Label-free electrochemical detection of short sequences related to the hepatitis B virus using 4,4'-diaminoazobenzene based on multiwalled carbon nanotube-modified GCE

A novel label-free electrochemical DNA biosensor based on 4,4'-diaminoazobenzene (4,4'-DAAB) and multiwalled carbon nanotube (MWNT)-modified glassy carbon electrode (GCE) for short DNA sequences related to the hepatitis B virus (HBV) hybridization detection was presented. Differential pulse voltammetry (DPV) was used to investigate hybridization event. The decrease in the peak current of 4,4'-DAAB was observed on hybridization of probe with the target. This electrochemical approach was sequence specific as indicated by the control experiments, in which no peak current change was observed when a noncomplementary DNA sequence was used. Numerous factors affecting the target hybridization were optimized to maximize the sensitivity. Under optimal conditions, this sensor showed a good calibration range between 7.94 x 10(-8) M and 1.58 x 10(-6) M, with HBV DNA sequence detection limit of 1.1 x 10(-8) M.     

A nucleic acid biosensor for the detection of a short sequence related to the hepatitis B virus using bis(benzimidazole)cadmium(II) dinitrate as an electrochemical indicator

A novel hybridization indicator, bis(benzimidazole)cadmium(II) dinitrate (Cd(bzim)(2)(NO(3))(2)), was utilized to develop an electrochemical DNA biosensor for the detection of a short DNA sequence related to the hepatitis B virus (HBV). The sensor relies on the immobilization and hybridization of the 21-mer single-stranded oligonucleotide from the HBV long repeat at the glassy carbon electrode (GCE). The hybridization between the probe and its complementary sequence as the target was studied by enhancement of the peak of the Cd(bzim)(2)(2+) indicator using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Numerous factors affecting the probe immobilization, target hybridization, and indicator binding reactions were optimized to maximize the sensitivity and speed of the assay time. With this approach, a sequence of the HBV could be quantified over the range from 1.49x10(-7)M to 1.06x10(-6)M, with a linear correlation of r=0.9973 and a detection limit of 8.4x10(-8)M. The Cd(bzim)(2)(2+) signal observed from the probe sequence before and after hybridization with a four-base mismatch containing sequence was lower than that observed after hybridization with a complementary sequence, showing good selectivity. These results demonstrate that the Cd(bzim)(2)(2+) indicator provides great promise for the rapid and specific measurement of the target DNA.     

HRP-HBVDNA探针在临检应用中的研究

本文介绍了一种简便的检测血清ＨＢＶＤＮＡ的方法。参照Ｒｅｎｚ等人的标记方法,构建了直接酶标ＨＲＰ ＨＢＶＤＮＡ探针。此探针经与固定在硝酸纤维素滤膜上的血清靶ＤＮＡ杂交后,可通过化学发光自显影检测技术观察结果。敏感度可检测０－１ｐｇ靶ＤＮＡ,相当于同位素探针的灵敏度。对６３份ＨＢｓＡｇＨＢｅＡｇ和Ａｎｔｉ ＨＢｃＥＬＩＳＡ阳性血清以及２４份ＨＢｓＡｇＡｎｔｉ ＨＢｃ阳性,ＨｂｅＡｇ阴性血清用ＨＲＰ ＨＢＶＤＮＡ探针进行检测,结果探针ＨＢＶＤＮＡ阳性率分别为１００％（６３）和５８％（１４）;对５０份ＨＢｓＡｇ,ＥＬＩＳＡ阴性和ＡＬＴ正常的血清,探针ＨＢＶＤＮＡ全部阴性。实验结果表明本方法具有很大的推广应用价值。     

间接核酸杂交方法的建立

建立了一种新的核酸杂交手段一间接核酸杂交方法,其突出的优点是用一种共同的核酸标记物就可检查不同的基因组或不同的基因。我们重组乙型肝炎病毒或EB病毒的核酸片段于噬菌体M_(13)mp8载体,以此重组的单链DNA为第一夹心层,用~(32)P标记的双链噬菌体DNA作为共同探针,检查乙型肝炎病毒和EB病毒的核酸,获得满意的结果。应用该法进行细胞内的原位杂交,检查细胞内存在的EB病毒基因效果亦佳。     

