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Biomedical subjects

Catherine J Murphy

Publications and source records attributed to Catherine J Murphy.

31 records · Page 2Linked to original sources
PubMed2005

Probing DNA structure with nanoparticles.

Semiconductor nanoparticles, also known as quantum dots, are receiving increasing attention for their biological applications. These nanomaterials are photoluminescent and are being developed both as dyes and as sensors. Here we describe our "sensor" use of quantum dots to detect different intrinsic DNA structures. Structural polymorphism in DNA may serve as a biological signal in vivo, highlighting the need for recognition of DNA structure in addition to DNA sequence in biotechnology assays.

Animals↗
PubMed2004

Immobilization of gold nanorods onto acid-terminated self-assembled monolayers via electrostatic interactions.

We report the immobilization of gold nanorods onto self-assembled monolayers (SAMs) of 16-mercaptohexadecanoic acid (16-MHA). The simple two step protocol involves formation of a SAM of 16-MHA molecules onto gold-coated glass slides and subsequent immersion of these slides into the gold nanorod solution. The nanorods, formed by a seed-mediated, surfactant-assisted synthesis protocol, are stabilized in solution due to surface modification by the surfactant cetyltrimethylammonium bromide (CTAB). Attractive electrostatic interactions between the carboxylic acid group on the SAM and the positively charged CTAB molecules are likely responsible for the nanorod immobilization. UV-vis spectroscopy has been used to follow the kinetics of the nanorod immobilization. The nature of interaction between the gold nanorods and the 16-MHA SAM has been probed by Fourier transform infrared spectroscopy (FTIR). The surface morphology of the immobilized rods is studied by scanning electron microscopy (SEM) and atomic force microscopy (AFM) measurements. SEM was also used to determine the density of the immobilized nanorods as a function of the pH of immobilization. Control over the surface coverage of the immobilized gold nanorods has been demonstrated by simple pH variation. Such well-dispersed immobilized gold nanorods with control over the surface coverage could be interesting substrates for applications such as surface-enhanced Raman spectroscopy (SERS).

Journal Article↗
PubMed2004

Room temperature, high-yield synthesis of multiple shapes of gold nanoparticles in aqueous solution.

A seed-mediated growth method was used to control the morphology and dimensions of Au nanocrystals by the manipulation of the experimental parameters in aqueous solution at room temperature. This chemical route produces various structural architectures with rod-, rectangle-, hexagon-, cube-, triangle-, and starlike profiles and branched (such as bi-, tri-, tetra-, and multipod) Au nanocrystals of various dimensions in high yield in the presence of a single surfactant, cetyltrimethylammonium bromide.

Journal Article↗
PubMed2004

Seeded high yield synthesis of short Au nanorods in aqueous solution.

Short gold nanorods of average lengths ranging between 20 and 100 nm (with corresponding aspect ratios of 2 and 4) were synthesized in excellent yield (approximately 97%). These nanorods were characterized by dark-field microscopy, UV-visible spectrophotometry, and transmission electron microscopy. Temporal evolution of rod shape had also been followed by UV-visible spectrophotometry and transmission electron microscopy and indicates that the nanorods briefly increase in length, then increase slightly in width, as they grow. The effect of the synthetic parameters on the rod dimension and yield was explored to find out suitable conditions to produce short nanorods; short nanorods have both plasmon bands in the visible region of the spectrum, which is a valuable property for sensor applications.

Journal Article↗
PubMed2004

Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe.

This paper explores the effects of structural modifications on the fast dynamics of DNA and the ability of time-resolved Stokes shift spectroscopy to measure those changes. The time-resolved Stokes shift of a synthetic coumarin base-pair replacement within an oligomer is measured between 40 ps and 40 ns. Comparisons are made between 17mers without modification, with a deleted base near the coumarin and with the coumarin placed near the end of the oligomer. The deletion of a next-to-nearest-neighbor base pair does not change the subnanosecond dynamics, but does cause an additional motion with a time constant of approximately 20 ns. A candidate for this motion is the flipping of the abasic sugar out of the helix and the concomitant intrusion of water into the interior of the helix. A nearby chain end causes little change in the dynamics after 1 ns but leads to a reduction in the amplitude of the dynamics between 40 ps and 1 ns. We suggest that at the chain end, where DNA on one side of the probe has been replaced by water, the charge- stabilizing dynamics have the same overall amplitude, but that much of the relaxation occurs before the start of the measurement time window.

