Meiling Lu

Binding of dimethylarsinous acid to Cys-13α of rat hemoglobin is responsible for the retention of arsenic in rat blood

The metabolism, disposition, and carcinogenicity of arsenic differ dramatically between humans and rats. To understand the molecular basis of these differences, we have characterized arsenic species in rats that were treated with inorganic arsenate (iAsV), monomethylarsonic acid (MMAV), or dimethylarsinic acid (DMAV) for up to 15 weeks. Arsenic significantly accumulated in the red blood cells (RBCs) of rats in the form of hemoglobin (Hb) complexed with dimethylarsinous acid (DMAIII), regardless of whether the rats were treated with iAsV, MMAV, or DMAV, suggesting rapid methylation of arsenic species followed by strong binding of DMAIII to rat Hb. The binding site for DMAIII was identified to be cysteine 13 in the alpha-chain of rat Hb with a stoichiometry of 1:1. Over 99% of the total arsenic (maximum 2.5-3.5 mM) in rat RBCs was bound to Hb for all rats examined (n = 138). In contrast, only 40-49% of the total arsenic (maximum approximately 10 muM) in rat plasma was bound to proteins. The ratios of the total arsenic in RBCs to that in plasma ranged from 88-423 for rats that were fed iAsV, 100-680 for rats that were fed MMAV, and 185-1393 for rats that were fed DMAV, when samples were obtained over the 15-week exposure duration. Previous studies have shown an increase in urothelial hyperplasia in rats fed DMAV. This is the first article reporting that treatment with iAsV in the drinking water also produces urothelial hyperplasia and at an even earlier time point than dietary DMAV. Dietary MMAV produced only a slight urothelial response. A correlation between the Hb-DMAIII complex and urothelial lesion severity in rats was observed. The lack of cysteine 13alpha in human Hb may be responsible for the shorter retention of arsenic in human blood. These differences in the disposition of arsenicals may contribute to the observed differences between humans and rats in susceptibility to arsenic carcinogenicity.

Dual modes of interaction between XRCC4 and polynucleotide kinase/phosphatase: implications for nonhomologous end joining.

XRCC4 plays a crucial role in the nonhomologous end joining (NHEJ) pathway of DNA double-strand break repair acting as a scaffold protein that recruits other NHEJ proteins to double-strand breaks. Phosphorylation of XRCC4 by protein kinase CK2 promotes a high affinity interaction with the forkhead-associated domain of the end-processing enzyme polynucleotide kinase/phosphatase (PNKP). Here we reveal that unphosphorylated XRCC4 also interacts with PNKP through a lower affinity interaction site within the catalytic domain and that this interaction stimulates the turnover of PNKP. Unexpectedly, CK2-phosphorylated XRCC4 inhibited PNKP activity. Moreover, the XRCC4·DNA ligase IV complex also stimulated PNKP enzyme turnover, and this effect was independent of the phosphorylation of XRCC4 at threonine 233. Our results reveal that CK2-mediated phosphorylation of XRCC4 can have different effects on PNKP activity, with implications for the roles of XRCC4 and PNKP in NHEJ.

Detection of Human Urinary 5-Hydroxymethylcytosine by Stable Isotope Dilution HPLC-MS/MS Analysis

