Masking oligonucleotides improve sensitivity of mutation detection based on guanine quenching

Guanine quenching of a fluorescence-labeled DNA probe is a powerful tool for detecting a mutation in a targeted site of a DNA strand. However, a different guanine adjacent to a targeted site can interfere with detection of a point mutation, resulting in unsatisfactory sensitivity. In the current study, we developed a simple method to improve sensitivity of the guanine quenching method using a masking DNA oligonucleotide. The simple addition of a masking DNA oligonucleotide was found to mask the interference of a different guanine in a target oligonucleotide on fluorescence and to enhance difference in the quenching ratio between wild-type and mutant oligonucleotides. Based on this strategy, we succeeded in discriminating various mutations from the wild-type YMDD motif of the hepatitis B virus DNA polymerase gene using guanine quenching with a masking oligonucleotide.     

Detection of point mutations in the HBV polymerase gene using a fluorescence intercalator in reverse micelles

We report a novel and simple method for mutation detection in DNA oligonucleotides using a double-stranded DNA specific dye (SYBR Green I) in nanostructured molecular assemblies, called reverse micelles. The intercalation of SYBR Green I into the duplex DNA exhibits fluorescent emission in a CTAB/isooctane reverse micellar system as well as in an aqueous solution. We found marked differences in the fluorescence intensity between perfectly matched and mismatched 52-mer synthetic oligonucleotides, which were designed to contain the YMDD motif of the hepatitis B virus (HBV) polymerase gene, in a reverse micellar solution. Using this method, we successfully detected a mutation in PCR-amplified oligonucleotides of the HBV polymerase gene in sera of four patients with chronic hepatitis B. This detection method does not require DNA immobilization, chemical modification of DNA, or any special apparatus; it only needs a normal fluorescence spectrophotometer, an inexpensive dye, and just 10 pmol of sample DNA.     

Dynamic changes of hepatitis B virus polymerase gene including YMDD motif in lamivudine-treated patients with chronic hepatitis B

The mutation of YMDD motif of hepatitis B virus (HBV) polymerase gene is the most frequent cause in HBV resistant to lamivudine. The aim of the study was to investigate variation features of HBV polymerase gene in chronic hepatitis B (CHB) patients before and after lamivudine treatment. From the serum samples of five CHB patients before and after 12 months of lamivudine treatment, HBV polymerase gene was amplificated and positive DNA fragments were cloned into JM105 competent cell. Twenty positive clones of every sample were checked with mismatched polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and YMDD variants were sequenced. Among five patients after 12 months of lamivudine treatment, M552I mutations in two patients with HBV DNA rebounding and D553G mutation in one non-responder were detected except two patients with negative HBV DNA consecutively. In summary, D553G mutation is probably one of the reasons that caused non-responders during lamivudine treatment. The mutations of YMDD motif occurred after lamivudine treatment are caused by the induction of lamivudine.     

5′-BIS-PYRENYLATED OLIGONUCLEOTIDES DISPLAY ENHANCED EXCIMER FLUORESCENCE UPON HYBRIDIZATION WITH DNA AND RNA

A simple one-step procedure was applied for synthesis of oligonucleotide conjugates bearing two pyrene residues at the 5′-phosphate of oligonucleotide. Excimer fluorescence intensity of the conjugates is highly sensitive to duplex formation: binding of the bis-pyrenylated oligonucleotides to their DNA and RNA targets leads 10-fold increase of fluorescence. The data show that excimer fluorescence intensity of the conjugates depends linearly on the concentration of target DNA and permits quantification of DNA in solution.     

