Homogeneous DNA Hybridization Research Articles

DNA Hybridization Assay Using Gold Nanoparticles and Electrophoresis Separation Provides 1 pM Sensitivity.

The efficiency of gold nanoparticle (AuNP) dimerization mediated by hybridization between two probe DNA molecules and a complementary target DNA molecule was maximized by examining several possible hybridization combinations. The uniformity of the size of the AuNPs, the use of surface modification appropriate for high hybridization efficiency, together with efficient blocking of nonspecific binding, all contributed to achieving a 1 pM detection limit following conventional gel electrophoresis separation of the DNA-modified AuNP multimers. This practical homogeneous DNA hybridization assay methodology will provide a rapid, cost-effective, and field-portable tool for clinical diagnosis.

A recyclable electrochemical sensing platform for breast cancer diagnosis based on homogeneous DNA hybridization and host-guest interaction between cucurbit [7]uril and ferrocene-nanosphere with signal amplification

Recently, many strategies have been developed to trace the breast cancer susceptibility gene (BRCA), which is closely related to the occurrence of breast cancer. In this work, a novel recyclable electrochemical sensing platform was constructed to detect BRCA DNA based on the homogeneous hybridization of this target sequence with ferrocene-labeled DNA/Au nanospheres (FcNS) and horseradish peroxidase-labeled DNA/Au nanospheres (HRPNS) concatamers, and the host-guest interaction between cucurbit [7]uril (CB [7]) adsorbed on the electrode and Fc on the hybridization complex. With the optimization of experimental conditions, the fabricated sensing platform showed improved sensitivity with a low detection limit of 25pM (S/N=3), contributed by the dual amplification of signal using FcNS and HRPNS concatamers, and high specificity for BRCA DNA. The captured complex was dissociated from CB [7]-modified electrode with the rise of pH value to recycle the sensing platform. Furthermore, this detection strategy displayed the reliability and applicability in the analysis of human serum samples, indicating great potential for applications in early diagnosis of breast cancer.

The novel pillar[5]arene derivative for recyclable electrochemical sensing platform of homogeneous DNA hybridization

In this work, a recyclable electrochemical sensing platform to detect breast cancer susceptibility gene (BRCA) was constructed by pillararenes based host–guest recognition and homogeneous DNA hybridization. BRCA target DNA (T-DNA) formed sandwich-type DNA via homogeneous hybridization with methylene blue labeled signal DNA and alkylamino modified capture DNA, which could form complexes with pillararenes. Such sandwich-type DNA was captured by a novel trithiocarbonate modified pillar[5]arene (P5A-CTA) which was immobilized on the Au electrode. With the help of enzyme amplification, the electrochemical detection signal of target DNA in sensing platform was apparently amplified. This sensing platform exhibited wide linear range and excellent specificity, and was particularly recyclable after simple washing with hot acetonitrile due to the reversible host–guest complexation between P5A-CTA and alkylamino modified DNA.

Robust Discrimination between Single Gold Nanoparticles and Their Dimers in Aqueous Solution for Ultrasensitive Homogeneous Bioassays

We propose a robust method to distinguish isolated single gold nanoparticles (AuNP monomers) and their dimers under Brownian motion, a key for ultrasensitive homogeneous bioassays, including AuNP sandwich assays. To detect dimers and distinguish them from a larger number of monomers in aqueous solution, single-particle polarization microscopy was performed. For the accurate detection of individual particles, the optical anisotropy and rotational diffusion time are measured because a dimer is much more anisotropic than the nearly spherical monomer and the rotational diffusion time of a dimer is four times that of a monomer. By employing an autocorrelation analysis, we defined a measure of distinguishing that simultaneously enables high detection probability and low error probability. The detection platform offers homogeneous DNA hybridization assays and immunoassays at the subpicomolar level.

