Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY® FL-labeled probe or primer

We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely positioned guanine. This approach makes use of an oligonucleotide probe or primer containing a BODIPY® FL-modified cytosine at its 5′-end. When such a probe was hybridized with a target DNA, its fluorescence was quenched by the guanine in the target, complementary to the modified cytosine, and the quench rate was proportional to the amount of target DNA. This widely applicable technique will be used directly with larger samples or in conjunction with the polymerase chain reaction to quantify small DNA samples.

PCR bias Toward the wild-type k-ras and p53 sequences: Implications for PCR detection of mutations and cancer diagnosis

PCR-based cancer diagnosis requires detection of rare mutations in k- ras, p53 or other genes. The assumption has been that mutant and wild-type sequences amplify with near equal efficiency, so that they are eventually present in proportions representative of the starting material. Work on factor IX suggests that this assumption is invalid for one case of near- sequence identity. To test the generality of this phenomenon and its relevance to cancer diagnosis, primers distant from point mutations in p53 and k-ras were used to amplify wild-type and mutant sequences from these genes. A substantial bias against PCR amplification of mutants was observed for two regions of the p53 gene and one region of k-ras. For k-ras and p53, bias was observed when the wild-type and mutant sequences were amplified separately or when mixed in equal proportions before PCR. Bias was present with proofreading and non-proofreading polymerase. Mutant and wild-type segments of the factor V, cystic fibrosis transmembrane conductance regulator and prothrombin genes were amplified and did not exhibit PCR bias. Therefore, the assumption of equal PCR efficiency for point mutant and wild-type sequences is invalid in several systems. Quantitative or diagnostic PCR will require validation for each locus, and enrichment strategies may be needed to optimize detection of mutants.

Analysis of killer immunoglobulin-like receptor genes in ankylosing spondylitis

Objectives: To assess the possible association of killer immunoglobulin-like receptor (KIR) genes, specifically KIR3DL1, KIR3DS1 and KIR3DL2, with ankylosing spondylitis (AS). Methods: 14 KIR genes were genotyped in 200 UK patients with AS and 405 healthy controls using multiplex polymerase chain reaction. Sequence-specific oligonucleotide probes were used to subtype 368 cases with AS and 366 controls for 12 KIR3DL2 alleles. Differences in KIR genotypes and KIR3DL2 allele frequencies were assessed using the χp2p test. Results: KIR3DL1 and KIR3DS1 gene frequencies were very similar in cases with AS and controls (odds ratio = 1.5, 95% confidence interval 0.8 to 3.0, and odds ratio = 1.02, 95% confidence interval 0.2 to 5.3, respectively). KIR3DL2 allele frequencies were not significantly different between cases with AS and controls. Conclusions: Neither the KIR gene content of particular KIR haplotypes nor KIR3DL2 polymorphisms contribute to AS.

Microbial identification by detection of ligation probes on DNA microarray

Microbes in natural and artificial environments as well as in the human body are a key part of the functional properties of these complex systems. The presence or absence of certain microbial taxa is a correlate of functional status like risk of disease or course of metabolic processes of a microbial community. As microbes are highly diverse and mostly notcultivable, molecular markers like gene sequences are a potential basis for detection and identification of key types. The goal of this thesis was to study molecular methods for identification of microbial DNA in order to develop a tool for analysis of environmental and clinical DNA samples. Particular emphasis was placed on specificity of detection which is a major challenge when analyzing complex microbial communities. The approach taken in this study was the application and optimization of enzymatic ligation of DNA probes coupled with microarray read-out for high-throughput microbial profiling. The results show that fungal phylotypes and human papillomavirus genotypes could be accurately identified from pools of PCR amplicons generated from purified sample DNA. Approximately 1 ng/μl of sample DNA was needed for representative PCR amplification as measured by comparisons between clone sequencing and microarray. A minimum of 0,25 amol/μl of PCR amplicons was detectable from amongst 5 ng/μl of background DNA, suggesting that the detection limit of the test comprising of ligation reaction followed by microarray read-out was approximately 0,04%. Detection from sample DNA directly was shown to be feasible with probes forming a circular molecule upon ligation followed by PCR amplification of the probe. In this approach, the minimum detectable relative amount of target genome was found to be 1% of all genomes in the sample as estimated from 454 deep sequencing results. Signal-to-noise of contact printed microarrays could be improved by using an internal microarray hybridization control oligonucleotide probe together with a computational algorithm. The algorithm was based on identification of a bias in the microarray data and correction of the bias as shown by simulated and real data. The results further suggest semiquantitative detection to be possible by ligation detection, allowing estimation of target abundance in a sample. However, in practise, comprehensive sequence information of full length rRNA genes is needed to support probe design with complex samples. This study shows that DNA microarray has the potential for an accurate microbial diagnostic platform to take advantage of increasing sequence data and to replace traditional, less efficient methods that still dominate routine testing in laboratories. The data suggests that ligation reaction based microarray assay can be optimized to a degree that allows good signal-tonoise and semiquantitative detection.