The sixth DNA base 5-hydroxymethylcytosine (5hmC) is the major oxidation product of the epigenetic modification 5-methylcytosine (5mC), mediating DNA demethylation in mammals. Reduced 5hmC levels are found to be linked with various tumors and neurological diseases; therefore, 5hmC is an emerging biomarker for disease diagnosis, treatment, and prognosis. Due to its advantages of being sterile, easily accessible in large volumes, and noninvasive to patients, urine is a favored diagnostic biofluid for 5hmC analysis. Here we developed an accurate, sensitive, and specific assay for quantification of 5mC, 5hmC, and other DNA demethylation intermediates in human urine. The urinary samples were desalted and enriched using off-line solid-phase extraction, followed by stable isotope dilution HPLC-MS/MS analysis for 5hmC and 5mC. By the use of ammonium bicarbonate (NH4HCO3) as an additive to the mobile phase, we improved the online-coupled MS/MS detection of 5mC, 5hmC, and 5-formylcytosine (5fC) by 1.8-14.3 times. The recovery of the method is approximately 100% for 5hmC, and 70-90% for 5mC. The relative standard deviation (RSD) of the interday precision is about 2.9-10.6%, and that of the intraday precision is about 1.4-7.7%. By the analysis of 13 volunteers using the developed method, we for the first time demonstrate the presence of 5hmC in human urine. Unexpectedly, we observed that the level of 5hmC (22.6 ± 13.7 nmol/L) is comparable to that of its precursor 5mC (52.4 ± 50.2 nmol/L) in human urine. Since the abundance of 5hmC (as a rare DNA base) is 1 or 2 orders of magnitude lower than 5mC in genomic DNA, our finding probably implicates a much higher turnover of 5hmC than 5mC in mammalian genomic DNA and underscores the importance of DNA demethylation in daily life.

DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway

Localized DNA melting may provide a general strategy for recognition of the wide array of chemically and structurally diverse DNA lesions repaired by the nucleotide excision repair (NER) pathway. However, it is not clear what causes such DNA melting and how it is driven. Here, we show a DNA wrapping–melting model supported by results from dynamic monitoring of the key DNA–protein and protein–protein interactions involved in the early stages of the Escherichia coli NER process. Using an analytical technique involving capillary electrophoresis coupled with laser-induced fluorescence polarization, which combines a mobility shift assay with conformational analysis, we demonstrate that DNA wrapping around UvrB, mediated by UvrA, is an early event in the damage-recognition process during E. coli NER. DNA wrapping of UvrB was confirmed by Förster resonance energy transfer and fluorescence lifetime measurements. This wrapping did not occur with readily denaturable damaged DNA substrates (“bubble” DNA), suggesting that DNA wrapping of UvrB plays an important role in the induction of DNA melting around the damage site. Analysis of DNA wrapping of mutant UvrB Y96A further suggests that a cooperative interaction between DNA wrapping of UvrA2B and contact of the β-hairpin of UvrB with the bulky damage moiety may be involved in the local DNA melting at the damage site.

Quantum Dots Enhanced Ultrasensitive Detection of DNA Adducts

Here we demonstrate that quantum dots (QD) can greatly improve the ultrasensitive capillary electrophoresis-laser induced fluorescence immunoassay of trace anti-benzo(a)pyrene diol epoxide (BPDE)-DNA adducts from sensitivity to separation. We for the first time show that the target QD-antibody-DNA complex is not only effectively separated but also effectively focused by capillary electrophoresis. With the online laser-induced fluorescence detection coupled, the low limits of detection of 6.6 x 10(-21) mol in mass and 120 fM in concentration are achieved for BPDE-DNA adducts. The achieved ultrasensitivity allows for human exposure biomonitoring and shows promising applications of QD in various DNA analyses, including DNA damage.

Identification of reactive cysteines in a protein using arsenic labeling and collision-induced dissociation tandem mass spectrometry.

Trivalent arsenicals have high affinity for thiols (such as free cysteines) in proteins. We describe here the use of this property to develop a collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) technique for the identification of reactive cysteines in proteins. A trivalent arsenic species, dimethylarsinous acid (DMA (III)), with a residue mass (103.9607) and mass defect distinct from the normal 20 amino acids, was used to selectively label reactive cysteine residues in proteins. The CID fragment ions of the arsenic-labeled sequences shifted away from the more abundant normal fragments that would otherwise overlap with the ions of interest. Along with the internal and immonium ions, the arsenic-labeled fragment ions served as MS/MS signatures for identification of the binding sites and for assessment of the relative reactivity of individual cysteine residues in a protein. Using this method, we have identified two highly reactive binding sites in rat hemoglobin (Hb): