Bare Probe Research Articles

Dosimetric evaluation of an intraoperative radiotherapy system: a measurement-based and Monte-Carlo modelling investigation

Intraoperative radiotherapy (IORT) is a specialised subset of radiotherapy, where a high radiation dose is delivered to a surgically exposed tumour bed in order to eradicate any remaining cancer cells. The aim of this study was to examine the dose characteristics of the Zeiss Intrabeam IORT device which provides near-isotropic emission of up to 50 kV X-rays. The EGSnrc Monte Carlo (MC) code system was used to simulate the device and percentage depth dose (PDD) data measured with a soft X-ray parallel-plate ionisation chamber were used for model verification. The model provided energy spectra, isodose curves and mean photon energies. In addition, EBT3 Gafchromic film was used to verify the MC model by examining PDDs and 2D dose distributions for various applicators. The differences between MC model and ionisation chamber measurements were within 3% for most points, with a maximum deviation of ~ 9%. Most of the simulated PDD points were within 5% of the film-measured data, with a maximum deviation of ~ 10%. The mean energy of the bare probe was found to be 21.19 keV. The mean photon energy from applicators ranged from 29.00 to 30.85 keV. Results of this study may be useful for future work on creating a system for treatment planning.

Sharp, high numerical aperture (NA), nanoimprinted bare pyramid probe for optical mapping.

The ability to correlate optical hyperspectral mapping and high resolution topographic imaging is critically important to gain deep insight into the structure-function relationship of nanomaterial systems. Scanning near-field optical microscopy can achieve this goal, but at the cost of significant effort in probe fabrication and experimental expertise. To overcome these two limitations, we have developed a low-cost and high-throughput nanoimprinting technique to integrate a sharp pyramid structure on the end facet of a single-mode fiber that can be scanned with a simple tuning-fork technique. The nanoimprinted pyramid has two main features: (1) a large taper angle (∼70°), which determines the far-field confinement at the tip, resulting in a spatial resolution of 275nm, an effective numerical aperture of 1.06, and (2) a sharp apex with a radius of curvature of ∼20nm, which enables high resolution topographic imaging. Optical performance is demonstrated through evanescent field distribution mapping of a plasmonic nanogroove sample, followed by hyperspectral photoluminescence mapping of nanocrystals using a fiber-in-fiber-out light coupling mode. Through comparative photoluminescence mapping on 2D monolayers, we also show a threefold improvement in spatial resolution over chemically etched fibers. These results show that the bare nanoimprinted near-field probes provide simple access to spectromicroscopy correlated with high resolution topographic mapping and have the potential to advance reproducible fiber-tip-based scanning near-field microscopy.

D-shape optical fiber probe dimension optimization for LSPR based bio-sensor

The evanescent wave absorption based photonic sensing platform has been developed using D-shaped fiber optic probes for refractive index (RI) mediated bio-sensors. The RI sensitivity of this bare probe was established using different sucrose solutions by optimizing the active de-cladded surface area of the fiber. A linear correlation between probe sensing area and RI sensitivity was observed for different probe lengths. Further, these bare probes have been functionalized using amine (–NH2) functional groups on the air-exposed core using the standard silane treatment process. This probe was demonstrated as a localized surface plasmon resonance (LSPR) monitoring platform by immobilizing the spherical gold nanoparticles (AuNPs). The effect of D-shaped length/area on absorption sensitivity was compared with bare and LSPR probes. The biosensing property of this LSPR probe was tested using Immunoglobulin antibody (HIgG). An exponential bimolecular binding kinetic has been observed during this antigen–antibody conjugation and the limit of detection was measured (0.6 µg/mL) by varying concentrations of antigen (GaHIgG). These fiber optic LSPR probes can be integrated into an optical system to develop an evanescent wave absorption-based biosensor.