Electrochemical DNA biosensor for the detection of interaction between di[azino-di(5,6-azafluorene)-kappa2-NN'] dibromicoppers and DNA

A new Cu(II) complex CuL(2)Br(2) (L = azino-di(5,6-azafluorene)-kappa(2)-NN') was synthesized, and a new method of electrochemical probe has been proposed for the determination of hepatitis B virus (HBV) based on its interaction with [CuL(2)](2+). This ligand, containing functional groups, as well as planar aromatic domains, is capable of binding to double-stranded DNA (dsDNA) more efficiently than to single-stranded DNA (ssDNA). Emphasis has been placed on the elucidation of the nature of the interaction by electrochemical techniques. The electroactive [CuL(2)](2+) could be employed as an electrochemical indicator to detect hybridization events in DNA biosensors. These biosensors have been constructed by immobilization of a probe DNA sequence from HBV onto glassy carbon electrode (GCE). After hybridization with the complementary target sequence, [CuL(2)](2+) was accumulated within the dsDNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range. Using this approach, complementary target sequences of HBV can be quantified over the range of 1.74 x 10(-9) to 3.45 x 10(-7) M, with a detection limit of 8.32 x 10(-10) M and a linear correlation coefficient of 0.9936.In addition, this approach is capable of detecting hybridization of complementary sequences containing one or three mismatched bases.     

Molecular cloning of human satellite DNA sequences and their use in detecting DNA polymorphism

A approximately 400 bp HaeIII human genomic satellite DNA band was cloned into pUC18 to construct a partial library. A fragment of bacteriophage M13 containing a sequence homologous to the human minisatellite core was cloned in pUC18 and was used as a probe to isolate a approximately 350 bp human satellite clone (pTRF5.6) from the partial library. Other clones from this library showed a wide variation in terms of size and hybridization to the pTRF5.6 clone. Human DNA from different individuals was digested with restriction enzymes, Southern transferred and probed with TRF5.6. Individual-specific complex pattern of DNA bands was produced. TRF5.6, therefore, could be useful as a probe for detecting genetic polymorphism.     

Demonstration of spontaneous XX/XY chimerism by DNA fingerprinting

Summary The M13 bacteriophage probe, which makes possible the establishment of DNA fingerprints, was used to study a phenotypically normal woman with a 46XY karyotype and her twin brother. Identical fingerprints and positive hybridzation with a series of Y-specific probes were obtained on blood samples from the siblings. DNA from a skin biopsy of the woman yielded a clearly different pattern and displayed no Y-specific hybridization, indicating that she is a spontaneous chimera. This study illustrates the use of DNA fingerprinting as a powerful and simple aid to the diagnosis of natural chimerism.     

Solution hybridization of crosslinkable DNA oligonucleotides to bacteriophage M13 DNA. Effect of secondary structure on hybridization kinetics and equilibria

Several DNA oligonucleotides have been photochemically modified with the furocoumarin 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) such that each contained a single HMT furan side monoadduct to thymidine at a unique 5' TpA 3' sequence. When these oligonucleotides were hybridized to their respective complements, the HMT adduct could be driven to form an interstrand crosslink by irradiation of the hybrid with 360 nm light. The ability to crosslink probe-target complexes has allowed us to determine the kinetics and the extent of hybridization in solution between these oligonucleotides and their complementary sequences in single-stranded bacteriophage M13 DNA. Our data indicate that these parameters are strongly influenced by the existence of local as well as global secondary structure in the viral DNA. During hybridization, rearrangement of this secondary structure so as to expose the target sequence can be rate-limiting. Upon attainment of equilibrium, only a portion of the target sequence may be hybridized to the probe with the remainder involved in intrastrand base-pairing. Using crosslinkable oligonucleotide probes hybridized and irradiated near the melting temperature of the respective probe-target complex one can partially overcome these secondary structure effects.     

