SPR-based DNA Detection with Metal Nanoparticles

In this short review paper, we summarize some of our ideas to utilize gold nanoparticles for the enhancement of surface plasmon resonance signals on DNA microarray. The hybridization of target-DNA capped gold nanoparticles with probe DNA on surface provides ca. ten times stronger optical contrast compared with that of target-DNA molecules. Our simulation result based on the Maxwell-Garnet theory explains well our experimental data and proves a potential of metallic nanoparticles for the substantial sensitivity enhancements for biosensor application in DNA diagnostics and bio-affinity studies, which leads to the fabrication of high resolution DNA microarrays.     

Biophysical characterization of complexation of DNA with oppositely charged Gemini surfactant 12-3-12

The interaction between DNA and cationic gemini surfactant trimethylene-1, 3-bis (dodecyldimethylammonium bromide) (12-3-12) has been investigated by the measurements of fluorescence, surface tension, UV spectrum and circular dichroism (CD). Micelle-like structure of 12-3-12 induced by DNA appears at critical aggregation concentration (CAC), which is much lower than critical micelle concentration (CMC) of 12-3-12 in DNA-free solution. CAC is independent of DNA concentration, but the CMC of the mixed solutions of DNA and 12-3-12(CMC(mix)) increases with the increasing of DNA concentration. The surface tensions of the mixed system are higher than that of the pure surfactant solution, much different from the so-called synergistic lowering of the surface tension for other polymer-surfactant systems. Phase separation occurs after the neutralization point and the precipitate redissolves with superfluous 12-3-12. Cationic surfactant 12-3-12 can exclude ethidium bromide (EB) from the DNA/EB complex, and this process does not depend on the DNA concentration but on the charge ratio of 12-3-12 to DNA. The binding constant of EB to DNA decreases sharply at the charge ratio from 0.5 to 1.0. Circular dichroism (CD) spectra show that DNA undergoes a conformational transition from native B-form to chiral psi-phase with increasing of 12-3-12.     

Development of a molecular diagnosis assay based on electrohybridization at plastic electrodes and subsequent PCR

Technologies enabling specific recognition of medically relevant nucleic acid sequences will play a pivotal role in future medical diagnosis. Whereas many approaches to molecular diagnosis systems include DNA microarrays on chips and fluorometric detection, the basis of our approach is the use of inexpensive components like plastic or metal thin film electrodes with low multiplexing and an electrochemical detection unit. To increase the sensitivity, PCR can be used as an intermediate step. For selective enrichment, specific nucleic acid probes were covalently attached at their 5′-ends to conducting polycarbonate/carbon fiber electrodes. Complementary oligonucleotides were enriched at the electrodes by cyclic inversion of an electrochemical potential, transferred into a PCR vial and thermally or electrochemically desorbed. The analysis of the PCR product shows the efficiency and selectivity of the electrochemical enrichment. Hybridization of DNA was shown by electrochemical methods, in this work especially by differential pulse voltammetry (DPV) using the single strand specific hybridization redox indicator osmium(VIII)-tetroxide, and potentiometric stripping analysis (PSA). This combination of experimental methods is the basis for a molecular diagnosis system including a disposable nucleic acid modified working electrode for specific enrichment, detection and quantification, and an optional capillary PCR module for fast amplification.     

Rapid analysis of amplified double-stranded DNA by capillary electrophoresis with laser-induced fluorescence detection

DNA amplification technology has been applied to clinical diagnosis of infectious disease, genetic disorder, and cancer. After in vitro amplification of a particular DNA region, the methods of analysis for these amplified samples play a pivotal role in clinical diagnosis. Conventional gel electrophoresis has been routinely used in the lab for checking DNA. The whole procedure is time consuming and requires more than 1 ng of DNA for detection. To achieve greater performance in DNA diagnosis, we demonstrated capillary electrophoresis with laser induced fluorescence detection for analysis of amplified DNA. The analysis of DNA could be completed within 3 min and the data is directly entered into the computer. Considering the automatic and rapid process, we believe that this method could be routinely utilized for the clinical diagnosis of amplified DNA products.     

