Epidemics of HIV Infection among Heavy Drug Users of Depressants Only, Stimulants Only, and Both Depressants and Stimulants in Mainland China: A Series, Cross-Sectional Studies.

Background: Heavy drug users was a global consensus high-risk population of HIV infection. However, the specific impact of drug on HIV infection has not yet been established. Depressants and stimulants were most widely used drugs in mainland China, and mix use of the two drugs was also serious. We assessed the HIV infection rate and trends in heavy drug users by analyzing data from the National Dynamic Management and Control Database for Drug Users (NDMCDDU). Methods: All heavy drug users with HIV test results in NDMCDDU from 2008 to 2016 were grouped into depressants only group (DOG), stimulants only group (SOG), and both depressants and stimulants group (DSG). We used joinpoint regression to examine trends of HIV infection rates. Multivariable logistic regression was used to examine factors related to HIV infection. Results: A total of 466,033 heavy drug users with 9522 cases of HIV infection were included in this analysis. HIV infection rate was estimated at 2.97% (95% CI 2.91-3.04%) of 265,774 users in DOG, 0.45% (95% CI 0.42-0.49%) of 140,895 users in SOG, and 1.65% (95% CI 1.55-1.76%) of 59,364 users in DSG. In DOG, a U-shaped curve of HIV infection rate decreased from 3.85% in 2008 to 2.19% in 2010 (annual percent change (APC) -12.9, 95% CI -19.3--6.0, p < 0.05), then increased to 4.64% in 2016 (APC 8.3, 95% CI 6.1-10.4, p < 0.05) was observed. However, SOG and DSG showed consistent increases from 0.15% in 2008 to 0.54% in 2016 (APC 8.2, 95% CI 4.8-11.8, p < 0.05) and from 0.78% in 2008 to 2.72% in 2016 (APC 13.5, 95% CI 10.7-16.4, p < 0.05), respectively. HIV infection rate of DOG in the southwest region presented a U-shaped trend. All groups showed significant increases in HIV infection in east and central regions. Conclusions: The U-shaped curve for HIV infection rate among DOG users and consistent increases among SOG and DSG users implies drug abuse is still a critical focus of HIV infection in China. It is urgently needed to reassess the effectiveness of current strategies on HIV prevention and control among drug users.

Alternate succession of aggregate-forming cyanobacterial genera correlated with their attached bacteria by co-pathways.

Freshwater lakes are threatened by harmful blooms characterized by Cyanobacterial Aggregates (CAs) that are normally aggregated with extracellular polysaccharides released by cyanobacteria to form a phycosphere. It is possible that mutualistic relationships exist between bacteria and cyanobacteria in these CAs wherein bacterial products supplement cyanobacterial growth, and cyanobacterial exudates, in turn, serve as substrates for bacteria, thus augmenting the stability of each constituent. However, little is known about the exact interaction between cyanobacteria and their attached bacteria in CAs. Therefore, in this study, we collected 26 CA samples from Lake Taihu, a large freshwater lake in China from March of 2015 to February of 2016. We then sequenced both the V4 regions of 16S rRNA genes and full metagenomes, resulting in 610 Mb of 16S rRNA gene data and 198.98 Gb of high-quality metagenomic data. We observed that two cyanobacteria genera (Microcystis and Dolichospermum) alternately dominated CAs along the sampling time and specific bacterial genera attached to different cyanobacteria genera dominated CAs. More specifically, Dolichospermum dominates CAs when water temperature is low and total nitrogen is high, while Microcystis dominates CAs when water temperature is high and total nitrogen is low. Moreover, we found specific bacterial genera attached to different cyanobacteria genera dominated CAs. The cyanobacteria-bacteria related pairs Dolichospermum-Burkholderia and Microcystis-Hyphomonas were detected by ecological networks construction. Bacterial communities in CAs were found to be more correlated with the cyanobacterial community (Mantel's r = 0.76, P = 0.001) than with environmental factors (Mantel's r = 0.27, P = 0.017). A potential codependent nitrogen-cycling pathway between cyanobacteria and their attached bacteria was constructed, indicating their functional link. Overall, these results demonstrated that mutualistic relationships do, indeed, exist between cyanobacteria and bacteria in CAs at both taxonomic and gene levels, providing biological clues potentially leading to the control of blooms by interventional strategies to disrupt bacteria-cyanobacteria relationships and co-pathways.