Base Pairing↗
PubMed2004

Platinum ion uptake by dendrimers: an NMR and AFM study.

The reaction of generation 2 and generation 4 poly(amidoamine) (PAMAM) dendrimers with K2PtCl2 was studied by several NMR methods. The time dependency of the Pt(II) complexation was followed with 195Pt NMR for both dendrimers and the equilibrium product was further characterized with (1)H NMR, and indirectly detected 13C NMR, in the case of the generation 2 dendrimer. After 2 days, a black precipitate of Pt(0) was observed, half the original 195Pt signal was lost, and approximately 20% of the initial Pt(II) was coordinated to the tertiary and secondary nitrogens of the generation 2 dendrimer. The uptake of Pt(II) by the generation 4 dendrimer was much slower, consistent with the steric crowding of the surface groups on the generation 4 dendrimer compared to the more open generation 2. After 10 days, 80% of the Pt(II) was deep within the generation 4 dendrimer; the remaining 20% was unreacted or bound near the surface nitrogens of a single dendrimer. The location and time course of the platinum ion uptake by the dendrimers provides valuable insight into the formation of Pt(0) nanoparticles made in the presence of dendrimers as stabilizers, visualized by atomic force microscopy.

Journal Article↗
PubMed2004

Optical detection of thymine dinucleoside monophosphate and its cis-syn photodimer by inorganic nanoparticles.

The Watson-Crick DNA double helix is an averaged ideal of multitudinous natural sequence-directed local structural deviations. By effectively derailing normal cellular physiological processes, damaged bases can induce noncanonical irregularities in the local structure of DNA if not efficiently repaired. Pyrimidine bases, especially thymine, are prone to dimerization when exposed to ultraviolet light. A [2 + 2] photocyclo-addition between adjacent thymine bases predominantly produces the cis-syn photodimer. These lesions, implicated in skin cancer, bend DNA by approximately 30 degrees due to their structural and conformational changes. Such changes in molecular properties can be detected by differential quenching of CdS nanoparticle luminescence and by surface-enhanced Raman scattering spectroscopy on metal nanoparticle substrates.

Cadmium Compounds↗
PubMed2003

Sodium-ion binding to DNA: detection by ultrafast time-resolved stokes-shift spectroscopy.

The nature of the counterion is shown to have a pronounced effect on the apparent dynamic polarity in the interior of DNA. Time-resolved Stokes-shift measurements in the 80 ps to 40 ns time range were made on a polarity-sensitive fluorophore (coumarin 102) that replaces a base pair in an oligonucleotide. With sodium counterions, the emission spectrum narrows with time, whereas with tetrabutylammonium counterions, it does not. Our interpretation is that a subpopulation of helices have sodium cations bound in a fashion that slows the normal dynamics.

Coumarins↗
PubMed2002

A fiber-optic fluorescence sensor for lithium ion in acetonitrile.

A novel fiber-optic fluorescence sensor based on a controlled-release reagent for the determination of lithium ion in organic solvents is proposed. The fluorogenic indicator 2-(2-hydroxyphenyl)benzoxazole is contained in a mini-polyethylene tube as the reagent reservoir and is brought into contact with the analyte solution by diffusion across a poly(vinyl chloride) (PVC) membrane to form a strongly fluorescent complex at the membrane/solution interface. The fluorescence signals produced are measured via two joined optical fibers positioned closely to the backside of the PVC membrane for light illumination and collection. The sensor is useful for measuring Li+ at concentrations in acetonitrile ranging from 1.0 x 10(-6) to 1.0 x 10(-2) M with a detection limit of 3.0 x 10(-7) M. The steady-state response can be reached within seconds, and the signal changes are fully reversible. The sensor shows minimal interference effects from other alkali metal and alkaline earth metal cations and has good stability and durability when stored in acetonitrile solutions.

Journal Article↗
PubMed2002

Complex local dynamics in DNA on the picosecond and nanosecond time scales.

Time-resolved Stokes shift measurements of the local structural relaxation of three DNA oligonucleotides are presented. Logarithmic relaxation is seen for over three decades in time (40 ps-40 ns), indicating a complex relaxation among a large number of conformational substates. The observed relaxation is the same in all the sequences. Sequence dependence of the localized dynamics of DNA does not appear within this time range. We infer that 30%-50% of the relaxation is faster than 40 ps, has a nonlogarithmic decay and has a sequence dependent amplitude.

Circular Dichroism↗