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At least 1,027 records · Page 57

DNA damage in oral cancer cells induced by nitrogen atmospheric pressure plasma jets

The nitrogen atmospheric pressure plasma jet (APPJ) was applied to induce DNA damage of SCC-25 oral cancer cells. Optical emission spectra were taken to characterize the reactive species produced in APPJ. In order to explore the spatial distribution of plasma effects, cells were placed onto photo-etched grid slides and the antibody H2A.X was used to locate double strand breaks of DNA inside nuclei using an immunofluorescence assay. The number of cells with double strand breaks in DNA was observed to be varied due to the distance from the irradiation center and duration of plasma treatment.

60 APPLIED LIFE SCIENCES↗

Spin transport and spin polarization properties in double-stranded DNA

We study the spin-dependent electron transport through a double-stranded DNA (dsDNA) using the Bogoliubov-de Gennes equations and non-equilibrium Green's function method. We calculate the spin-dependent electron conductance and spin-polarization for different lengths, helix angles, twist angles of dsDNA, the environment-induced dephasing factors, and hopping integral. It is shown that the conductance decreases by increasing the length and dephasing factor. Also, we show that the spin-polarization depends on the helical symmetry and the length of DNA. It is shown that the double-stranded DNA can act as a perfect spin filter. Finally, we show that the sign of spin polarization can be inverted from +1 (−1) to −1 (+1) for some values of hopping integral.

60 APPLIED LIFE SCIENCES↗

Intense photoluminescence from dried double-stranded DNA and single-walled carbon nanotube hybrid

Semiconducting single-walled carbon nanotubes (SWNTs) show near-infrared photoluminescence (PL) when they are individually isolated. This was an obstacle to use photonic properties of SWNTs on a solid surface. We show that SWNTs wrapped with DNA maintain intense PL under the dry conditions. SWNTs are well isolated individually by DNA even when the DNA-SWNT hybrids are agglomerated. This finding opens up application of SWNTs to photonic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

An improved DNA force field for ssDNA interactions with gold nanoparticles

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones “protecting” hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the “protection” by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis and characterisation of platinum (II) salphen complex and its interaction with calf thymus DNA

A platinum (II) salphen complex was synthesised by condensation reaction of 2,4-dihydroxylbenzaldehyde and o-phenylenediamine with potassium tetrachloroplatinate to obtain N,N′-Bis-4-(hydroxysalicylidene)-phenylenediamine-platinum (II). The structure of the complex was confirmed by {sup 1}H and {sup 13}C NMR spectroscopy, FTIR spectroscopy, CHN elemental analyses and ESI-MS spectrometry. The platinum (II) salphen complex with four donor atoms N{sub 2}O{sub 2} from its salphen ligand coordinated to platinum (II) metal centre were determined. The binding mode and interaction of this complex with calf thymus DNA was determined by UV/Vis DNA titration and emission titration. The intercalation between the DNA bases by π-π stacking due to its square planar geometry and aromatic rings structures was proposed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

60 APPLIED LIFE SCIENCES↗

Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5–50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length l{sub p} of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with l{sub p} ∼ 50 nm.

60 APPLIED LIFE SCIENCES↗

Local conformational perturbations of the DNA molecule in the SG-model

Within the formalism of the Fokker–Planck equation, the influence of nonstationary external force, random force, and dissipation effects on dynamics local conformational perturbations (kink) propagating along the DNA molecule is investigated. Such waves have an important role in the regulation of important biological processes in living systems at the molecular level. As a dynamic model of DNA was used a modified sine-Gordon equation, simulating the rotational oscillations of bases in one of the chains DNA. The equation of evolution of the kink momentum is obtained in the form of the stochastic differential equation in the Stratonovich sense within the framework of the well-known McLaughlin and Scott energy approach. The corresponding Fokker–Planck equation for the momentum distribution function coincides with the equation describing the Ornstein–Uhlenbek process with a regular nonstationary external force. The influence of the nonlinear stochastic effects on the kink dynamics is considered with the help of the Fokker– Planck nonlinear equation with the shift coefficient dependent on the first moment of the kink momentum distribution function. Expressions are derived for average value and variance of the momentum. Examples are considered which demonstrate the influence of the external regular and random forces on the evolution of the average value and variance of the kink momentum. Within the formalism of the Fokker–Planck equation, the influence of nonstationary external force, random force, and dissipation effects on the kink dynamics is investigated in the sine–Gordon model. The equation of evolution of the kink momentum is obtained in the form of the stochastic differential equation in the Stratonovich sense within the framework of the well-known McLaughlin and Scott energy approach. The corresponding Fokker–Planck equation for the momentum distribution function coincides with the equation describing the Ornstein–Uhlenbek process with a regular nonstationary external force. The influence of the nonlinear stochastic effects on the kink dynamics is considered with the help of the Fokker–Planck nonlinear equation with the shift coefficient dependent on the first moment of the kink momentum distribution function. Expressions are derived for average value and variance of the momentum. Examples are considered which demonstrate the influence of the external regular and random forces on the evolution of the average value and variance of the kink momentum.