未经抗病毒治疗慢乙肝患者YMDD变异检测及HBV基因分型

目的 :探讨未接受拉米呋啶及干扰素抗病毒治疗的慢性乙型肝炎患者中YMDD是否存在变异及HBV的基因亚型。方法 :采用PCR荧光分子信标探针检测技术及PCR微板核酸杂交 ELISA技术进行HBVYMDD变异株 (YIDD YVDD)及HBV基因分型检测。结果 :2 9例慢性乙肝患者HBVYMDD变异阳性 6例 ,阳性率为 2 0 6%。 5例变异阳性中 3例为YIDD阳性 ,2例为YVDD阳性 ,6例均为YMDD野生株和变异株同时存在 ;HBV基因亚型以C、B、D亚型为主 ,分别占41 3% ( 1 2 2 9)、2 4 1 % ( 7 2 9)、2 0 6% ( 6 2 9)。结论 :在未经抗病毒治疗的慢乙肝患者中存在YMDD变异株 ,临床上在应用拉米呋啶对慢性乙型肝炎患者进行抗病毒治疗前 ,应对患者是否存在YMDD变异加以重视 。     

Substitution at rt269 in Hepatitis B Virus Polymerase Is a Compensatory Mutation Associated with Multi-Drug Resistance

The emergence of compensatory mutations in the polymerase gene of drug resistant hepatitis B virus (HBV) is associated with treatment failure. We previously identified a multi-drug resistant HBV mutant, which displayed resistance towards lamivudine (LMV), clevudine (CLV), and entecavir (ETV), along with a strong replication capacity. The aim of this study was to identify the previously unknown compensatory mutations, and to determine the clinical relevance of this mutation during antiviral therapy. In vitro mutagenesis, drug susceptibility assay, and molecular modeling studies were performed. The rtL269I substitution conferred 2- to 7-fold higher replication capacity in the wild-type (WT) or YMDD mutation backbone, regardless of drug treatment. The rtL269I substitution alone did not confer resistance to LMV, ETV, adefovir (ADV), or tenofovir (TDF). However, upon combination with YMDD mutation, the replication capacity under LMV or ETV treatment was enhanced by several folds. Molecular modeling studies suggested that the rtL269I substitution affects template binding, which may eventually lead to the enhanced activity of rtI269-HBV polymerase in both WT virus and YMDD mutant. The clinical relevance of the rtL269I substitution was validated by its emergence in association with YMDD mutation in chronic hepatitis B (CHB) patients with sub-optimal response or treatment failure to LMV or CLV. Our study suggests that substitution at rt269 in HBV polymerase is associated with multi-drug resistance, which may serve as a novel compensatory mutation for replication-defective multi-drug resistant HBV.     

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5′-nucleases with an energy minimization algorithm that utilizes the 5′-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5′-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific ‘bridge’ probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37°C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.     

荧光分子信标探针检测拉米夫定耐药基因的研究

建立荧光分子信标探针方法,探讨乙肝病毒对拉米夫定耐药的发生及病程进展。观察77例乙肝病人口服拉米夫定治疗前及治疗后12个月及24个月肝功能(ALT)及免疫学指标及检测HBVDNA含量,并采用PCR荧光分子信标技术检测YMDD耐药突变株(包括YIDDYVDD突变株)。结果表明,口服拉米夫定12个月或24个月,近半数病人血清HBVDNA转阴(小于01pgml),35%(2777)的病人出现e抗原血清转换或单纯e抗原转阴,而e抗原血清转换绝大多数发生于HBVDNA低于100pgml血清的病人。30%(2376)的病人出现YMDD耐药(YIDDYVDD),在HBVDNA小于10pgml(106拷贝ml)的病人中YMDD耐药株与野生株共存。加大口服拉米夫定剂量,绝大多数YMDD耐药株仍不能转变为YMDD野生株。提示中国乙肝患者YMDD耐药后不适合加大剂量继续使用拉米夫定治疗 。     

DNA bioassays based on the fluorescence ‘turn off’ of silver nanocluster beacon

Recognition and quantification of oligonucleotide sequences play important roles in medical diagnosis. In this study, a new fluorescent oligonucleotide‐stabilized silver nanocluster beacon (NCB) probe was designed for sensitive detection of oligonucleotide sequence targets. This probe contained two tailored DNA strands. One strand was a signal probe strand containing a cytosine‐rich strand template for fluorescent silver nanocluster (Ag NC) synthesis and a detection sections at each end. The other strand was a fluorescence enhancing strand containing a guanine‐rich section for signal enhancement at one end and a linker section complementary to one end of the signal probe strand. After synthesis of the Ag NCs and hybridization of the two strands, the fluorescence intensity of the as‐prepared silver NCB was enhanced 200‐fold compared with the Ag NCs. Two NCBs were designed to detect two disease‐related oligonucleotide sequences, and results indicated that the two target oligonucleotide sequences in the range 50.0–600.0 and 50.0–200.0 nM could be linearly detected with detection limits of 20 and 25 nM, respectively. The developed fluorescence method using NCBs for oligonucleotide sequence detection was sensitive, facile and had potential for use in bioanalysis and diagnosis.     