Distance and Temperature Dependency in Nonoverlapping and Conventional Förster Resonance Energy-Transfer

Förster resonance energy-transfer (FRET) is a powerful and widely applied bioanalytical tool. According to the definition of FRET by Förster, for energy-transfer to take place, a substantial spectral overlap between the donor emission and acceptor excitation spectra is required. Recently also a phenomenon termed nonoverlapping FRET (nFRET) has been reported. The nFRET phenomenon is based on energy-transfer between a lanthanide chelate donor and a spectrally nonoverlapping acceptor and thus obviously differs from the conventional FRET, but the mechanism of nFRET and resulting implications to assay design have not been thoroughly examined. In this work, a homogeneous DNA-hybridization assay was constructed to study the distance and temperature dependency of both nFRET and conventional FRET. Capture oligonucleotides were labeled at the 5'-end with a Eu(III)-chelate, and these conjugates hybridized to complementary tracer oligonucleotides labeled with an organic fluorophore at various distances from the 3'-end. The distance dependency was studied with a fluorometer utilizing time-resolution, and the temperature dependency was studied using a frequency-domain (FD) luminometer. Results demonstrated a difference in both the distance and temperature dependency between conventional FRET and nFRET. On the basis of our measurements, we propose that in nFRET thermal excitation occurs from the lowest radiative state of the ion to a higher excited state that is either ionic or associated with a ligand-to-metal charge-transfer state.

Single Gold Nanoparticles Counter: An Ultrasensitive Detection Platform for One-Step Homogeneous Immunoassays and DNA Hybridization Assays

In this paper, we present for the first time a single gold nanoparticle counter (SGNPC) in solution based on the photon bursting in a highly focused laser beam (less than 1 fL) due to the plasmon resonance scattering and Brownian motion of gold nanoparticles (GNPs). The photon burst intensity of single 36 nm GNPs is several tens to hundreds times stronger than that of quantum dots (QDs) and organic dyes. The relationship between the photon burst counts and GNPs concentration shows an excellent linearity. The linear range is over 4 orders of magnitude, and the detection limit of GNPs (36 nm) is 17 fM. On the basis of this single nanoparticle technique, we developed an ultrasensitive and highly selective detection platform for homogeneous immunoassay and DNA hybridization assays using GNPs as probes, which were 2-5 orders of magnitude more sensitive than current homogeneous methods. We used this technology to construct homogeneous sandwich immunoassays for cancer biomarkers, such as carcinoembryonic antigen (CEA) and alpha fetal protein (AFP), and aptamer recognition for thrombin. The detection limits are 130 fM for CEA, 714 fM for AFP and 2.72 pM for thrombin. Our method was successfully applied for direct determination of CEA, AFP and thrombin levels in sera from healthy subjects and cancer patients. In homogeneous DNA hybridization detection, we chose methylenetetrahydrofolate reductase (MTHFR) gene as a target. This assay successfully distinguished DNA sequences with single base mismatches, and the detection limits for the target were at 1 fM level.

Label-free and homogeneous DNA hybridization detection using gold nanoparticles-based chemiluiminescence system

We find that the catalytic activity of gold nanoparticles (GNPs) on luminol-H 2O 2 chemiluminescence (CL) system is greatly enhanced after it is aggregated by 0.5 M NaCl. We use this observation to design a CL detection of DNA hybridization. It is based on that the single- and double-stranded oligonucleotides have different propensities to adsorb on GNPs in colloidal solution, and the hybridization occurred between the probe DNA and target DNA can result in aggregation of the GNPs, producing strong CL emission. In the assay, no covalent functionalization of the GNPs, the probe, or the target DNA is required. The assay, including hybridization and detection, occurs in homogenous solution. The detection limit of target DNA (3 σ) was estimated to be as low as 1.1 fM. The sensitivity was increased more than 6 orders of magnitude over that of GNPs-based colorimetric method. The present CL method for DNA hybridization detection offers the advantages of being simple, cheap, rapid and sensitive.

Fluorescent lanthanide chelates for biological systems

Certain lanthanide chelate complexes are known to emit strong fluorescence with very distinct physical properties that are different from those of organic fluorescent compounds: the fluorescence of lanthanide complexes is long-lived with the half decay-time of several hundreds microseconds to 2 ms. The complexes are excited by UV light and emit fluorescence in the visible region. The emission profile is very sharp and the wavelength is specific to each metal, for instance, Eu3+ complexes emit at 615 nm and Tb3+ at 545 nm regardless of the ligand. These properties show that the complexes can be excellent fluorescence labels for proteins and DNAs and, when time-resolved fluorometry is employed, provide highly sensitive detection methods in biotechnology. Among many labels we have developed, BHHCT-Eu3+ and BPTA-Tb3+ are suitable for immunoassay, DNA hybridization assay, and DNA chip technology. Homogeneous DNA hybridization assay systems using fluorescence resonance energy transfer and fluorescence intercalators will be introduced.