Detection of Hepatitis B Virus (HBV) DNA at femtomolar concentrations using a silica nanoparticle-enhanced microcantilever sensor

We report Hepatitis B Virus (HBV) DNA detection using a silica nanoparticle-enhanced dynamic microcantilever biosensor. A 243-mer nucleotide of HBV DNA precore/core region was used as the target DNA. For this assay, the capture probe on the microcantilever surface and the detection probe conjugated with silica nanoparticles were designed specifically for the target DNA. For efficient detection of the HBV target DNA using silica nanoparticle-enhanced DNA assay, the size of silica nanoparticles and the dimension of microcantilever were optimized by directly binding the silica nanoparticles through DNA hybridization. In addition, the correlation between the applied nanoparticle concentrations and the resonant frequency shifts of the microcantilever was discussed clearly to validate the quantitative relationship between mass loading and resonant frequency shift.HBV target DNAs of 23.1 fM to 2.31 nM which were obtained from the PCR product were detected using a silica nanoparticle-enhanced microcantilever. The HBV target DNA of 243-mer was detected up to the picomolar (pM) level without nanoparticle enhancement and up to the femtomolar (fM) level using a nanoparticle-based signal amplification process. In the above two cases, the resonant frequency shifts were found to be linearly correlated with the concentrations of HBV target DNAs. We believe that this linearity originated mainly from an increase in mass that resulted from binding between the probe DNA and HBV PCR product, and between HBV PCR product and silica nanoparticles for the signal enhancement, even though there is another potential factor such as the spring constant change that may have influenced on the resonant frequency of the microcantilever.     

Hybridization assay of hepatitis B virus by QCM peptide nucleic acid biosensor

Although the analyses of HBV genomic DNA have traditionally been performed with commercial techniques, the high cost and long time consumed have hindered their applications in routinely diagnosis and prognosis of infection. We construct peptide nucleic acid (PNA) piezoelectric biosensor for real-time monitoring of hybridization of hepatitis B virus (HBV) genomic DNA. The PNA probe can combine to target DNA sequences more effectively and specifically than a DNA probe. The PNA probe was designed and immobilized on the surface of the biosensor to substitute the conventional DNA probe for direct detection of HBV genomic DNA without previous amplification by PCR. The hybridization assay was completed in 50 min. The detection limit was 8.6 pg/L and the clinical specificity was 94.44% compared with real time-PCR (RT-PCR). The PNA probe was able to distinguish sequences that differ only in one base. Detection sensitivity can be improved and detection time can be decreased by adding RecA protein-coated complementary ssDNA which complement to HBV gene regions. The QCM system we designed has the advantages of being rapid, label-free and highly sensitive and can be a useful supplement to commercial assay methods in clinical chemistry.     

A sensitive colorimetric detection of virus DNA and oncogene

Advantage of cloning probe DNA fragment in phage M13 DNA was taken to provide a larger single stranded DNA as a hybridization probe. High level of direct enzyme labels was introduced via the M13 DNA moiety as well as probe DNA. A highly sensitive colorimetric detection of virus DNA and oncogene was developed.     

乙型肝炎病毒DNA在患者血清及肝组织中存在状态的研究

对29例肝炎,1例尸检肝组织和血清中乙型肝炎病毒的DNA(HBV DNA)进行了研究,发现HBsAg( )/HBeAg( )患者中,有9/17(52.94％)血清HBV DNA阳性;HBsAg( )/抗-HBe( )患者中,2/6(33.33％)也为阳性。从30例肝组织中提取DNA经琼脂糖电泳,Southern吸印转移及分子杂交试验结果表明,27例HBV DNA阳性,全部有游离型HBV DNA。27例中有5例经用标记pBR322探针杂交排除非特异杂交带后,在高分子量区有HBV DNA特异的杂交带,提示有HBV DNA整合。     

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-H₂O₂ 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 (3σ) 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.     