乙肝治疗耐药基因突变的焦磷酸测序技术诊断

目的:建立焦磷酸测序技术检测拉米夫定和阿德福韦酯治疗乙肝所致乙肝病毒基因耐药突变的定量检测方法,为临床乙肝耐药诊断和治疗提供依据。方法:针对乙肝病毒DNA聚合酶基因序列上4个常见基因突变位点的6种突变形式,分别克隆构建野生型和突变型质粒作为标准品,应用生物信息学手段设计目标基因通用PCR引物和各突变点的焦磷酸测序引物,建立焦磷酸测序的突变检测方法。对接受拉米夫定、阿德福韦酯治疗的慢性乙型肝炎患者血清标本进行检测。结果:构建了乙肝病毒四种常见耐药性突变的标准株和变异株克隆,建立了分别或同时检测拉米夫定、阿德福韦酯耐药突变的焦磷酸测序方法,对68例临床耐药或疑似耐药的患者血清标本进行检测,双脱氧测序验证,检出拉米夫定耐药突变32例,阿德福韦酯耐药突变5例,其中焦磷酸测序检出20例为混合突变,而双脱氧测序显示为6例。结论:成功建立了焦磷酸测序定量检测拉米夫定、阿德福韦酯耐药基因突变的方法,构建了乙肝病毒耐药基因突变的标准质粒,为临床动态监测乙肝病毒变异病毒株、指导合理用药奠定了基础。     

Detection of mixed populations of wild-type and YMDD hepatitis B variants by pyrosequencing in acutely and chronically infected patients

ABSTRACT: BACKGROUND: Lamivudine (LAM) is associated with the highest known rate of resistance mutations amongnucleotide analogs used to treat chronic hepatitis B virus (HBV) infection. Despite this, LAMcontinues in widespread use, especially in combination therapies. The primary LAMresistance mutation (rtM204V/I) occurs in the YMDD motif of HBV polymerase. The aim ofthis study was to characterize Brazilian HBV isolates from acute and chronic cases by directsequencing, and to identify HBV quasispecies in the YMDD motif using a pyrosequencingmethod capable of detecting single-nucleotide polymorphisms. HBV DNA from serumsamples of 20 individuals with acute HBV infection and 44 with chronic infectionundergoing antiviral therapies containing LAM were analyzed by direct sequencing andpyrosequencing methods. RESULTS: Phylogenic analyses of direct-sequenced isolates showed the expected genotypes (A, D andF) for the Brazilian population in both acute and chronic infections. However, withingenotype A isolates, subgenotype A2 was more frequently detected in acute cases than inchronic cases (P = 0.012). As expected, none of the individuals with acute hepatitis B hadLAM-resistant isolates as a dominant virus population, whether detected by direct sequencingor pyrosequencing. However, pyrosequencing analyses showed that 45% of isolates (9/20)had minor subpopulations (4-17%) of LAM-resistant isolates. Among chronic patientsundergoing LAM treatment, YMDD mutants were frequently found as a dominant viruspopulation. In cases where wild-type virus was the dominant population, subpopulations ofYMDD variants were usually found, demonstrating the complexity of HBV quasispecies. CONCLUSIONS: YMDD variants were frequently detected as a minor population in acute HBV infection. Theoccurrence of pre-existing variants may lead to a high frequency of resistant mutants duringantiviral therapy in the chronic phase. In chronic infection, detection of YMDD variantsbefore virological or biochemical breakthrough might contribute to making better therapychoices and thus improving treatment outcome.     