Electrical contactless microfluidic flow quantification

Precise sensing of microfluidic flow is essential to advancing lab-on-a-chip development and the downstream medical applications. Contactless microfluidic flow interrogation is noninvasive, nonperturbative, and fouling-free. However, known real non-contact flow sensing technologies are limited to quantifying bulk fluids. Here, we develop an electrical approach to contactless quantification of aqueous microfluidic flow. We found that the electric potential generated by the ubiquitous contact electrification of a microfluidic flow with fluidic channel walls is interrogatable by using a probe electrode at a distance over centimeters from the microfluidic flow, and the measured voltage response demonstrates linear relationship to the microfluidic flow rate with a resolution of sub-microliter per minute (in a 1-Hz bandwidth), providing an ideal, high-precision contactless flow transduction pathway. In addition to this primary finding, by using a monolayer-graphene coated probe electrode, in comparison with a typical bare probe electrode, an overall enhancement in flow-sensory resolution of 36.4% is attained.

Monte Carlo calculation of the TG-43 dosimetry parameters for the INTRABEAM source with spherical applicators

Objective: The relative TG-43 dosimetry parameters of the INTRABEAM (Carl Zeiss Meditec AG, Jena, Germany) bare probe were recently reported by Ayala Alvarez et al (2020 Phys. Med. Biol. 65 245041). The current study focuses on the dosimetry characterization of the INTRABEAM source with the eight available spherical applicators according to the TG-43 formalism using Monte Carlo (MC) simulations. Approach: This report includes the calculated dose-rate conversion coefficients that determine the absolute dose rate to water at a reference point of 10 mm from the applicator surface, based on calibration air-kerma rate measurements at 50 cm from the source on its transverse plane. Since the air-kerma rate measurements are not yet provided from a standards laboratory for the INTRABEAM, the values in the present study were calculated with MC. This approach is aligned with other works in the search for standardization of the dosimetry of electronic brachytherapy sources. As a validation of the MC model, depth dose calculations along the source axis were compared with calibration data from the source manufacturer. Main results: The calculated dose-rate conversion coefficients were 434.0 for the bare probe, and 683.5, 548.3, 449.9, 376.5, 251.0, 225.6, 202.8, and 182.6 for the source with applicators of increasing diameter from 15 to 50 mm, respectively. The radial dose and the 2D anisotropy functions of the TG-43 formalism were also obtained and tabulated in this document. Significance: This work presents the data required by a treatment planning system for the characterization of the INTRABEAM system in the context of intraoperative radiotherapy applications.

Effective energy assessment during breast cancer intraoperative radiotherapy by low-energy X-rays: A Monte Carlo study.

The study reported in the present paper aimed to evaluate the effective energy (Eeff) of X-rays emitted from the surface of a bare X-ray probe and from different spherical applicators with various diameters, which are widely employed for low kV intraoperative radiotherapy (IORT) of breast cancer. A previously validated Monte Carlo model of the INTRABEAM system along with applicator diameters of 1.5-5cm (with 0.5cm increments) was employed for this purpose. The results show that the presence of the applicator can considerably harden the X-rays produced by the bare probe so that Eeff increases by a factor of about 2.6. Variations of applicator diameter also affects the X-ray effective energy. Specifically, increasing the applicator diameter from 1.5 to 3cm and 3.5-5cm resulted in an increase in the Eeff by 8.8% and 14.6%, respectively. The validity of the calculated Eeff values was confirmed by a reasonable agreement between the obtained probability density distributions (PDDs) for the full X-ray energy spectrum and those for the corresponding single effective energies, for different applicator diameters. The Eeff values obtained for different applicator diameters and the bare probe alone can be used as an alternative for the corresponding full energy spectra, in Monte Carlo-based dosimetry simulations of low-energy therapeutic X-rays, as well as for determining quality conversion factors of any ion chambers employed for low kV-IORT absolute dosimetry.