Surface functionalized exosomes as targeted drug delivery vehicles for cerebral ischemia therapy.

The safe and effective delivery of drugs is a major obstacle in the treatment of ischemic stroke. Exosomes hold great promise as an endogenous drug delivery nanosystem for the treatment of cerebral ischemia given their unique properties, including low immunogenicity, innate stability, high delivery efficiency, and ability to cross the blood-brain barrier (BBB). However, exosome insufficient targeting capability limits their clinical applications. In this study, the c(RGDyK) peptide has been conjugated to the exosome surface by an easy, rapid, and bio-orthogonal chemistry. In the transient middle cerebral artery occlusion (MCAO) mice model, The engineered c(RGDyK)-conjugated exosomes (cRGD-Exo) target the lesion region of the ischemic brain after intravenous administration. Furthermore, curcumin has been loaded onto the cRGD-Exo, and administration of these exosomes has resulted in a strong suppression of the inflammatory response and cellular apoptosis in the lesion region. The results suggest a targeting delivery vehicle for ischemic brain based on exosomes and provide a strategy for the rapid and large-scale production of functionalized exosomes.

Notification Rate of Tuberculosis among Migrants in China 2005-2014: A Systematic Review and Meta-analysis.

BACKGROUND: Migrations have been reported to be associated with the high risk of tuberculosis (TB), but there is no systematic analysis of the available data for TB among migrant in China. The aim of this study was to examine the notification rate of active and sputum smear-positive TB by a systematic review and meta-analysis. METHODS: A systematic review and meta-analysis were performed to examine the notification rate of active and sputum smear-positive TB among migrants in China. Two reviewers searched the cross-sectional studies published in PubMed, EMBASE, SciFinder, and Web of Science in English and in CNKI and Wanfang databases in Chinese. Pooled estimates of notification rate of TB among migrants were calculated using a random effects model. Meta-regression analysis and subgroup analysis stratified by year, region were also performed. RESULTS: Seventy eligible studies met the inclusion criteria for the final analysis. The overall notification rate of active TB and sputum smear-positive cases among migrants were 53.12 (95% confidence interval [CI]: 47.32-59.63) and 24.53 (95% CI: 22.01-27.34) per 100,000 populations, respectively. The notification rate of active TB significantly increased from 50.95 (95% CI: 41.11-63.14) per 100,000 populations in 2005 to 84.62 (95% CI: 78.00-91.80) per 100,000 populations in 2014 while that of smear-positive TB was constant during the study time (P = 0.79). The geographic difference was identified both for active and sputum smear-positive TB, with the higher notification rates mainly distributing along the eastern coastal areas. CONCLUSIONS: The pooled estimate of active TB and sputum smear-positive TB among migrants was lower than the national notification rate among general population, but the gap between our data and national notification rate among general population is narrowed down during 2005-2014.

Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing.

The cyanobacterial genus Microcystis is well known as the main group that forms harmful blooms in water. A strain of Microcystis, M. panniformis FACHB1757, was isolated from Meiliang Bay of Lake Taihu in August 2011. The whole genome was sequenced using PacBio RS II sequencer with 48-fold coverage. The complete genome sequence with no gaps contained a 5,686,839 bp chromosome and a 38,683 bp plasmid, which coded for 6,519 and 49 proteins, respectively. Comparison with strains of M. aeruginosa and some other water bloom-forming cyanobacterial species revealed large-scale structure rearrangement and length variation at the genome level along with 36 genomic islands annotated genome-wide, which demonstrates high plasticity of the M. panniformis FACHB1757 genome and reveals that Microcystis has a flexible genome evolution.

B-cell lymphoma 2 rs17757541 C>G polymorphism was associated with an increased risk of coronary artery disease in a Chinese population.

The goal of our study was to evaluate the genetic effects of sixteen single nucleotide polymorphisms (SNPs) in apoptosis-related genes on the development of coronary artery disease (CAD) through a case-control study. A total of 1979 individuals, including 826 CAD cases (aged 67.27 ± 10.26 years) and 1153 non-CAD controls (aged 59.13 ± 10.51 years), were enrolled into the study. The genotypes were determined using a custom-by-design 48-Plex SNPscanTM Kit. The results showed that the BCL2 rs17757541 C>G polymorphism was associated with increased risk of CAD in homozygote comparison and recessive genetic model. However, no association between the other fifteen SNPs and CAD risk was observed. Stratified analyses indicated a significantly increased risk of CAD associated with the BCL2 rs17757541 C>G polymorphism among males and younger patients. Therefore, the results indicated that there is a close correlation between the BCL2 rs17757541 C>G polymorphism and CAD, which suggests that this SNP site should be further studied as a potential biomarker for CAD.

