An optimized protocol for rapid and sensitive application of southern (Northern) hybridization by using fluorescein labeling and detecting system

An optimized complete protocol that produces consistent Southern hybridization results (RFLP) for as many as 240 samples in 36 h is presented. Signals can be detected from 0.1 g genomic DNA. The protocol can be adapted to Northern hybridization by using 0.05 M NaOH as transfer buffer in a downward blotting method. Probes can be removed in stripping solution containing 2–5 mM EDTA. The protocol using this system has many advantages over the conventional radioactive method as safety, rapidness, sensitivity, and signal quality.     

cDNA芯片表面核酸固定化的优化

cDNA芯片技术表面核酸固定化影响因素众多,其中涉及选择载体、固定于玻片的DNA片段浓度、玻片DNA片段的固定方法、玻片预处理方法、DNA片段的变性、溶解DNA片段的点样液等等.针对这些因素进行了优化筛选实验,以便于提高cDNA芯片技术检测基因表达的效率.     

Whole-mount in situ hybridization of small invertebrate embryos using laboratory mini-columns

To facilitate the handling of small invertebrate embryos during whole-mount in situ hybridization, a method of solution exchange using laboratory mini-columns was developed. This protocol speeds time-consuming aspiration of buffers, and avoids accidental loss of the embryos, by gently pushing solutions through the column using air pressure from a syringe after each incubation. The next buffer is then added using a pipettor. Embryos are retained on a filter within the column. As many columns as desired may be processed in parallel for different probes or stages.     

An optimized protocol for the identification of diatoms,flagellated algae and pathogenic protozoa with phylochips

In the past decade, molecular probe‐based methods have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that are devoid of distinct morphological features. However until recently, these methods had the major drawback of being limited to the identification of only one or just a few species at a time. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single‐glass slide, the so‐called phylochip. There are numerous microarray protocols in the literature. These protocols share the same principles, but vary in details, e.g. labelling approach or detergent concentration in the washing buffer. In this study, we show that even small variations in hybridization protocols can have a strong impact on the outcome of the microarray hybridization. An optimized protocol for species identification on phylochips is presented. The optimized protocol is the result of a joined effort of three laboratories to develop phylochips for microbial species identification.     

Improved procedure for fluorescence in situ hybridization on tissue microarrays

BACKGROUND: The recently developed tissue microarray (TMA) technology allows the arrangement of up to a thousand tissue specimens on a single microscope slide. This technology enables researchers to perform gene copy number studies on very large series of archival formalin-fixed tissues using fluorescence in situ hybridization (FISH). However, the hybridization properties of individual archival specimens can vary considerably. Therefore a highly optimized protocol is needed to fulfill the task of producing evaluable hybridization signals simultaneously in hundreds of specimens in a TMA. METHODS: The performance of two different FISH protocols, the standard protocol for paraffin embedded tissues and our new optimized protocol, was tested on TMAs using probes for the HER-2 and ZNF217 genes as well as the chromosome 17 centromere. RESULTS: The new protocol resulted in greatly increased signal intensity and an almost 30% increase in the number of tissue samples with evaluable hybridization signals. CONCLUSIONS: Our improved protocol for FISH on TMAs provides standardized hybridization conditions leading to high-quality hybridization signals in the majority of specimens. The increases in the signal intensity and the number of evaluable samples are extremely important for the successful analyses of TMAs by FISH and will allow the utilization of the TMA technology in its full potential.     

Enumeration of Vibrio vulnificus on membrane filters with a fluorescently labeled oligonucleotide probe specific for kingdom-level 16S rRNA sequences.

Vibrio vulnificus was enumerated on membrane filters after hybridization with a fluorescent oligonucleotide eubacterial probe. Cells were hybridized in liquid buffer or directly on membrane filters. There was no significant difference between fluorescent oligonucleotide direct counts and acridine orange direct counts (P > 0.05). Liquid buffer hybridization was preferable to direct filter hybridization.     