玉米 rbcL 基因与兰藻 rbcS 基因定向融合及它们在宿主大肠杆菌中的表达

二磷酸核酮糖羧化酶/氧化酶(简称Rubisco, EC, 4.1.1.39)是绿色植物光合作用中参与固定CO2的关键酶。在高等植物，该酶是由8个分子量为55KD的大亚基(LSU)和8个分子量为14KD的小亚基(SSU)构成的16聚体。每个大亚基有四个活性中心，具有双向催化功能，其编码基因位于叶绿体基因组大单拷贝区;小亚基功能还不清楚，它由核基因组编码且有几个拷贝;未成熟小亚基N端有一段transit peptide，靠它的定向跨越叶绿体膜。迄今为止，取自几种植物材料的这二种亚基的氨基酸顺序和编码基因的核苷酸顺序分析业已完成。为该酶的遗传操作奠定了必要的基础。 由于Rubisco与人类利用太阳能和提高作物产量直接相关，所以成为通过生物技术进行改造的重大项目。 巢状假囊细菌(Anacyslis nidulans) R2是一种不含限制性内切酶的单细胞原核生物，能营光合作用，其Rubisco大亚基的氨基酸顺序与玉米的LSU同源性高达80%，但是第四个活性部位(Leu 456位)与玉米不同(Sys, 459位)，由此导致其对CO2的亲合力降低。另一方面，其rbcL与rbcS仅相隔93个bp，且同属一个操纵子。这意味着有可能用同源DNA片段等位交换的办法来改造其rbcL基因。 根据现有的资料，设计出玉米rbcL与兰藻rbcS定向重组于pUC119的兰图：先从pANP1155中切出0.7kb含蓝藻rbcS的PstI-HindIII片段，克隆进pUC119的lacZ启动子下游得pTAS28，采用Reverse primer作引物进行核苷酸顺序分析，确认蓝藻rbcS基因座落在pTAS28正链上。随后从pZmc460中切出包含玉米rbcL基因1.7kb的BglII-HincII片段，将它插入pTAS28的HincⅡ-BamHⅠ双酶切位点，得到pTMN3;为了比较，在另一个质粒pTMN7于1.7kb片段之前加进0.1kb的PstI-HaeIII蓝藻DNA。根据玉米rbcL基因核苷酸顺序（1218-1251）合成一个Oligonucleotide probe，对这三个质粒的总RNA抽提物进行Northern Blot，得到明显的杂交斑点;接着用菌体总蛋白冻干品进行了Western分析，并以新鲜的玉米和烟草叶片为对照，得到阳性结果。显然这二种基因重组之后仍能在宿主E. coli中正常表达。 真正的挑战应是下一步用上述二种质粒转化兰藻A. nidulans R2，考查其能否整合进基因组并表现出较低的氧化酶活性。