Monte Carlo calculation of the relative TG-43 dosimetry parameters for the INTRABEAM electronic brachytherapy source

The INTRABEAM system (Carl Zeiss Meditec AG, Jena, Germany) is an electronic brachytherapy (eBT) device designed for intraoperative radiotherapy applications. To date, the INTRABEAM x-ray source has not been characterized according to the AAPM TG-43 specifications for brachytherapy sources. This restricts its modelling in commercial treatment planning systems (TPSs), with the consequence that the doses to organs at risk are unknown. The aim of this work is to characterize the INTRABEAM source according to the TG-43 brachytherapy dosimetry protocol. The dose distribution in water around the source was determined with Monte Carlo (MC) calculations. For the validation of the MC model, depth dose calculations along the source longitudinal axis were compared with measurements using a soft x-ray ionization chamber (PTW 34013) and two synthetic diamond detectors (microDiamond PTW TN60019). In our results, the measurements in water agreed with the MC model calculations within uncertainties. The use of the microDiamond detector yielded better agreement with MC calculations, within estimated uncertainties, compared to the ionization chamber at points of steeper dose gradients. The radial dose function showed a steep fall-off close to the INTRABEAM source (10 mm) with a gradient higher than that of commonly used brachytherapy radionuclides (192Ir, 125I and 103Pd), with values of 2.510, 1.645 and 1.232 at 4, 6 and 8 mm, respectively. The radial dose function partially flattens at larger distances with a fall-off comparable to that of the Xoft Axxent® (iCAD, Inc., Nashua, NH) eBT system. The simulated 2D polar anisotropy close to the bare probe walls showed deviations from unity of up to 55% at 10 mm and 155°. This work presents the MC calculated TG-43 parameters for the INTRABEAM, which constitute the necessary data for the characterization of the source as required by a TPS used in clinical dose calculations.

Impact of spherical applicator diameter on relative biologic effectiveness of low energy IORT X-rays: A hybrid Monte Carlo study.

Low-kV IORT (Low kilovoltage intraoperative radiotherapy) using INTRABEAM machine and dedicated spherical applicators is a candidate modality for breast cancer treatment. The current study aims to quantify the RBE (relative biologic effectiveness) variations of emitted X-rays from the surface of different spherical applicators and bare probe through a hybrid Monte Carlo (MC) simulation approach. A validated MC model of INTRABEAM machine and different applicator diameters, based on GEANT4 Toolkit, was employed for RBE evaluation. To doing so, scored X-ray energy spectra at the surface of each applicator diameter/bare probe were used to calculate the corresponding secondary electron energy spectra at various distances inside the water and breast tissue. Then, MCDS (Monte Carlo damage simulation) code was used to calculate the RBE values according to the calculated electron spectra. Presence of spherical applicators can increase the RBE of emitted X-rays from the bare probe by about 22.3%. In return, changing the applicator diameter has a minimal impact (about 3.2%) on RBE variation of emitted X-rays from each applicator surface. By increasing the distance from applicator surface, the RBE increments too, so that its value enhances by about 10% with moving from 2 to 10mm distance. Calculated RBE values within the breast tissue were higher than those of water by about 4% maximum value. Ball section of spherical IORT applicators can affect the RBE value of the emitted X-rays from INTRABEAM machine. Increased RBE of breast tissue can reduce the prescribed dose for breast irradiation if INTRABEAM machine has been calibrated inside the water.

Influence of breast tissue composition on dosimetric characteristics of therapeutic low energy X-rays