[Strategy of selecting 16S rRNA hypervariable regions for metagenome-phylogenetic marker genes based analysis].

The advent of next generation sequencing technology enables parallel analysis of the whole microbial community from multiple samples. Particularly, sequencing 16S rRNA hypervariable tags has become the most efficient and cost-effective method for assessing microbial diversity. Due to its short read length of the 2nd-generation sequencing methods that cannot cover the full 16S rRNA genomic region, specific hypervariable regions or V-regions must be selected to act as the proxy. Over the past decade, selection of V-regions has not been consistent in assessing microbial diversity. Here we evaluated the current strategies of selecting 16S rRNA hypervariable regions for surveying microbial diversity. The environmental condition was considered as one of the important factors for selection of 16S rRNA hypervariable regions. We suggested that a pilot study to test different V-regions is required in bacterial diversity studies based on 16S rRNA genes.

Association of polymorphisms of cytosine arabinoside-metabolizing enzyme gene with therapeutic efficacy for acute myeloid leukemia.

BACKGROUND: The cytosine arabinoside (Ara-C)-based chemotherapy is the major remedial measure for acute myeloid leukemia (AML). Deoxycytidine kinase (DCK) and cytidine deaminase (CDA) are the key enzymes in the metabolism of Ara-C. Many single nucleotide polymorphisms (SNPs) and haplotypes of DCK and CDA, which contribute to susceptibility to Ara-C, have been identified in Africans and Europeans. However, there has been no report about the relation among three SNPs in DCK (rs115543896, rs72552079, and rs111454937) and two SNPs in CDA (rs2072671 and rs60369023), and their clinical response to Ara-C for a Chinese population. In this study, we aimed to investigate whether these five SNPs are associated with the therapeutic outcomes of Ara-C-based chemotherapy regimens in patients with AML. METHODS: A total of 151 Chinese patients with AML were enrolled in our study. SNPs genotyping were performed using the MassARRAY system by means of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) method. RESULTS: The results illustrated that DCKrs111454937 AA genotype was more frequent in patients with higher platelet count, and A allele frequency was significantly higher in the group £40 years, lower white blood cell (WBC) count patients group and the group with platelet counts > 60'10(9)/L. Meanwhile, both DCKrs72552079 TC (OR = 1.225, 95%CI = 1.225 - 9.851, P = 0.0192) and CDArs60369023 GA (OR = 9.851, 95%CI = 1.31 - 77.93, P = 0.0263) significantly improved Ara-C-based chemotherapy response. While DCKrs11554389 AA (OR = 0.147, 95%CI = 0.027 - 0.801, P = 0.0267) was associated with the decrease of Ara-C-based chemotherapy response. CONCLUSION: It is evident that the DCK and CDA polymorphisms might be the important markers for the AML patients' therapy outcomes in a Chinese population.

Polymorphisms of dihydropyrimidine dehydrogenase gene and clinical outcomes of gastric cancer patients treated with fluorouracil-based adjuvant chemotherapy in Chinese population.

BACKGROUND: Dihydropyrimidine dehydrogenase (DPD), a key enzyme involved in the catabolism of 5-fluorouracil (5-FU), is the attractive candidate for pharmacogenetic research on efficacies and toxicities of 5-FU. The aim of this study is to explore the association between polymorphisms of dihydropyrimidine dehydrogenase gene (DPYD) and clinical outcomes of gastric cancer patients treated with fluorouracil-based adjuvant chemotherapy in the Chinese population. METHODS: Three hundred and sixty-two patients with gastric cancer in the Chinese population were treated with fluorouracil-based adjuvant chemotherapy. The single nucleotide polymorphic genotypes of DPYD were determined by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) using DNA samples isolated from peripheral blood collected before treatment. RESULTS: The average response rate for chemotherapy was 46.7%. A significantly different distribution of the rs1801159 (c2=8.76, P=0.012) genotypes was observed. Homozygous genotype rs1801159A/A was over-represented in responsive patients. Conversely, carriers of the rs1801159A/G genotype were prevalent in non-responsive patients. In the haplotype association analysis, there was significant difference in global haplotype distribution between the groups (c2=3.96, P=0.0465). CONCLUSIONS: These results suggest that polymorphisms of rs1801159 in DPYD may be used as valuable predictors of the response to fluorouracil-based chemotherapy for gastric cancer patients in the Chinese population. Well-designed, comprehensive, and prospective studies on determining these polymorphisms of DPYD as predictive markers for gastric cancer in response to fluorouracil-based therapies are warranted.