A homogeneous DNA hybridization system by using a new luminescence terbium chelate.

Homogeneous DNA hybridization assay based on the luminescence resonance energy transfer (LRET) from a new luminescence terbium chelate, N,N,N(1),N(1)-[2,6-bis(3'-aminomethyl-1'-pyrazolyl)-4-phenylpyridine]tetrakis(acetic acid) (BPTA)-Tb(3+) (lambda(ex) = 325 nm and lambda(em) = 545 nm) to an organic dye, Cy3 (lambda(ex) = 548 nm and lambda(em) = 565 nm), has been developed. In the system, two DNA probes whose sequences are complementary to the two different consecutive sequences of a target DNA are used; one of the probes is labeled with the Tb(3+) chelate at the 3'-end, and the other is with Cy3 at the 5'-end. Labeling of the Tb(3+) chelate is accomplished via the linkage of a biotin-labeled DNA probe with the Tb(3+) chelate-labeled streptavidin. Strong sensitized emission of Cy3 was observed upon excitation of the Tb(3+) chelate at 325 nm, when the two probe DNAs were hybridized with the target DNA. The sensitivity of the assay was very high compared with those of the previous homogeneous-format assays using the conventional organic dyes; the detection limit of the present assay is about 30 pM of the target DNA strand.

Homogeneous DNA hybridization assay by using europium luminescence energy transfer.

Homogeneous DNA hybridization assay based on luminescence resonance energy transfer (LRET) from a tetradentate beta-diketonate europium chelate, 4,4'-bis(1' ',1' ',1' ',2' ',2' ',3' ',3' '-heptafluoro-4' ',6' '-hexanedion-6' '-yl)-chlorosulfo-o-terphenyl (BHHCT)-Eu(3+) (lambda(ex) = 340 nm and lambda(em) = 615 nm), to an organic dye, Cy5 (lambda(ex) = 643 nm and lambda(em) = 669 nm) has been developed, in which two DNA probes whose sequences comprises the whole complementary strand to the target DNA, are used; one probe having a biotin label on the 3'-terminus and the other a Cy5 label on the 5'-terminus. After hybridization, streptavidin labeled with BHHCT-Eu(3+) was added to the hybridization solution, and in the presence of the target DNA, the sensitized emission of Cy5 was observed when the hybridized complex was irradiated at 340 nm. In the absence of the target DNA, no emission was observed from Cy5.

Pseudomonas monteilii sp. nov., isolated from clinical specimens.

We propose the name Pseudomonas monteilii for a new species of gram-negative, rod-shaped, motile bacteria that were nonhemolytic on blood agar and were isolated from clinical sources. The 10 strains of P. monteilii were incapable of liquefing gelatin. They grew at 10 degrees C but not at 41 degrees C, produced fluorescent pigments, catalase, and cytochrome oxidase, and possessed the arginine dihydrolase system. They were capable of respiratory but not fermentative metabolism. They did not hydrolyze esculin or starch and were able to use benzylamine, alpha-aminobutyrate, D-ribose, L-arabinose, butyrate, valerate, isovalerate, isobutyrate, inositol, phenylacetate, D-alanine, and amylamine. They possessed L-phenylalanine arylamidase, L-lysine arylamidase, L-alanine arylamidase, gamma-glutamyl-transferase, glycyl-phenylalanine arylamidase, L-tryptophan arylamidase, glycyl-L-alanine arylamidase, esterase C4, esterase C6, esterase C8, esterase C9, esterase C10, and esterase C18. DNA relatedness studies revealed that P. monteilii strains formed a homogeneous DNA hybridization group. A total of 57 strains representing previously described or partially characterized taxa belonging to the genus Pseudomonas were 6 to 54% related to P. monteilii. The highest hybridization values were obtained with strains belonging to or related to Pseudomonas putida biovar A. The average G+C content of the DNA was 60.5 +/- 0.5 mol% for four of the P. monteilii strains studied. The type strain of P. monteilii is CFML 90-60 (= CIP 104883); it was isolated from bronchial aspirate and has a G+C content of 60 mol%. The clinical significance of these organisms is not known.