Intraoperative radiotherapy using low energy X-rays (low-kV IORT) is a candidate modality for early-stage breast cancer irradiation. The patient treatment planning in this type of radiotherapy is based on the acquired dosimetry data inside the water, while the difference of breast tissue composition respect to the water may change the dosimetric characteristics of employed low energy X-rays. The impact of different breast tissue compositions on dosimetric characteristics of low energy X-rays was assessed through Monte Carlo (MC) simulation in the current study.A validated MC model of INTRABEAM machine along with 2.5 and 5 cm diameter applicator, based on the GEANT4 MC Toolkit, was used to calculate the percentage depth dose (PDD) curves of the bare probe and mentioned applicator diameters inside different breast compositions of 30% and 70% glandular weight as well as the calcified breast. Finally, obtained PDD results were quantitatively compared with corresponding data inside the water.The results showed that the 70% glandular breast composition has the best accordance to the water so that the mean difference between the acquired PDDs for the bare probe, 2.5, and 5 cm diameter applicator respect to the water was obtained as 5.6%, 4.1%, and 4.9%, respectively. On the other hand, the calcified breast substantially changes the dosimetric features of low energy X-rays, so that the mean difference between the PDD data respect to the water can reach to about 78%.Based on the findings, it can be concluded that the breast tissue composition can affect the employed dosimetry data for patient treatment planning in the low-kV IORT method, especially in the case of calcified breast. Considering the variations of breast tissue composition can improve the accuracy of the delivered dose to the patient.

A novel periodically tapered structure-based gold nanoparticles and graphene oxide – Immobilized optical fiber sensor to detect ascorbic acid

This work presents a study, analysis, design, and characterization of a localized surface plasmon resonance (LSPR) based ascorbic acid (AA) sensor with improved sensitivity compared to those already reported. Various multi-tapered (four, five, and eight tapered) optical fiber sensors (OFSs) have been developed and characterized in this study. Along with these, different nanomaterials (NMs), such as gold nanoparticles (AuNPs) and graphene oxide (GO), are immobilized over the bare probe. Further, NMs immobilized probes are functionalized with ascorbate oxidase. The AuNPs are well studied in the past with the variation in size, shape and surface functionalization and have been found to be well-suited NMs for biosensing applications. On the other hand, GO-based material is equally promising in the nanostructure-based optical sensing due to their broad surface area, high electrical conductivity, good chemical stability, and excellent mechanical behavior. The performance parameters of the proposed sensor, such as sensitivity (8.3 nm/mM), correlation correlator (0.9724), and limit of detection (51.94 µM) are greatly improved over the previous designs. A wide range of characterization and validation of NMs immobilized structures are reported here. It indicates a great potential in the practical implementation of LSPR based OFSs for routine diagnostics.

Transvaginal ultrasound probes are human papillomavirus-free following low-level disinfection: cross-sectional multicenter survey.

To assess the frequency of detection of high-risk human papillomavirus (hrHPV) on transvaginal ultrasound (TVS) probes and keyboards and evaluate operator compliance with national recommendations for prevention of cross-infection during TVS. This was a multicenter observational survey involving 46 public and private centers, in the Paris region of France, in which at least five consecutive TVS examinations were performed per day. We audited 676 TVS procedures. We recorded preventive hygiene actions undertaken by the operator at three stages: (1) during TVS; (2) during probe disinfection; and (3) during preparation of the probe for the next TVS. After probe disinfection, we collected one sample from the bare probe and one from the ultrasound keyboard; following probe preparation for the next examination, an additional sample was obtained from the covered probe. The samples were tested for presence of hrHPV DNA using the Cobas® 4800 System. We did not detect hrHPV DNA in samples collected from uncovered or covered probes (0%; 95% CI, 0.00-0.55%). Keyboard samples were positive for hrHPV in two cases (0.3%; 95% CI, 0.04-1.07%). During TVS, the operator avoided touching the keyboard with a hand that had touched the patient's vulva in 86% of cases and held the probe with a gloved hand in 68%. Before probe disinfection, the operator wore new gloves, or performed hand disinfection in 8% of cases. The probe disinfection technique used was adequate in 87% of cases, not performed at all in 12% and insufficient in 1%. Before preparing the probe for the next scan, the operators disinfected their hands or used new gloves in 81% of cases. The probe cover and the coupling gel used complied with recommendations in 98% and 46% of cases, respectively. Of the seven preventive hygiene actions recommended in national guidelines, all were performed in 2%, three to six in 95% and two in 3% of observations. In four (9%) centers, disinfection was not performed in over half the observations. No evidence of hrHPV DNA was found on TVS probes and probe covers following low-level disinfection, despite suboptimal compliance with hygiene guidelines. Routine TVS practice could be made easier and safer with a global approach to probe disinfection and hand hygiene. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Monte Carlo based analysis and evaluation of energy spectrum for low-kV IORT spherical applicators