Fast and Non-Toxic In Situ Hybridization without Blocking of Repetitive Sequences

Formamide is the preferred solvent to lower the melting point and annealing temperature of nucleic acid strands in in situ hybridization (ISH). A key benefit of formamide is better preservation of morphology due to a lower incubation temperature. However, in fluorescence in situ hybridization (FISH), against unique DNA targets in tissue sections, an overnight hybridization is required to obtain sufficient signal intensity. Here, we identified alternative solvents and developed a new hybridization buffer that reduces the required hybridization time to one hour (IQFISH method). Remarkably, denaturation and blocking against repetitive DNA sequences to prevent non-specific binding is not required. Furthermore, the new hybridization buffer is less hazardous than formamide containing buffers. The results demonstrate a significant increased hybridization rate at a lowered denaturation and hybridization temperature for both DNA and PNA (peptide nucleic acid) probes. We anticipate that these formamide substituting solvents will become the foundation for changes in the understanding and performance of denaturation and hybridization of nucleic acids. For example, the process time for tissue-based ISH for gene aberration tests in cancer diagnostics can be reduced from days to a few hours. Furthermore, the understanding of the interactions and duplex formation of nucleic acid strands may benefit from the properties of these solvents.     

Fluorescence in situ hybridization method for co-localization of mRNA and GEP

Co-localization studies using green fluorescent protein (GFP) and fluorescence immunohistochemistry have become commonplace. However, co-localization studies using GFP and mRNA in situ hybridization are rare, in large part because typical in situ hybridization reaction conditions often lead to the loss of GFP fluorescence. Here, we describe a new fluorescence mRNA in situ hybridization protocol using cRNA riboprobes that leaves GFP fluorescence intact. This protocol is based on a urea-based hybridization buffer and the Tyramide Signal Amplification system. This protocol should provide researchers engaged in the use of GFP with a solid starting point for adapting their own in situ hybridization protocols.     

Electric field directed nucleic acid hybridization on microchips.

Selection and adjustment of proper physical parameters enables rapid DNA transport, site selective concentration, and accelerated hybridization reactions to be carried out on active microelectronic arrays. These physical parameters include DC current, voltage, solution conductivity and buffer species. Generally, at any given current and voltage level, the transport or mobility of DNA is inversely proportional to electrolyte or buffer conductivity. However, only a subset of buffer species produce both rapid transport, site specific concentration and accelerated hybridization. These buffers include zwitterionic and low conductivity species such as: d- and l-histidine; 1- and 3-methylhistidines; carnosine; imidazole; pyridine; and collidine. In contrast, buffers such as glycine, beta-alanine and gamma-amino-butyric acid (GABA) produce rapid transport and site selective concentration but do not facilitate hybridization. Our results suggest that the ability of these buffers (histidine, etc.) to facilitate hybridization appears linked to their ability to provide electric field concentration of DNA; to buffer acidic conditions present at the anode; and in this process acquire a net positive charge which then shields or diminishes repulsion between the DNA strands, thus promoting hybridization.     

Theoretical aspects of genomic variation screening using DNA microarrays

We present a theoretical model for typical microarray-based single nucleotide polymorphism (SNP) assay of small genomic DNA amount. We derived the adsorption isotherm expressing the on-array hybridization efficiency in terms of genomic target sequence and concentration, oligonucleotide probe sequence and surface density, hybridization buffer, and temperature. This isotherm correctly describes the surface probe density effects, the sensitivity peak, and the melting temperature depression, and is in accord with published experiments. We discuss optimization of parallel SNP genotyping. Our estimates show that SNP detection at a single temperature in aqueous hybridization buffer is restricted by DNA regions that differ by less than 20% in GC content. We predict that the variety of genotyped SNPs could be substantially extended using an assay design with high probe density and a large fraction of probes hybridized.     