DNA biosensors that reason

Despite the many designs of devices operating with the DNA strand displacement, surprisingly none is explicitly devoted to the implementation of logical deductions. The present article introduces a new model of biosensor device that uses nucleic acid strands to encode simple rules such as "IF DNA_strand(1) is present THEN disease(A)" or "IF DNA_strand(1) AND DNA_strand(2) are present THEN disease(B)". Taking advantage of the strand displacement operation, our model makes these simple rules interact with input signals (either DNA or any type of RNA) to generate an output signal (in the form of nucleotide strands). This output signal represents a diagnosis, which either can be measured using FRET techniques, cascaded as the input of another logical deduction with different rules, or even be a drug that is administered in response to a set of symptoms. The encoding introduces an implicit error cancellation mechanism, which increases the system scalability enabling longer inference cascades with a bounded and controllable signal-noise relation. It also allows the same rule to be used in forward inference or backward inference, providing the option of validly outputting negated propositions (e.g. "diagnosis A excluded"). The models presented in this paper can be used to implement smart logical DNA devices that perform genetic diagnosis in vitro.     

乙型肝炎病毒e抗原定量检测的性能验证和临床应用探索

乙型肝炎病毒e抗原(hepatitis B e antigen, HBeAg)的定量检测对乙型肝炎临床诊疗具有一定的重要性,但其定量检测还未成为常规检验项目。本研究对HBeAg定量检测系统进行性能验证,比较HBeAg定量和定性检测的相关性和一致性,分析HBeAg定量结果和乙型肝炎病毒DNA(hepatitis B virus DNA, HBV DNA)的关系,为HBeAg定量检测在临床诊疗的应用提供依据。通过收集710例2019年3月至5月于复旦大学附属华山医院就诊的慢性乙型肝炎患者血清样本,参照美国临床实验室标准化协会(The Clinical & Laboratory Standards Institute, CLSI)相关文件的要求,对雅培ARCHITECTi4000SR全自动免疫分析仪检测的HBeAg定量试剂的精密度、分析灵敏度、线性范围/可报告范围、携带污染率进行验证和评价;采用化学发光微粒子免疫检测技术(chemiluminescence microparticle immuno assay, CMIA)对618例患者进行HBeAg定性和定量检测;采用荧光定量PCR对慢性乙型肝炎患者进行HBV DNA检测,比较HBV DNA和HBeAg定量结果的相关性。本研究证实HBeAg定量试剂检测性能验证结果良好;HBeAg定量和定性检测相关性良好;126例同时有HBeAg定量检测和HBV DNA定量检测的结果显示,两种方法呈正相关且一致性良好。HBeAg定量检测可用于常规实验室检测来辅助HBV感染的临床诊疗。     

Processing DNA molecules as text

Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg’s movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing—the creation of variations and combinations of existing DNA—using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction.

Electronic supplementary material

The online version of this article (doi:10.1007/s11693-010-9059-y) contains supplementary material, which is available to authorized users.     

Studying the effect of a charged surface on the interaction of bleomycin with DNA using an atomic force microscope

The cleavage of DNA caused by the antitumoral drug bleomycin has been investigated using atomic force microscopy (AFM). This work deals with the effect that adsorbing DNA onto a positively- or negatively-charged surface has on the double-strand cleavage of DNA by Fe(III)/bleomycin. Quantitative analysis of the number of breaks per DNA molecule, in bulk and at the surface of the mica substrate, has been performed by analyzing AFM images. It turns out that the cleavage of DNA is strongly inhibited by a positively-charged surface. Our experiments can be interpreted using a simple electrostatic model. This paper is a first step in the study of DNA accessibility to ligand such as bleomycin, using AFM in liquids.Olivier Piétrement and David Pastré have contributed equally to the work.     