用蛋白质工程的方法改良枯草杆菌蛋白酶E(Subtilisin E)的抗氧化性

以含有蛋白酶E基因(aprE)的单链M13mp18-aprE DNA为模板,合成的寡核苷酸5′-3′为诱变引物,用缺口双链法对aprE进行Met-222-Ala点突变。经菌落印迹杂交筛选,选出阳性噬斑。用SaⅡ酶解M13mp18-aprE得到aprE,将它和pPZW103重组,转化中性、碱性蛋白酶缺失宿主菌DB104。经含卡那霉素和脱脂奶粉板筛选和比较aprE限制性内切酶NcoⅠ和SacⅡ水解电泳图谱分析,完成构建一个分泌抗氧化的枯草杆菌蛋白酶E的工程菌PW8888。     

Determination of hepatitis B virus DNA in serum by molecular hybridization

Hepatitis B virus (HBV) DNA was detected by direct spotting of alkali-denatured serum on a nitrocellulose filter and molecular hybridization with cloned HBV DNA as the probe. Measurement of the autoradiographic signals as the intensity of hybridization allowed the quantitation of HBV DNA content in serum specimens in reference to cloned HBV DNA. Direct spotting of denatured serum was approximately three times as sensitive as the conventional method in which proteinase-treated serum was extracted with phenol-chloroform. The intensity of hybridization with 25 specimens of HB virion concentrates correlated well with DNA polymerase activity (r = 0.89, P less than 0.01).     

A new and versatile reagent for incorporating multiple primary aliphatic amines into synthetic oligonucleotides.

A novel and versatile phosphoramidite, N-Fmoc-O1-DMT-O2-cyanoethoxydiisopropylamino-phosphinyl-3-am ino-1,2-propanediol (1, Fig. 1), has been synthesized and used to incorporate primary aliphatic amines into synthetic oligonucleotides. Its convenient preparation and use in solid phase oligonucleotide synthesis is described. Using phosphoramidite 1, an amino-modified oligonucleotide probe complementary to M13mp18 DNA was constructed with five primary amines attached to the 5'-terminus. The amino-modified oligonucleotide was subsequently labeled with biotin and employed in a dot-blot hybridization assay. As little as 0.5 ng of M13mp18 target DNA was colorimetrically detected.     

Hypervariable DNA fingerprinting in Escherichia coli: minisatellite probe from bacteriophage M13.

Extensive restriction-fragment-length polymorphism was revealed in Escherichia coli strains by using a region of the bacteriophage M13 genome as a DNA hybridization probe. This variation was observed across natural strains, in clinical samples, and to a lesser extent in laboratory strains. The sequence in M13 which revealed this fingerprint pattern was a region of the gene III coat protein, which contains two clusters of a 15-base-pair repeat. Oligonucleotides made to a consensus of these repeats also revealed the fingerprint profile. While this consensus sequence has significant homology to the lambda chi site sequence, an oligonucleotide made of the chi sequence did not reveal polymorphic fingerprint patterns in E. coli. The strain variation revealed by the M13 and M13-derived oligonucleotide probes will be useful for bacterial characterization and should find use in studies of bacterial evolution and population dynamics. The findings raise questions about what these repeated sequences are and why they are so variable.     

The characterization of arabms1: an Arabidopsis thaliana sequence homologous to bacteriophage M13 repeat element

A genomic DNA fragment was isolated from the genome of Arabidopsisthaliana via hybridization with bacteriophage M13 protein IIIrepeat element. A 45 bp region of the A. thaliana DNA fragmenthas a repeating 12 bp structure that shows sequence homologyto both the M13 repeat and to a rice minisatellite-like element.Hybridization of digests of A. thaliana genomic DNA with theminisatellite DNA generates a multilocus DNA fingerprint withlow polymorphism. Key words: Minisatellite, M13 repeat element, Arabidopsis thaliana