RNA Interference-Guided Targeting of Hepatitis C Virus Replication with Antisense Locked Nucleic Acid-Based Oligonucleotides Containing 8-oxo-dG Modifications

The inhibitory potency of an antisense oligonucleotide depends critically on its design and the accessibility of its target site. Here, we used an RNA interference-guided approach to select antisense oligonucleotide target sites in the coding region of the highly structured hepatitis C virus (HCV) RNA genome. We modified the conventional design of an antisense oligonucleotide containing locked nucleic acid (LNA) residues at its termini (LNA/DNA gapmer) by inserting 8-oxo-2’-deoxyguanosine (8-oxo-dG) residues into the central DNA region. Obtained compounds, designed with the aim to analyze the effects of 8-oxo-dG modifications on the antisense oligonucleotides, displayed a unique set of properties. Compared to conventional LNA/DNA gapmers, the melting temperatures of the duplexes formed by modified LNA/DNA gapmers and DNA or RNA targets were reduced by approximately 1.6-3.3°C per modification. Comparative transfection studies showed that small interfering RNA was the most potent HCV RNA replication inhibitor (effective concentration 50 (EC₅₀): 0.13 nM), whereas isosequential standard and modified LNA/DNA gapmers were approximately 50-fold less efficient (EC₅₀: 5.5 and 7.1 nM, respectively). However, the presence of 8-oxo-dG residues led to a more complete suppression of HCV replication in transfected cells. These modifications did not affect the efficiency of RNase H cleavage of antisense oligonucleotide:RNA duplexes but did alter specificity, triggering the appearance of multiple cleavage products. Moreover, the incorporation of 8-oxo-dG residues increased the stability of antisense oligonucleotides of different configurations in human serum.     

Gene Correction by RNA‐DNA Oligonucleotides

An oligonucleotide composed of a contiguous stretch of RNA and DNA residues has been developed to facilitate the correction of single‐base mutations of episomal and chromosomal targets in mammalian cells. The design of the oligonucleotide exploited the highly recombinogenic RNA‐DNA hybrids and featured hairpin capped ends avoiding destruction by cellular helicases or exonucleases. The RNA‐DNA oligonucleotide (RDO) was designed to correct a point mutation in the tyrosinase gene and caused a permanent gene correction in mouse albino melanocytes, determined by clonal analysis at the level of genomic sequence, protein and phenotypic change. Recently, we demonstrated correction of the tyrosinase gene using the same RDO in vivo, as detected by dark pigmentation of several hairs and DOPA staining of hair follicles in the treated skin of albino mice. Such RDOs might hold a promise as a therapeutic method for the treatment of skin diseases. However, the frequency of gene correction varies among different cells, indicating that cellular activities, such as recombination and repair, may be important for gene conversion by RDOs. As this technology becomes more widely utilized in the scientific community, it will be important to understand the mechanism and to optimize the design of RDOs to improve their efficiency and general applicability.     

靶向C—Raf-1基因的反义核酸抗乙型肝炎病毒活性研究

目的：通过体内外实验验证靶向c-Raf-1基因的反义核酸是否具有抑制乙型肝炎病毒（HBV）的活性。方法：设计靶向c-Raf-1基因的反义核酸,并在细胞水平进行体外抗HBV活性筛选,通过RT-PCR检测c-Raf-1基因mRNA水平的变化,通过体内药效学实验进一步验证反义核酸的抗HBV效果。结果：经体外筛选,靶向c-Raf-1基因的反义核酸Raf-3145具有相对明显的抑制HBV表面抗原（HBsAg）的作用,并可剂量依赖性地抑制c-Raf-1基因的表达;体内药效学结果显示,反义核酸Raf-3145在30 mg/kg剂量下对HBsAg的表达具有一定的抑制作用。结论：经体内外活性评价,初步确定了靶向宿主基因c-Raf-1的反义核酸具有一定的抑制HBsAg表达的活性,也进一步验证了c-Raf-1基因可以作为抗HBV药物设计的候选靶点。     

Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses.

Branched oligonucleotides (bDNA) have been synthesized containing a unique primary segment and a set of identical secondary fragments covalently attached to the primary sequence through branch points. The primary sequence is designed to hybridize (directly or indirectly) to a target nucleic acid, such as hepatitis B virus (HBV) or hepatitis C virus (HCV) genomic DNA or RNA, respectively. The secondary fragments are used to direct the binding of multiple copies of a small oligonucleotide labelled with alkaline phosphatase. Assays for the presence of HBV and HCV based on the application of these branched amplification multimers have been devised. It is possible to detect as few as 1,000 hepatitis viral genomes directly.     

