermo effects were used to cause double helix defects in DNA. FRET radii were experimentally estimated in background electrolyte solution (0.01 M NaNO3) and proved to be 3.9 +- 0.3 nm and the data are in satisfactory agreement with the t…
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling…