60 APPLIED LIFE SCIENCES↗

Electronic transport in methylated fragments of DNA

We investigate the electronic transport properties of methylated deoxyribonucleic-acid (DNA) strands, a biological system in which methyl groups are added to DNA (a major epigenetic modification in gene expression), sandwiched between two metallic platinum electrodes. Our theoretical simulations apply an effective Hamiltonian based on a tight-binding model to obtain current-voltage curves related to the non-methylated/methylated DNA strands. The results suggest potential applications in the development of novel biosensors for molecular diagnostics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Optically controlled multiple switching operations of DNA biopolymer devices

We present optically tunable operations of deoxyribonucleic acid (DNA) biopolymer devices, where a single high-resistance state, write-once read-many-times memory state, write-read-erase memory state, and single low-resistance state can be achieved by controlling UV irradiation time. The device is a simple sandwich structure with a spin-coated DNA biopolymer layer sandwiched by two electrodes. Upon irradiation, the electrical properties of the device are adjusted owing to a phototriggered synthesis of silver nanoparticles in DNA biopolymer, giving rise to multiple switching scenarios. This technique, distinct from the strategy of doping of pre-formed nanoparticles, enables a post-film fabrication process for achieving optically controlled memory device operations, which provides a more versatile platform to fabricate organic memory and optoelectronic devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Internal twisting motion dependent conductance of an aperiodic DNA molecule

The influence of internal twisting motion of base-pair on conductance of an aperiodic DNA molecule has been studied. Double-stranded DNA molecule with sequence GCTAGTACGTGACGTAGCTAGGATATGCCTGA on one chain and its complement on the other chain is used. The molecule is modeled using Hamiltonian Tight Binding, in which the effect of twisting motion on base onsite energy and between bases electron hopping constant was taking into account. Semi-empirical theory of Slater-Koster is employed in bringing the twisting motion effect on the hopping constants. In addition to the ability to hop from one base to other base, electron can also hop from a base to sugar-phosphate backbone and vice versa. The current flowing through DNA molecule is calculated using Landauer–Büttiker formula from transmission probability, which is calculated using transfer matrix technique and scattering matrix method, simultaneously. Then, the differential conductance is calculated from the I-V curve. The calculation result shows at some region of voltages, the conductance increases as the frequency increases, but in other region it decreases with the frequency.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion

By using tight binding Hamiltonian model, charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion is studied. The DNA chain used is 32 base pairs long poly(dA)-poly(dT) molecule. The molecule is contacted to electrode at both ends. The influence of environment on charge transport in DNA is modeled as variation of backbone disorder. The twisting motion amplitude is taking into account by assuming that the twisting angle distributes following Gaussian distribution function with zero average and standard deviation proportional to square root of temperature and inversely proportional to the twisting motion frequency. The base-pair twisting motion influences both the onsite energy of the bases and electron hopping constant between bases. The charge transport properties are studied by calculating current using Landauer-Buttiker formula from transmission probabilities which is calculated by transfer matrix methods. The result shows that as the backbone disorder increases, the maximum current decreases. By decreasing the twisting motion frequency, the current increases rapidly at low voltage, but the current increases slower at higher voltage. The threshold voltage can increase or decrease with increasing backbone disorder and increasing twisting frequency.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The impact of new Geant4-DNA cross section models on electron track structure simulations in liquid water

The most recent release of the open source and general purpose Geant4 Monte Carlo simulation toolkit (Geant4 10.2 release) contains a new set of physics models in the Geant4-DNA extension for improving the modelling of low-energy electron transport in liquid water (<10 keV). This includes updated electron cross sections for excitation, ionization, and elastic scattering. In the present work, the impact of these developments to track-structure calculations is examined for providing the first comprehensive comparison against the default physics models of Geant4-DNA. Significant differences with the default models are found for the average path length and penetration distance, as well as for dose-point-kernels for electron energies below a few hundred eV. On the other hand, self-irradiation absorbed fractions for tissue-like volumes and low-energy electron sources (including some Auger emitters) reveal rather small differences (up to 15%) between these new and default Geant4-DNA models. The above findings indicate that the impact of the new developments will mainly affect those applications where the spatial pattern of interactions and energy deposition of very-low energy electrons play an important role such as, for example, the modelling of the chemical and biophysical stage of radiation damage to cells.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DNA molecules deviate from shortest trajectory when driven through hydrogel