Low-kV IORT is an increasing modality for breast cancer treatment. Soft X-rays from INTRABEAM (Carl Zeiss Meditec AG, Oberkochen, Germany), a dedicated IORT device along with special spherical applicators are employed for this purpose. A Monte Carlo model of INTRAMBEAM and spherical applicators are introduced in the current study to evaluate the dosimetric and physical characteristics of emitted X-rays from the bare probe and different applicator diameters.X-ray probe and different applicator diameters of 1.5cm to 5cm were simulated by GEANT4 Monte Carlo Toolkit. Then, the validity of the simulated model was evaluated by comparing the Monte Carlo based PDD (percentage depth dose) and anisotropy data with those reported by the manufacturer. Finally, the physical characteristics of X-rays such as the mean and most probable energy as well as the LET of secondary electrons were obtained and analyzed.There was a good agreement between the simulated and reported PDDs for bare probe and different applicator diameters. The anisotropy values were also within an exemplary range reported by the manufacturer. The X-ray mean energy shifts from 25.6keV to 28.6keV with variations of applicator diameter. The maximum variation of the secondary electron LET was 9% with changing the applicator diameter.The usefulness of GEANT4 Toolkit for Monte Carlo based commissioning of INTRABEAM machine was confirmed in the current study. The variations of the applicator diameter slightly changed the physical characteristics of low-kV X-rays and LET of secondary electrons which cannot considerably affect the relative biologic effectiveness (RBE) for different applicator diameters.

Poly(N-isopropylacrylamide) Response to Salt Concentration and Anion Identity: A Brush-on-Brush Study.

The stability of poly(N-isopropylacrylamide) (PNIPAM) brush-modified colloidal silica particles was compared to asymmetric and symmetric PNIPAM brush direct force measurements in the presence of 1, 10, and 500 mM aqueous salt solution of KCl, KNO3, and KSCN between 10 and 45 °C. Dynamic light scattering measurements highlighted subtle variations in the salt-mediated thermoresponse, while atomic force microscopy (AFM) force curves between a bare silica or PNIPAM brush-modified colloid probe and a planar PNIPAM brush elucidated differences in brush interactions. The AFM force curves in the presence of KCl primarily revealed steric interactions between the surfaces, while KNO3 and KSCN solutions exhibited electrosteric interactions on approach as a function of the chaotropic nature of the ion and the solution concentration. The symmetric PNIPAM brush interaction highlighted significant variations between KCl and KSCN at 1 and 500 mM concentrations, while the approach and retraction force curves were relatively similar at 10 mM concentration. The combination of these techniques enabled the stability of PNIPAM brush-modified colloidal dispersions in the presence of electrolyte to be better understood with specific ion binding and the solution Debye length playing a significant role.

Common-path all-fiber optical coherence tomography probe based on high-index elliptical epoxy-lensed fiber

We propose and demonstrate high-index elliptical epoxy-lensed fiber probes designed specifically for endoscopic common-path (CP) swept-source optical coherence tomography (OCT) imaging inside wet tissues. The high-index epoxy lens uses a beam expansion region of a few hundred microns, which is capped with a spherical surface mounted at the end of an optical fiber. The probe is designed to operate inside wet tissues and shows improved performance over a long imaging depth, compared to bare or simple half-ball-lensed fiber probes. It allows optimal CP-OCT imaging in wet tissues by providing a stable reference power level and optimal beam waist for a long imaging depth. We have fabricated an array of these probes and one with a beam expansion region length of 288 μm and with a lens surface radius of 61 μm exhibiting 25-dB signal-to-noise ratio improvement compared to a bare fiber probe at 1.5-mm distance in water. The proposed probe is tested using a phantom sample comprising several layers of tape in water. The OCT images show that the probe is capable of high-resolution imaging over a distance of 1.5 mm.