Association of mitochondrial haplogroup D and risk of esophageal cancer in Taihang Mountain and Chaoshan areas in China.

Both the Taihang Mountain area in north-central China and Chaoshan area in the southeastern littoral of China are areas with high risk of esophageal cancer (EC). Our previous study confirmed that populations from the two areas might share similar matrilineal backgrounds and found that mitochondrial DNA (mtDNA) haplogroup D, especially subhaplogroups D4a and D5a, might be genetic background markers of EC in Chaoshan area. Here, to further determine whether D4a, D5a, and D might be susceptibility markers for EC in the two high-risk areas, we performed a case-control study with larger samples and analyzed the distributions of these three haplogroups in subjects (controls [n = 898] and patients [n = 768]) from the two areas. D4a haplogroup was significantly associated with increased risk of EC in Taihang Mountain subjects, especially women. D5 haplogroup was associated with EC at the general population level in the Taihang Mountain area and in subjects ≤ 60 years, especially women ≤ 60 years, in the Chaoshan area. D haplogroup was associated with EC only in subjects ≤ 60 years, especially men ≤ 60 years, in the Chaoshan area. D4a and D5 showing positive association with EC in the Taihang Mountain area became the predominant subhaplogroups of D in Chaoshan controls. In conclusion, D, D4a, and D5 haplogroups might be susceptibility markers for EC in the two high-risk areas in China, particularly D4a and D5 for the Taihang Mountain area and D and D5 for the Chaoshan area.

[Characterization of reaction kinetics between ligand and receptor on the solid and liquid interface based on optical waveguide lightmode spectroscopy].

The present paper describes the use of optical waveguide lightmode spectroscopy (OWLS) for study of the binding interaction of the vascular endothelial growth factor (VGEF) with VEGF receptor 2 (VEGFR2). VEGF were immobilized in the surface of an 3-amino 3-propyltriethoxy silane (APTES) modified sensor chip. The solutions with different concentration of VEGFR2 were injected to the system to investigate the kinetic character with OWLS on the solid and liquid interface. The receptor binding and dissociation on the interface, quantified by association and dissociation rate coefficients ka and kd, were determined by the OWLS experiments. The k(a) and k(d) is 6.86 x 10(5) L x mol(-1) x s(-1) and 1.15 x 10(-3) s(-1), respectively. The results show that OWLS method could meet the requirement of kinetic determination of ligand--receptor interaction in applications for related fundamental research and pharmaceutical development.

Application of nanofiber-packed SPE for determination of salivary-free cortisol using fluorescence precolumn derivatization and HPLC detection.

Salivary cortisol has emerged as an easy-to-collect biologic marker of stress in many researches. In this study, we present a method for the determination of salivary-free cortisol using HPLC method with fluorescence precolumn derivatization, which is based on a novel extraction from the strongly acidic medium (fluorescent derivatives of cortisol in sulfuric acid medium) by electrospun polystyrene nanofibers packed SPE. For high-throughput sample extraction, an array pretreatment device based on nanofibers packed SPE micro-column was designed. The LOD of cortisol was 0.01 microg/L (S/N=3). The RSDs (n=6) for all analytes were below 8.0%, and the recoveries were 110, 102.4, and 99.4% (n=3) for saliva spiked with 0.1, 10, and 20 microg/L of cortisol, respectively. The proposed method was then successfully applied in the determination of free cortisol in human saliva. The salivary cortisol concentrations in the real samples ranged from 0.22 to 7.45 microg/L. The nanofiber-packed SPE overcame the low extraction recovery and bad clean-up effect of the conventional methods, and increased the sensitivity and selectivity of the method.

[Electrochemical detection of toxin gene in Listeria monocytogenes].