Carnitine palmitoyltransferase II deficiency: Diagnosis by molecular analysis of blood

Four missense mutations have been reported to be associated with the typical, adult form of carnitine palmitoyltransferase II (CPT II) deficiency: Three amino acid substitutions (R631C, P50H and D553N) appear to be rare, while the S113L mutation was found to be common in a group of European patients with CPT II deficiency.We analyzed genomic DNA from 20 American patients with recurrent episodes of myoglobinuria as well as DNA from 10 normal controls in order to determine the frequency of the reported missense mutations in our patient population.The three previously described rare mutations were not found in our group of patients. The S113L mutation was found in 19 of our patients: 5 patients were homozygous, 14 patients were heterozygous.Given the high frequency of this mutation in our series of patients we concluded that the clinical diagnosis of CPT II deficiency can be confirmed by a 'blood test' without resorting to a muscle biopsy.     

Natural lipid extracts and biomembrane-mimicking lipid compositions are disposed to form nonlamellar phases, and they release DNA from lipoplexes most efficiently

A viewpoint now emerging is that a critical factor in lipid-mediated transfection (lipofection) is the structural evolution of lipoplexes upon interacting and mixing with cellular lipids. Here we report our finding that lipid mixtures mimicking biomembrane lipid compositions are superior to pure anionic liposomes in their ability to release DNA from lipoplexes (cationic lipid/DNA complexes), even though they have a much lower negative charge density (and thus lower capacity to neutralize the positive charge of the lipoplex lipids). Flow fluorometry revealed that the portion of DNA released after a 30-min incubation of the cationic O-ethylphosphatidylcholine lipoplexes with the anionic phosphatidylserine or phosphatidylglycerol was 19% and 37%, respectively, whereas a mixture mimicking biomembranes (MM: phosphatidylcholine/phosphatidylethanolamine/phosphatidylserine /cholesterol 45:20:20:15 w/w) and polar lipid extract from bovine liver released 62% and 74%, respectively, of the DNA content. A possible reason for this superior power in releasing DNA by the natural lipid mixtures was suggested by structural experiments: while pure anionic lipids typically form lamellae, the natural lipid mixtures exhibited a surprising predilection to form nonlamellar phases. Thus, the MM mixture arranged into lamellar arrays at physiological temperature, but began to convert to the hexagonal phase at a slightly higher temperature, ∼ 40-45 °C. A propensity to form nonlamellar phases (hexagonal, cubic, micellar) at close to physiological temperatures was also found with the lipid extracts from natural tissues (from bovine liver, brain, and heart). This result reveals that electrostatic interactions are only one of the factors involved in lipid-mediated DNA delivery. The tendency of lipid bilayers to form nonlamellar phases has been described in terms of bilayer “frustration” which imposes a nonzero intrinsic curvature of the two opposing monolayers. Because the stored curvature elastic energy in a “frustrated” bilayer seems to be comparable to the binding energy between cationic lipid and DNA, the balance between these two energies could play a significant role in the lipoplex-membrane interactions and DNA release energetics.     

Multiplexed DNA Methylation Analysis in Colorectal Cancer Using Liquid Biopsy and Its Diagnostic and Predictive Value

Early diagnosis of colorectal cancer (CRC) is of high importance as prognosis depends on tumour stage at the time of diagnosis. Detection of tumour-specific DNA methylation marks in cfDNA has several advantages over other approaches and has great potential for solving diagnostic needs. We report here the identification of DNA methylation biomarkers for CRC and give insights in our methylation-sensitive restriction enzyme coupled qPCR (MSRE-qPCR) system. Targeted microarrays were used to investigate the DNA methylation status of 360 cancer-associated genes. Validation was done by qPCR-based approaches. A focus was on investigating marker performance in cfDNA from 88 patients (44 CRC, 44 controls). Finally, the workflow was scaled-up to perform 180plex analysis on 110 cfDNA samples, to identify a DNA methylation signature for advanced colonic adenomas (AA). A DNA methylation signature (n = 44) was deduced from microarray experiments and confirmed by quantitative methylation-specific PCR (qMSP) and by MSRE-qPCR, providing for six genes’ single areas under the curve (AUC) values of >0.85 (WT1, PENK, SPARC, GDNF, TMEFF2, DCC). A subset of the signatures can be used for patient stratification and therapy monitoring for progressed CRC with liver metastasis using cfDNA. Furthermore, we identified a 35-plex classifier for the identification of AAs with an AUC of 0.80.     

The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction

The Escherichia coli dam adenine-N6 methyltransferase modifies DNA at GATC sequences. It is involved in post-replicative mismatch repair, control of DNA replication and gene regulation. We show that E. coli dam acts as a functional monomer and methylates only one strand of the DNA in each binding event. The preferred way of ternary complex assembly is that the enzyme first binds to DNA and then to S-adenosylmethionine. The enzyme methylates an oligonucleotide containing two dam sites and a 879 bp PCR product with four sites in a fully processive reaction. On lambda-DNA comprising 48,502 bp and 116 dam sites, E. coli dam scans 3000 dam sites per binding event in a random walk, that on average leads to a processive methylation of 55 sites. Processive methylation of DNA considerably accelerates DNA methylation. The highly processive mechanism of E. coli dam could explain why small amounts of E. coli dam are able to maintain the methylation state of dam sites during DNA replication. Furthermore, our data support the general rule that solitary DNA methyltransferase modify DNA processively whereas methyltransferases belonging to a restriction-modification system show a distributive mechanism, because processive methylation of DNA would interfere with the biological function of restriction-modification systems.     

非标记表面增强拉曼光谱在DNA检测中的应用

表面增强拉曼光谱(SERS)是一种超灵敏的生化分析技术,已经被广泛运用于细胞、核酸、蛋白质等生物分子的检测,在生物医学领域表现出了巨大的应用潜力。近年来,将表面增强拉曼光谱技术应用于遗传物质DNA的精准检测,引起了人们广泛的关注。本文简要叙述了表面增强拉曼光谱技术的基本原理及其在DNA检测中的优势,主要介绍了非标记的DNA-SERS检测应用进展,其中包括本项目组的相关工作。研究表明,非标记DNA-SERS技术有望成为一种快速、准确的临床诊断方式。     

Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness

We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent characterization of the loading process of the genome inside the phi29 bacteriophage capsid. Our emphasis is on the modelling of double-stranded DNA as a flexible thick polymer (tube) instead of a beads-and-springs chain. By using finite-size scaling to extrapolate our results to genome lengths appropriate for phi29, we find that the thickness-induced force may account for up to half the one measured experimentally at high packing densities. An analogous agreement is found for the total work that has to be spent in the packaging process. Remarkably, such agreement can be obtained in the absence of any tunable parameters and is a mere consequence of the DNA thickness. Furthermore, we provide a quantitative estimate of how the persistence length of a polymer depends on its thickness. The expression accounts for the significant difference in the persistence lengths of single and double-stranded DNA (again with the sole input of their respective sections and natural nucleotide/base-pair spacing).     

Optical biosensor-based characterization of anti-double-stranded DNA monoclonal antibodies as possible new standards for laboratory tests

The serum determination of circulating anti-double-stranded (ds)DNA autoantibodies is a routine measure for the laboratory diagnosis of systemic lupus erythematosus. Since available assays differ substantially and no feasible calibrator is available, the aim of this study was to evaluate a recently introduced surface plasmon resonance (SPR) biosensor chip for binding studies between dsDNA and anti-dsDNA autoantibodies and to demonstrate its usefulness for the characterization of new monoclonal antibody (mAb) standards and standardization of assays.We characterized two human and one murine monoclonal anti-dsDNA antibodies by measuring the kinetic on- and off-rates using the biosensor and calculating functional affinity (avidity) as the ratio of these. Obtained equilibrium dissociation constants were verified by an independent method and inhibition experiments were performed to determine reactivities to DNA of various length and composition.While all mAbs exhibited comparable avidities, which could be confirmed by gel shift experiments, one of them proved to have slower association and dissociation kinetics. This was the only mAb providing positive results in the Farr RIA. In inhibition experiments with ss- and ds-oligonucleotides 10, 24 and 42 bp in length, the mAbs acted substantially different.The study demonstrates how putative standards for the anti-dsDNA determination can be characterized using SPR biosensor technology. Our results suggest that kinetic rate constants seem to be decisive in explaining the behaviour of mAbs. Different reactivities to various DNA species should be taken into account with respect to varying DNA sources in commonly used laboratory assays.     

Nanopore sensor for fast label-free detection of short double-stranded DNAs

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with γ-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.     

血循环DNA在淋巴瘤中的研究进展

近年来血循环DNA用于基因诊断已成为研究热点,血循环DNA是指血浆中具有DNA双螺旋结构的核苷酸片段,逐渐成为一项新的肿瘤标记物。研究发现肿瘤患者血循环DNA较正常人有很大差异,不同疾病条件下其含量有不同程度的升高,且逐渐成为替代当前需采集肿瘤组织作为标本的无创方法。尽管血循环DNA的来源尚不清楚,通过监测血循环DNA总水平变化及相关肿瘤基因的异常改变,可以实现恶性肿瘤的早期诊断及预后评估。特别是许多国外文献报道,它与淋巴瘤的关系非常密切,无论血循环DNA的定性或定量研究,包括淋巴瘤常见的基因重排或者病毒相关血浆DNA,与淋巴瘤的诊断、治疗反应及预后直接相关。现将近几年国内外血循环DNA在淋巴瘤中的应用进行综述,对研究前景做简单展望。     

A suite of DNA methylation markers that can detect most common human cancers

Cancer-specific DNA methylation from the tumor derived fraction of cell free DNA found in blood samples could be used for minimally invasive detection and monitoring of cancer. The knowledge of marker regions with cancer-specific DNA methylation is necessary to the success of such a process. We analyzed the largest cancer DNA methylation dataset available—TCGA Illumina HumanMethylation450 data with over 8,500 tumors—in order to find cancer-specific DNA methylation markers for most common human cancers. First, we identified differentially methylated regions for individual cancer types and those were further filtered against data from normal tissues to obtain marker regions with cancer-specific methylation, resulting in a total of 1,250 hypermethylated and 584 hypomethylated marker CpGs. From hypermethylated markers, optimal sets of six markers for each TCGA cancer type were chosen that could identify most tumors with high specificity and sensitivity [area under the curve (AUC): 0.969-1.000] and a universal 12 marker set that can detect tumors of all 33 TCGA cancer types (AUC >0.84). In addition to hundreds of new DNA methylation markers, our approach also identified markers that are in current clinical use, SEPT9 and GSTP1, indicating the validity of our approach and a significant potential utility for the newly discovered markers. The hypermethylated markers are linked to polycomb associated loci and a significant fraction of the discovered markers is within noncoding RNA genes; one of the best markers is MIR129-2. Future clinical testing of herein discovered markers will confirm new markers that will improve minimally invasive diagnosis and monitoring for multiple cancers.     

精子DNA损伤检测技术的研究进展

精子DNA完整性与男性生育力之间的关系是近些年来生殖医学研究领域的热点之一,精子DNA损伤已成为反映男性生育力的一个新指标。精子DNA的损伤原因有很多,有时可能是多种因素共同作用的结果。生殖系统疾病、环境污染、吸烟、微量元素及各种理化因素等原因都可能导致精子DNA完整性受损。常见的精子DNA完整性检测技术有原位末端标记法、精子染色体扩散实验、精子染色质结构分析试验、单细胞凝胶电泳、荧光原位杂交技术和8-羟基脱氧鸟苷测定法等。随着检验技术的不断发展,关于精子DNA损伤的检测技术也在不断更新改进。本文主要就近十年来精子DNA损伤机制、检测技术的相关研究进展作一综述,提示现有的精子DNA完整性检测技术尚不能满足临床和科研需要,急需找到一种理想的检测方法为男性不育的诊断和治疗提供重要依据。