Method for reducing measurement errors of a Langmuir probe with a protective RF shield

Probe measurements were conducted in the middle cross-section of an inductive, low-pressure xenon plasma using a straight cylindrical Langmuir probe with a bare metal shield that protected the probe from radio frequency interference. As a result, reliable radial distributions of the plasma parameters were obtained. Subsequent analyses of these measurements revealed that the electron energy distribution function (EEDF) deviated substantially from the Maxwellian functions and that this deviation depended on the length of the probe shield. To evaluate the shield's influence on the measurement results, in addition to the probe (which was moved radially as its shield length varied in the range of lsh1 = lmax–0), an additional L-shaped probe was inserted at a different location. This probe was moved differently from the first probe and provided confirmational measurements in the common special position where lsh1 = 0 and lsh2 ≠ 0. In this position, the second shield decreased all the plasma parameters. A comparison of the probe datasets identified the principles of the relationships between measurement errors and EEDF distortions caused by the bare probe shields. This dependence was used to correct the measurements performed using the first probe by eliminating the influence of its shield. Physical analyses based on earlier studies showed that these peculiarities are caused by a short-circuited double-probe effect that occurs in bare metal probe protective shields.

Note: Additionally refined new possibilities of plasma probe diagnostics.

In two previous Notes published in this journal, a method of measuring probe sheath thickness and ion mass was described using Langmuir probe diagnostics in low pressure xenon plasma close to Maxwellian substance. According to the first Note, this method includes two stages: (i) in a special experiment with known ion mass, the Bohm and Child-Langmuir-Boguslavsky (CLB) equations for cylindrical Langmuir probes used in this xenon plasma were solved jointly to determine the probe sheath thicknesses and Bohm coefficient CBCyl ≈ 1.13; and (ii) in a general experiment, with known CBCyl, the same equations could be solved to obtain the probe sheath thicknesses and the mean ion mass. In the second Note, the (i) stage of this method was refined: the results of the CLB probe sheath model application, which were termed "evaluations," were corrected using the step-front probe sheath model, which was closer to reality in the special experiment with the xenon plasma. This process resulted in a Bohm coefficient of CBCyl ≈ 1.23 for the cylindrical probe. In the present Note, corrected xenon plasma parameters without the influence of the bare probe protective shield were used for the (i) stage of this diagnostic method. This action also refined the Bohm coefficient, lowering it to CBCyl ≈ 0.745 for cylindrical probes. This advance makes the new diagnostics method more objective and reliable.

Graphene oxide coated U-bent plastic optical fiber based chemical sensor for organic solvents

This study describes the development of a refractive index (RI) based fiber optic chemical sensor using a U-bent plastic optical fiber (BPOF) probe made of 0.5 mm polymethylmethacrylate (PMMA) core and optimum bend diameter of 1.4 mm coated with graphene oxide (GO) film. GO film on BPOF sensor surface significantly enhance the RI sensitivity of the sensor as well as its chemical resistance due to improved refractive index contrast and (PMMA) surface passivation by GO respectively. GO was chemisorbed to hexamethylenediamine (HMDA) functionalized BPOF probe surface by identifying the optimum GO concentration (100 μg/ml) and incubation time (24 h). An enhanced RI sensitivity of 9.42 ± 0.37 (ΔA845nm/ΔRIU) was achieved using GO coating of thickness 3.3 μm, which is 3.6 times higher than that of the bare BPOF probe. The RI sensitivities in presence of organic solvents including methanol, ethanol and isopropyl alcohol are found to be 12.75 ± 1.19, 9.97 ± 0.66 and 13.93 ± 0.92 (ΔA845nm/ΔRIU) respectively. GO film over BPOF was stable even after incubation of the probes in the alcohols over 12 h. In addition, GO-BPOF probes were able to tolerate acetone environment for a prolonged duration of 30 min as opposed to 10 min in case of the bare probes due to improved chemical resistance. Hence, the GO-BPOF could potentially be utilized as a sensitive RI sensor not only for aqueous solutions but also for reactive organic solvents such as alcohols and acetone which are known to damage the PMMA surface.