植物高赖氨酸蛋白质的分离和纯化及其N端序列核苷酸探针的合成

禾谷类作物水稻和小麦是人们的主要植物性食物来源．而这些作物种子蛋白质中人类不能合成的必需氨基酸含量不平衡，造成了优质蛋白质的缺乏和人体对蛋白质利用的极大浪费．大约有二分之一的谷类种子蛋白质和四分之一的大豆蛋白质不能被合理地利用。大多数禾本科作物包括水稻和小麦的种子蛋白质中第一限制性氨基酸是赖氨酸，纠正其不平衡现象可大大提商蛋白质的营养价值。本研究在高赖氨酸植物种的筛选、高赖氨酸种子储藏蛋白质的纯化及其基因的分离等方面开展了工作。 选用与禾本科亲缘关系较远的8个植物种为研究材料，它们分别属于榛科，十字花科、胡桃科、豆科、胡麻科和松科。氨基酸组分分析确定豆科和十字花科的三个植物种赖氨酸含量在5.5%以上，其中豆科植物四棱豆(Pso phocarpus tetragonolobus)种子全蛋白赖氨酸含量达7.9%．用5种提取液提取了四棱豆种子的清蛋白、球蛋白和全蛋白。经测定发现0.025M Tris.HCl(pH7.4)提取液提取的清蛋白赖氨酸含量高最．通过自然胶电泳，SDS-PAGB电泳，非变牲IEF和变性IEF／SDS双向电泳，对四棱豆种子清蛋白进行了定性研究。用变性IEF/ SDS双向电泳分析出60多种蛋白质和蛋白质亚基及多肽。研究中改进了等电聚焦电泳纯化蛋白质的方法，经处理的胶板显现出清晰的蛋白质带型，不需染色即可确定带的位置，从切下的胶条中洗脱的蛋白质，其纯度达到双向电泳纯和HPLC纯。用三种电溶方法(SDS-PAGE非变性IEF，变性IEF)纯化出三十一种蛋白质或多肽分子。分别进行了分子量确定和氨基酸组分分析，发现了一个赖氨酸含量高达11.4%的蛋白质，其分子量为18KD，并制备了该蛋白质的抗体，测定了18KD蛋白质N端30个氨基酸残基的顺序，根据这一顺序设计合成了一组17个核苷酸的基因探针．经鉴定单链DNA探针的纯度和总量达到了设计要求。用尿素法与CTAB法结合提取了四棱豆幼苗核基因组DNA，其分子量在50Kb以上，达到了构建GenormicDNA文库的要求．用bamHI EcoRI和HindⅢ三种酶切割提取的DNA，得到了分子量大小不同的片段。 对四棱豆种子蛋白质的定性、高赖氨酸蛋白质的纯化、18KD蛋白N端序列分析及寡核苷酸探针的合成以及GcnomicDNA的提取与酶切，尚未见有资料报道．这些工作为克隆高赖氨酸基因打下了良好的基础，对改良禾本科作物蛋白质品质意义深远．

Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

Molecular diversity of the HLA-C gene identified in a Caucasian population

A DNA typing procedure, based on a two stage polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing strategy, has been developed and applied to DNA from 1000 healthy individuals from the Northern Ireland region. The two-stage procedure involves human leukocyte antigen (HLA-C) identification through the use of a medium resolution PCR-SSOP system, followed by four secondary group specific PCR-SSOP systems, to enable allele resolution. The PCR-SSOP systems were designed for the identification of HLA-Cw alleles with possible discrimination within exons 2 and 3 of the HLA-C gene, i.e., HLA-Cw*01-Cw*16. PCR-SSP tests were designed for the resolution of HLA-Cw*17 and -Cw*18 alleles. The systems can also be used independently of each other if selective allele resolution is required. HLA-Cw allele frequencies occuring within the Northern Ireland population have been compiled, along with estimations of HLA-B/Cw haplotype frequencies. (C) American Society for Histocompatibility and Immunogenetics, 2002. Published by Elsevier Science Inc.

Visualising single molecules of HIV-1 and miRNA nucleic acids

Background
The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19–26 nucleotides in length.

Results
We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1–2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection.