An Activated GOPS‐poly‐L‐Lysine‐ Coated Glass Surface for the Immobilization of 60mer Oligonucleotides

To explore a method for enhancing the immobilization and hybridization efficiency of oligonucleotides on DNA microarrays, conventional protocols of poly‐L‐lysine coating were modified by means of surface chemistry, namely, the slides were prepared by the covalently coupling of poly‐L‐lysine to a glycidoxy‐modified glass surface. The modified slides were then used to print microarrays for the detection of the SARS coronavirus by means of 60mer oligonucleotide probes. The characteristics of the modified slides concerning immobilization efficiency, hybridization dynamics, and probe stripping cycles were determined. The improved surface exhibited high immobilization efficiency, a good quality uniformity, and satisfactory hybridization dynamics. The spotting concentration of 10 μmol/L can meet the requirements of detection; the spots were approximately 170 nm in diameter; the mean fluorescence intensity of the SARS spots were between 3.2 × 10⁴ and 5.0 × 10⁴ after hybridization. Furthermore, the microarrays prepared by this method demonstrated more resistance to consecutive probe stripping cycles. The activated GOPS‐PLL slide could undergo hybridization stripping cycles for at least three cycles, and the highest loss in fluorescence intensity was found to be only 11.9 % after the third hybridization. The modified slides using the above‐mentioned method were superior to those slides treated with conventional approaches, which theoretically agrees with the fact that modification by surface chemistry attaches the DNA covalently firmly to the slides. This protocol may have great promise in the future for application in large‐scale manufacture.     

Specific inhibition of hepatitis B viral gene expression in vitro by targeted antisense oligonucleotides.

A 21-mer oligodeoxynucleotide complementary to the polyadenylation signal for human hepatitis B virus (HBV) was complexed to a soluble DNA-carrier system that is targetable to hepatocytes via asialoglycoprotein receptors present on those cells. A cell line, HepG2 (2.2.15) that possesses asialoglycoprotein receptors and is permanently transfected with hepatitis B virus (ayw subtype) was exposed to complexed antisense DNA or controls. In the presence of complexed antisense DNA, the concentration of hepatitis B surface antigen in medium was 80% lower than controls after 24 h. Furthermore, during the next 6 days, there was no significant increase in surface antigen concentration in the presence of complexed antisense DNA. The inhibition could be effectively blocked by competition with an excess of free asialoglycoprotein. Total protein synthesis remained unchanged by exposure to complexed antisense sequences under identical conditions. In addition, HBV DNA in the medium and cell layers after 24-h exposure to complexed antisense sequences was 80% lower than in controls. The data indicate that antisense oligonucleotides complexed by a soluble DNA-carrier system can be targeted to cells via asialoglycoprotein receptors resulting in specific inhibition of hepatitis B viral gene expression and replication.     

Luminescent and hydrophilic LaF3–polymer nanocomposite for DNA detection

Luminescent LaF₃–Ce³⁺/Tb³⁺ nanocrystals have been successfully prepared via a simple wet chemical technique. For the next bioapplication, these nanoparticles dispersed in cyclohexane have also been functionalized with poly(St‐co‐MAA), based on a designed oil‐in‐water microemulsion system. These polymer‐coated nanospheres are water‐soluble and bioconjugable. Unlike semiconductor quantum dots, the as‐prepared lanthanum fluoride nanocrystals possess non‐size‐dependent emissions and completely stable photocycles. With functionalized LaF₃ nanospheres as fluorescence probes, a fluorescence method was developed for the rapid quantitative analysis of DNA, due to the quenching effect of fluorescence by the DNA. Under optimum conditions, the fluorescence intensity was proportional to the concentration of the introduced DNA over the range 2.5–35 µg/mL for calf thymus DNA (ctDNA) and 2.5–30 µg/mL for fish sperm DNA (fsDNA), respectively. Copyright © 2008 John Wiley & Sons, Ltd.