Two dimensional α-MoO3-x nanoflakes as bare eye probe for hydrogen peroxide in biological fluids

We report a rapid and facile method for detection of hydrogen peroxide (H2O2) in biological fluids using sub-stoichiometric two-dimensional (2D) molybdenum trioxide (α-MoO3-x) nanoflakes. The two-dimensional nanoflakes, initially blue in color, is oxidized after interaction with hydrogen peroxide thereby changing its oxidation state to form α-MoO3. The change in oxidation state of nanoflakes transforms from blue to a visually distinct hazy blue color with change in absorption spectrum. The phenomenal property is explored here in sensing up to 34 nM as limit of detection. The efficacy of the detection system was analyzed by “zone of inhibition” based agar diffusion assay with different concentrations of H2O2. The current approach is highly accurate, effective and reproducible for quantification of physiological concentration of H2O2 in biological fluid such as human urine.

Elevating the Precision of Plasma Probe Diagnostics by Elimination of Bare Probe Protective Shields’ Influence

Probe diagnostics of the low pressure inductive xenon plasma were conducted using classic cylindrical Langmuir probes with conventional protection of their circuits against radio frequency interferences by bare metal shields. The dimensions of their probetips were determined in the special experiment that provided negligible local plasma distortions. Accurate probe measurements were used to determine the spatial plasma parameter distributions in a gas discharge unit of an ion thruster model which helped to develop its ion-extracting grate. The subsequent analysis of probe measurements showed that in these experiments, the plasma electron energy distribution function (EEDF) was quite noticeably deviated from the Maxwell function depending on the main probe shield length that varied from maximum to zero. Use of an additional probe in the special position where its shield was rather long with zero shield length of the main probe showed that the additional shield lowered all plasma parameters. Comparison of both probes’ data identified the principled relationship between measurement errors and EEDF distortions caused by bare probe shield and this dependence was used to correct the initial probe measurements. Therefore plasma probe diagnostics became more precise due to the lowered influence of the bare probe protective shields. Its physical analysis based on previous authors’ works showed that this effect was caused by a shortcircuited double-probe phenomenon in the bare metal shields.

Trifunctional fluorescent unnatural nucleoside: Label free detection of T-T/C-C base mismatches, abasic site and bulge DNA

The detection and targeting of both the mismatched and abasic DNA is highly important which would ultimately help in designing new diagnostics and chemotherapeutics. Furthermore, sensing and targeting the bulge sequence with a fluorescent probe would be useful to study the role of bulges in nucleic acid function or could have significant therapeutic potential. Thus, detection of specific bulges by small fluorescent molecules is an attractive research area since the past several years. Many attempts have been made to prepare such compounds. We report herein a label free strategy for the detection of pyrimidine base mismatches (T/T and C/C), sensing of abasic site, and pyrimidine base bulge DNA using an unnatural tetrazolylpyrene nucleoside (TPyBDo) as a bare fluorescent probe. The H-bonding/hydrophobic force mediated interactions allow the sensing of all three deformed DNA via an enhancement of fluorescence signal using our simple “Just-Mix and Read” strategy. The binding of the probe to all the three deformed DNA duplexes is accompanied by an increase in the thermal melting stability of the deformed DNAs. That the probe binds efficiently to the minor groove near the deformed site was evident from spectroscopic studies. All the spectral evidences open up a multitude of possibilities for using our probe, tetrazolylpyrene nucleoside, as an efficient fluorescent light-up bio-probe for label free DNA detection.