Conclusions
Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1–2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence.

Immobilization of streptavidin in sol-gel films: Application on the diagnosis of hepatitis C virus

Recent advances have accelerated the development of biosensors for the analysis of specific gene sequences. In this kind of biosensor, a DNA probe is immobilized on a transducer and the hybridization with the target DNA is monitored by suitable methodology. In the present work, the streptavidin (STA) was encapsulated in thin films siloxane-poly(propylene oxide) hybrids prepared by sol-gel method and deposited on the graphite electrode surface by dip-coating process. Biotinylated 18-mer probes were immobilized through STA and a novel amperometric DNA biosensor for the detection and genotyping of the hepatitis C virus (genotypes 1, 2A/C, 2B and 3) is described. The HCV RNA from serum was submitted to reverse transcriptase-linked polymerase chain reaction (RT-PCR) and biotin-labeled cDNA was obtained. Thus, the cDNA was hybridized to the target-specific oligonucleotide probe immobilized on the graphite electrode surface and following the avidin-peroxidase conjugate was added. The enzymatic response was investigated by constant potential amperometry at -0.45 V versus Ag/AgCl using H2O2 and KI solutions. HCV RNA negative and positive controls and positive samples of sera patients were analyzed and the results were compared to commercial kit. The proposed methodology appeared to be suitable and convenient tool for streptavidin immobilization and diagnose of HCV disease. (c) 2006 Elsevier B.V. All rights reserved.

Strategies for detecting DNA hybridisation using surface plasmon fluorescence spectroscopy

Die Anregung und Emission von Fluorophoren nahe planaren Metalloberflächen und schiefen Gittern wurde mittels Oberflächenplasmonen Fluoreszenz Spektroskopie (SPFS) untersucht. Die Fluorophore konnten durch das evaneszente Plasmonenfeld angeregt und die einzelnen Abregungskanäle identifiziert werden.Die Sensorarchitektur für den Nachweis der Hybridisierung bestand aus auf einer Streptavidin-Matrix immobilisierten unmarkierten Sondensträngen. Cy5 markierte Zielsequenzen wurden aus der Lösung hybridisiert und die Adsorptionskinetiken konnten oberflächensensitiv detektiert werden.Ein neues Detektionsschema für unmarkierte Zielstränge wurde mittels fluoreszenzmarkirten Sondensträngen realisiert. Die Hybridisierung führte zu der Bildung von steifen helikalen Bereichen in der Probe und separierte den Farbstoff von der Metalloberfläche. Reduzierte Fluorezenzlöschung zeigte daher das Hybridisierungsereignis an.Die Verwendung eines potentiellen Förster-Paares zur Detektion von DNA Hybridisierung wurde untersucht. Donor und Akzeptor wurden an Ziel- und Sondenstrang immobilisiert und das Hybridisierungsereignis konnte anhand der Auslöschung der Donor-Fluorezenz nachgewiesen werden.Schließlich wurde der Einsatz von einzelstrangbindenden Proteinen (SSB) zur Steigerung der Sensitivität bezüglich Basenfehlpaarungen betrachtet. Verdrängungsreaktionen zwischen Proteinen und markierten Zielsträngen wurden anhand von SPS und Fluorezenzkinetiken studiert.

Localization of DJ-1 mRNA in the mouse brain

DJ-1 is mutated in autosomal recessive, early onset Parkinson's disease but the exact localization of the DJ-1 gene product in the mammalian brain is largely unknown. We aimed to evaluate the DJ-1 mRNA expression pattern in the mouse brain. Serial coronal sections of brains of five male and five female adult mice were investigated by using in situ hybridization with a DJ-1 specific 35S-labeled oligonucleotide probe. Hybridized sections were analyzed after exposure to autoradiography films and after coating with a photographic emulsion. DJ-1 was heterogeneously expressed throughout the mouse central nervous system. A high expression of DJ-1 mRNA was detected in neuronal and non-neuronal populations of several structures of the motor system such as the substantia nigra, the red nucleus, the caudate putamen, the globus pallidus, and the deep nuclei of the cerebellum. Furthermore, DJ-1 mRNA was also highly expressed in non-motor structures including the hippocampus, the olfactory bulb, the reticular nucleus of the thalamus, and the piriform cortex. The high expression of DJ-1 mRNA in brain regions involved in motor control is compatible with the occurrence of parkinsonian symptoms after DJ-1 mutations. However, expression in other regions indicates that a dysfunction of DJ-1 may contribute to additional clinical features in patients with a DJ-1 mutation.