Adaptor long-range PCR procedure for clone-specific characterization and chromosomal localization

An efficient adaptor long-range PCR (ALR-PCR) procedure was developed to detect genomic rearrangements in high-plasticity genomic regions between closely related strains of bacteria. The method was precisely optimized using a combination of high-speed experimental steps for the chromosomal localization and elucidation of deletions, inversions, duplications, or inserted sequences within a clone-specific flanking region. The advantages of this strategy are: (i) ready-to-use polymerase mixtures and Master mix (ready-to-use reaction mixtures with polymerase MasterAmp and buffer 2x Premix 4); (ii) a 5-min ligation procedure; (iii) rapid purification of DNA digests; (iv) optimized DNA template concentration protocol to avoid nonspecific amplification and high backgrounds; (v) long-range PCR protocol to obtain at least 9.6 kb single PCR products; (vi) two-step PCR cycling with the same annealing and extension temperature at 68 degrees C; (vii) simple design of the adaptors according to the preferred restriction endonuclease enzyme; and (viii) simple technology and equipment required. The application of this method for a tester-specific suppressive subtractive hybridization (SSH) clone of Brucella melitensis 16M revealed an 837-bp deletion and a 7255-bp DNA transfer from one chromosomal location to another for Brucella abortus 2308 used as a driver.     

Enhanced nucleic acid capture and flow cytometry detection with peptide nucleic acid probes and tunable-surface microparticles

New methods for automated, direct nucleic acid purification and detection are required for the next generation of unattended environmental monitoring devices. In this study we investigated whether tunable-surface bead chemistry and peptide nucleic acids (PNA) could enhance the recovery and detection of intact rRNA in both test tube and automated suspension array hybridization formats. Intact rRNA was easily captured and detected on PNA-coated Lumavidin beads from 0.1 ng total RNA with a 15-min hybridization in pH 7 buffer, representing 1.7 x 10(3) cell equivalents of total RNA. DNA-conjugated beads in pH 5 hybridization buffer required an overnight hybridization to achieve a detectable signal at 0.1 ng target RNA. Standard DNA hybridization conditions (pH 7) were one order of magnitude less sensitive than the tunable-surface (pH 5) condition. The PNA-conjugated particles were 100x more sensitive than the tunable-surface DNA particles in the automated format, with a detection limit of 0.1 ng total RNA. The detection limits for total RNA on PNA-conjugated microparticles is immediately conducive to the detection and characterization of microorganisms in low-biomass environments or to the identification of rare sequences in a complex sample mixture, without using PCR.     

Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments

A protocol was developed for the efficient recovery of intact, high molecular weight rRNA from different environmental matrices. Critical variables were identified in sample processing that influenced yield and integrity of recovered nucleic acid. Most notably, the order of addition and the buffer to sample volume ratio profoundly influenced the efficiency of nucleic acid recovery from sediment material when utilizing a guanidine thiocyanate-beta-mercaptoethaol extraction buffer. Addition of one sample volume to five buffer volumes contributed to an order of magnitude increase in recovery relative to reverse order of addition (buffer addition to sample). An optimized extraction protocol was used to evaluate rRNA yield by seeding samples with whole cells and radiolabeled nucleic acid. Recovery of intact rRNA was confirmed by polyacrylamide gel electrophoresis, which was also used to provide another estimate of quantity. This optimized protocol was used to measure depth-related changes in biomass distribution in Lake Michigan deep-water sediments. This revealed a biomodal biomass distribution; a maximum near the water/sediment interface and a secondary peak associated with the oxic/suboxic boundary. A significant portion of the community at the oxic/suboxic boundary was composed of non-methanogenic Archaea.     

FLUCTUATING ASYMMETRY IN A SALIX HYBRID SYSTEM: THE IMPORTANCE OF GENETIC VERSUS ENVIRONMENTAL CAUSES

To examine the effects of hybridization and environmental stress on developmental instability, we examined fluctuating asymmetry (FA), the variance in random deviations from perfect symmetry in bilaterally symmetrical traits, for leaf symmetry in a Salix hybrid system. An abiotic environmental stress (water stress), an interspecific biotic stress (pathogen attack), and an intraspecific biotic stress (competition) were examined to determine which factors increase developmental instability. None of these three environmental stressors significantly increased FA. However, genetic stress through hybridization was detected; hybrid plants showed significantly higher levels of FA than parental species. In contrast to hybridization providing greater developmental stability through heterozygosity, these results suggest that complex, nonadditive interactions provided developmental stability and that developmental instability increased when coadapted gene complexes were disrupted through hybridization. In addition, plant biomass was significantly, negatively correlated with FA, suggesting that those individuals that were more able to buffer themselves against the disruptive effects of environmental stress may have a selective advantage over those that are less able to buffer themselves against these disruptive effects.     