Dynamic fluorescence-based single-molecule imaging of $λ$-DNA molecules driven through agarose hydrogels by DC electric fields reveals that passage through the hydrogel (98.5% water content) induces mobility orthogonal to the external field. Tortuous paths followed by the DNA molecules, which are heavily entangled in the hydrogel mesh as their contour length is nearly 100 times the hydrogel mesh size of 200 nm, cause them to appear to diffuse orthogonal to the driving force. The higher the driving field, from 2 to 16 V/cm, the higher the off-axis dispersion is, over the same time interval. In this work we measure the off-axis displacement distribution over 3 orders of magnitude of probability density and find a master curve after normalizing for time (t) elapsed, but the power of time for normalizing increases with the external field, from t 0.25 to t 0.6 with increasing field. Comparing trajectories over the same distance traveled in the electric field direction, we observe whereas for the highest field strengths DNA molecules come closest to taking the shortest trajectory between two points in space, deviations from the shortest trajectory grow larger and larger (up to 40% larger) as one approaches the case of small yet finite external field strength.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Compact quantum dot surface modification to enable emergent behaviors in quantum dot-DNA composites

Quantum dot (QD) biological imaging and sensing applications often require surface modification with single-stranded deoxyribonucleic acid (ssDNA) oligonucleotides. Furthermore, ssDNA conjugation can be leveraged for precision QD templating via higher-order DNA nanostructures to exploit emergent behaviors in photonic applications. Use of ssDNA-QDs across these platforms requires compact, controlled conjugation that engenders QD stability over a wide pH range and in solutions of high ionic strength. However, cur-rent ssDNA-QD conjugation approaches suffer from limitations, such as the requirement for thick coatings, low control over ssDNA labeling density, requirement of large amounts of ssDNA, or low colloidal or photostability, restraining implementation in many applications. Here, we combine thin, multidentate, phytochelatin-3 (PC3) QD passivation techniques with strain-promoted copper-free alkyne-azide click chemistry to yield functional ssDNA-QDs with high stability. This process was broadly applicable across QD sizes (i.e.,λ em = 540, 560, 600 nm), ssDNA lengths (i.e., 10–16 base pairs, bps), and sequences (poly thymine, mixed bps). The resulting compacts sDNA-QDs displayed a fluorescence quenching efficiency of up to 89% by hybridization with complementary ssDNA-AuNPs. Further-more, ssDNA-QDs were successfully incorporated with higher-order DNA origami nanostructure templates. Finally, this approach, combining PC3 passivation with click chemistry, generates ssDNA-PC3-QDs that enable emergent QD properties in DNA-based devices and applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions

In human cells, the oxidative DNA lesion 8,5'-cyclo-2'-deoxyadenosine (CydA) induces prolonged stalling of RNA polymerase II (Pol II) followed by transcriptional bypass, generating both error-free and mutant transcripts with AMP misincorporated immediately downstream from the lesion. Here, we present biochemical and crystallographic evidence for the mechanism of CydA recognition. Pol II stalling results from impaired loading of the template base (5') next to CydA into the active site, leading to preferential AMP misincorporation. Such predominant AMP insertion, which also occurs at an abasic site, is unaffected by the identity of the 5´-templating base, indicating that it derives from nontemplated synthesis according to an A rule known for DNA polymerases and recently identified for Pol II bypass of pyrimidine dimers. Subsequent to AMP misincorporation, Pol II encounters a major translocation block that is slowly overcome. The translocation block combined with the poor extension of the dA.rA mispair reduce transcriptional mutagenesis. Moreover, increasing the active-site flexibility by mutation in the trigger loop, which increases the ability of Pol II to accommodate the bulky lesion, and addition of transacting factor TFIIF facilitate CydA bypass. Thus, blocking lesion entry to the active site, trans-lesion A rule synthesis, and translocation block are common features of transcription across different bulky DNA lesions.

59 BASIC BIOLOGICAL SCIENCES↗

Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6

Significance The loading of the core Mcm2-7 helicase onto origin DNA is essential for the formation of replication forks and genomic stability. Here, we report two cryo-electron microscopy (cryo-EM) structures that capture helicase loader–helicase complexes just prior to DNA insertion. These pre-loading structures, combined with a computational simulation of the dynamic transition from the pre-loading state to the loaded state, provide crucial insights into the mechanism required for topologically linking the helicase to DNA. The helicase loading system is highly conserved from yeast to human, which means that the molecular principles described here for the yeast system are likely applicable to the human system.

59 BASIC BIOLOGICAL SCIENCES↗