Listeria monocytogenes (LM) is a food-borne pathogen inducing listeriosis, an illness characterized by encephalitis, septicaemia, and meningitis. Listeriolysin O (LLO) is absolutely required for virulence by L. monocytogenes, and is found only in virulent strains of the species. One of the best ways to detect and confirm the pathogen is detection of one of the virulence factors, LLO, produced by the microorganism. This paper focused on the electrical method used to detect the LLO toxin gene in food products and organism without labeling the target DNA. The electrochemical sensor was obtained by immobilizing single-stranded oligonucleotides onto the gold electrode with the mercaptan activated by N-hydroxysulfosuccinimide (NHS) and N-(3-dimethylamion)propyl-N'-ethyl carbodiimidehydrochloride (EDC). The hy-bridization reaction that occurred on the electrode surface was evidenced by Cyclic Voltammetry (CV) analysis using [Co(phen)3](ClO4)3 as an indicator. The covalently immobilized single-stranded DNA could selectively hybridize to its complementary DNA in solution to form double-stranded DNA on the gold surface. A significant increase of the peak cur-rent of Cyclic Voltammetry (CV) upon hybridization of immobilized ssDNA with PCR amplification products in the solu-tion was observed. This peak current change was used to monitor the amount of PCR amplification products. Factors deter-mining the sensitivity of the electrochemical assay, such as DNA target concentration and hybridization conditions, were investigated. The coupling of DNA to the electrochemical sensors has the potential of the quantitative evaluation of gene.

[Genomic analysis of DNA-protein interaction by chromatin immunoprecipitation].

Chromatin immunoprecipitation (ChIP) is an effective technique to analyze the interactions of DNA binding proteins with the genome in vivo. ChIP coupled with high density microarray (ChIP-chip) or high-throughput sequencing (ChIP-Seq) has generated large amount of data and expected to allow the development of a network describing the cellular transcriptional regulation. Here, we reviewed the ChIP, ChIP-chip, and ChIP-Seq techniques as well as their perspectives. Focus is given to data analysis of ChIP-Seq and the applications of ChIP-chip and ChIP-Seq.

XPC Lys939Gln polymorphism is associated with the decreased response to platinum based chemotherapy in advanced non-small-cell lung cancer.

BACKGROUND: Platinum-based chemotherapeutics are the most common regimens for advanced non-small-cell lung cancer (NSCLC) patients, and genetic factors are thought to represent important determinants of drug efficacy. We prospectively assessed the status of the XPC Ala499Val and Lys939Gln gene polymorphisms and investigated whether these SNPs can predict the response to cisplatin/carboplatin-based regimens in advanced NSCLC patients in a Chinese population. METHODS: The treatment outcomes of 96 advanced NSCLC patients who were treated with platinum-based chemotherapy were evaluated. The polymorphic status of xeroderma pigmentosum group C (XPC) gene was genotyped by the 3-D polyacrylamide gel-based DNA microarray method. RESULTS: The distributions of XPC Lys939Gln genotypes differed significantly between the response group (complete + partial responses) and the non-response group (stable + progressive disease; P = 0.022). The heterozygous A/C genotype carriers had a poorer response rate than the wild A/A genotype carriers in stage III (OR, 0.074; 95%CI, 0.008 - 0.704; P = 0.023). The XPC Ala499Val polymorphisms were not associated with response to platinum-based chemotherapy. CONCLUSION: Polymorphisms of the XPC gene, Lys939Gln, may be a predictive marker of treatment response for advanced NSCLC patients in stage III.

[Detection of single nucleotide polymorphisms of Jak2 gene in multiple myeloma by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry].

This study was purposed to investigate the practicality of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) for detection of single nucleotide polymorphisms (SNP) on jak2 gene in multiple myeloma (MM) cells. The DNA fragment containing 2 SNPs of jak2 (C428T and C643T) was amplified using PCR and was purified. The purified product was used as the template for primer extension (PEX). The small products of allele-specific reaction were purified, the SNPs on jak2 gene of 5 patients with MM and 5 healthy persons were detected by MALDI-TOF MS. The results showed that the distribution of genotype C428T and C643T was not different between MM patients and healthy persons, both of which are homozygous T/T. In conclusion, the method based on MALDI-TOF MS and PEX technique for detecting SNP in jak2 gene is rapid, accurate and reliable method, and can be used in clinical practice.

Correlation of the SNPs of FGFR1, FGF10, FGF18 with nonsyndromic cleft lip with or without palate in Chinese population.