Adenosine A2A receptor gene expression in the normal striatum and after 6-OH-dopamine lesion

Adenosine A2A receptors are present on enkephalinergic medium sized striatal neurons in the rat and have an important function in the modulation of striatal output. In order to establish more accurately whether adenosine transmission is a generalized phenomenon in mammalian striatum we compared the A2A R expression in the mouse, rat, cat and human striatum. Secondly we compared the modulation of enkephalin gene expression and A2A receptor gene expression in rat striatal neurons after 6-OH-dopamine lesion of the substantia nigra. Hybridization histochemistry was performed with a 35S-labelled radioactive oligonucleotide probe. The results showed high expression of A2A adenosine receptor genes only in the medium-sized cells of the striatum in all examined species. In the rat striatum, expression of A2A receptors was not significantly altered after lesion of the dopaminergic pathways with 6-OH-dopamine even though enkephalin gene expression was up-regulated. The absence of a change in A2A receptor gene expression after 6-OH-dopamine treatment speaks against a dependency on dopaminergic innervation. The maintained inhibitory function of A2A R on motor activity in spite of dopamine depletion could be partly responsible for the depression of locomotor activity observed in basal ganglia disorders such as Parkinson's disease.

Expression of adenosine A2a receptors gene in the olfactory bulb and spinal cord of rat and mouse

The expression of adenosine A2a receptors (A2aR) in the mammalian striatum is well known. In contrast the exact distribution of A2aR in other regions of the central nervous system remains unclear. The aim of this study was to investigate the A2aR gene expression in the rat olfactory bulb and spinal cord, two regions which are seldom included in mapping studies. Secondly, we compared the A2aR expression in the rat and in the mouse brain. Hybridization histochemistry was performed with an S35-labelled radioactive oligonucleotide probe. The results show strong expression of A2aR in the mouse and rat striatum in accordance with previous reports. In the olfactory bulb a weak but specific expression of A2aR was found in the granular cell layer in both species. In contrast, no significant expression of the A2aR gene was observed in other parts of the brain or the rat spinal cord. The presence of the A2aR in the mammalian olfactory bulb suggests a functional role for this receptor in olfaction.

Detection of enterotoxigenic Escherichia coli in foods by polymerase chain reaction

Enterotoxigenic Escherichia coli (ETEC) causes significant morbidity and mortality in infants of developing countries and is the most common cause of diarrhea in travelers to these areas. Enterotoxigenic Escherichia coli infections are commonly caused by ingestion of fecally contaminated food. A timely method for the detection of ETEC in foods would be important in the prevention of this disease. A multiplex polymerase chain reaction (PCR) assay which has been successful in detecting the heat-labile and heat-stable toxins of ETEC in stool was examined to determine its utility in foods. This PCR assay, preceded by a glass matrix and chaotropic DNA extraction, was effective in detecting high numbers of ETEC in a variety of foods. Ninety percent of 121 spiked food samples yielded positive results. Samples of salsa from Guadalajara, Mexico and Houston, Texas were collected and underwent DNA extraction and PCR. All samples yielded negative results for both the heat-labile and heat-stable toxins. Samples were also subjected to oligonucleotide probe analysis and resulted in 5 samples positive for ETEC. Upon dilution testing, it was found that positive PCR results only occurred when 12,000 to 1,000,000 bacteria were present in 200 mg of food. Although the DNA extraction and PCR method has been shown to be both sensitive and specific in stool, similar results were not obtained in food samples. ^