A modified hybridization protocol for low-density diagnostic DNA microarrays

To promote the application of DNa microarrays for clinical diagnosis, the problems of cross-hybridization and low signal intensity in the hybridization processes has been addressed. We tested a new hybridization protocol for low-density diagnostic DNA microarrays, by skipping the purification step during sample labeling, while elevating the hybridization temperature from 42°C to 52°C, adding a step of distilled water rinsing immediately after hybridization and before the low stringency washing steps. It was found that the modified hybridization protocol works well in our study, which increased detection sensitivity and eliminated nonspecific signals.     

Simultaneous Detection of FISH Signals and Bromo-Deoxyuridine Incorporation in Fixed Tissue Cultured Cells

FISH (Fluorescence in situ hybridization) is a powerful technique that detects and localises specific DNA sequences on metaphase chromosomes, interphase nuclei or chromatin fibres. When coupled to BrdU (5-Bromo 2-deoxy-uridine) labeling of newly replicated DNA, the replication properties of different DNA sequences can be analysed. However, the technique for the detection of BrdU incorporation is time consuming, and relies on acidic pH buffer treatments, that prevent use of pH sensitive fluorochromes such as FITC (Fluoro-isothiocianate) during FISH. In this work, we describe a simplified protocol that allows the simultaneous detection of FISH signals and BrdU incorporation. Since the technique does not involve paraformaldehyde for cell fixation, or formamide for denaturation of the target DNA and in post-hybridisation washes, it represents a safer alternative to classical FISH techniques.     

寡核苷酸探针制备的优化

目的:探讨寡核苷酸微阵列制备中适合使用的探针浓度、探针缓冲液pH值、离子强度、优化杂交条件。方法:选取人白细胞抗原DQA1位点,针对多态性集中的外显子2设计一对保守引物及16条特异性分型探针;分别用ddH2O和0.1、0.2mol/L碳酸盐缓冲液(pH=7)稀释探针至100μmol/L;选取合适的缓冲液浓度后,调碳酸盐缓冲液为5.0、6.0、7.0、8.0、9.0、10.0等6种pH值,选取最优pH值及离子强度,分别溶解探针至20、50、100、200μmol/L,比较上述不同条件的杂交结果。结果:用0.1mol/L、pH9的碳酸盐缓冲液溶解探针杂交效果最佳;探针浓度为20μmol/L时信号弱,其他浓度下无显著差别。结论:通过探针制备的优化可以提高杂交效率,探针浓度与杂交信号强度无明显正相关。     

A one-day double-labelling technique for tissue specimens: Immunogold-silver staining forin situ hybridization combined with alkaline phosphatase-anti-alkaline phosphatase (APAAP) immunohistochemistry for antigens

Summary An improved technique is described that addresses the problems of sensitivity, specificity, the use of hazardous radioactive equipment and time consumption in immunohistochemical labelling and double labelling ofin situ hybridization of tissue specimens. It consists of a two-step protocol in which digoxigenin-uridine triphosphate (UTP) labelled riboprobes in thein situ hybridization step are visualized by the immunogold-silver staining method, and double labelling of tissue antigens is achieved by the application of an alkaline phosphatase-anti-alkaline phosphatase staining step. We tested this protocol using snap-frozen tissue sections of synovial tissue from patients with rheumatoid arthritis. The target mRNA was detected by perforin or cathepsin D riboprobes, the double labelling was performed using anti-collagen type IV and alpha-smooth muscle actin antibodies. It is concluded that, in comparison with an established three-to four-day double-labelling protocol used in many laboratories, this one-day combination is currently the most rapid assay of reliable quality for double labelling ofin situ hybridization products and tissue antigens.