OBJECTIVE: To explore the relationship between the polymorphisms in gene FGFR1, FGF10, FGF18 and the nonsyndromic cleft lip with or without cleft palate (NS CLP) in Chinese population. METHODS: Genomic DNA was isolated from peripheral lymphocytes of 75 patients with NS CLP and their parents and 75 unimpaired healthy children. The polymorphisms in FGFR1 gene rs13317, p.E467K, p.M369I and p.S393S, FGF10 gene rs1448037 and FGF18 gene rs4043716 were detected by applying three-dimensional (3-D) polyacrylamide gel microarray technology. The data were performed using statistical analysis: the genotype frequency and allele frequency between patients with NSCL/P and control subjects were performed. Haplotype relative risk (HRR), family based association test (FBAT), and transmission disequilibrium test (TDT) in nuclear family were performed. RESULTS: There were no polymorphism in FGFR1 gene p. E467K, p. M369I and p.S393S site, the corresponding base was all G. The polymorphisms of rs13317 and rs1448037 were detected and their genotype frequency and allele frequency showed no significant difference between 75 patients with NSCL/P and 75 normal children. TDT, HRR and FBAT were also no significant differences. The genotype frequency of gene FGF18 rs4043716 showed significant difference, but allele frequency were no significant difference. TDT, HRR and FBAT were also no significant difference. CONCLUSION: Our studies suggest an association between gene FGF18 rs4043716 and the NS CLP in Chinese population, and no association among gene FGFR1 rs13317, p. E467K, p. M369I, p. S393S and gene FGF10 rs1448037.

[Study on the genotyping of single nucleotide polymorphisms for a large number of samples by three-dimensional polyacrylamide gel-based microarray method].

OBJECTIVE: To genotype single nucleotide polymorphisms (SNPs) in a large number of samples by applying three-dimensional polyacrylamide gel-based microarray. METHODS: The method relies on copolymerization of acrylamide-modified PCR products with acrylamide monomers and acryl-modified slides to prepare gel-based microarray. Then array is hybridized with a pair of specific probes and the two universal dual-color fluorescent detectors labeled with Cy3 or Cy5 respectively (Tag1 and Tag2). Electrophoresis is used in post-hybridization to remove the nonspecifically bound targets and mismatches. Finally, genotyping is based on the images captured through two-color fluorescent scanning. RESULTS: The 3-D gel-immobilization of nucleic acids has a high immobilization yield and good hybridization efficiency. As universal dual-color fluorescent detectors are used, it is not required that specific probes be labeled for all SNPs, therefore the expense for synthesis can be reduced considerably. Electrophoresis in post-hybridization can enhance the capability for discriminating a single nucleotide mismatch from the perfectly matched sequence and improve the signal-to-noise ratio significantly. CONCLUSION: The gel-based microarray is a rapid, simple and high-throughput method for SNPs genotyping and may be very competitive in the efficiency, fidelity and cost for constructing DNA microarrays, which will hold significant promise for applications in human DNA diagnostics.

Gel-pad microarrays templated by patterned porous silicon for dual-mode detection of proteins.

A proof-of-concept study demonstrated the feasibility of a novel gel-pad microarray on porous silicon chips, by initiation of an atom transfer radical propagation (ATRP) polymerisation of (polyethylene glycol) methacrylate (PEGMA) with surface Si-H species, stepwise chemical conversions of the gel membrane to an NTA-Ni2+/histidine-tagged protein system, and matrix-assisted laser desorption/ionisation mass spectroscopy (MALDI MS) and fluorescence detections.

Probing DNA hybridization efficiency and single base mismatch by X-ray photoelectron spectroscopy.

We demonstrated the use of X-ray photoelectron spectroscopy (XPS) to study DNA hybridization. Target DNA labeled with hexachloro-fluorescein (HEX) was hybridized to DNA arrays with four different probes. Each probe dot of the hybridized arrays was detected with XPS. The XPS Cl2p peak areas were found to decrease with an increase in mismatched bases in DNA probes. The Cl2p core-level peak area ratio of a probe perfectly matched to one, two and three base-mismatched probes accorded well with the results of conventional fluorescent imaging, which shows that XPS is a potential tool for analyzing DNA arrays. The DNA arrays' hybridization efficiency was assessed by the molar ratio of chlorine to phosphorus in a DNA strand, which was determined from the relevant XPS Cl2p and P2p core-level peak areas after hybridization. This could provide a new method to detect DNA hybridization efficiency.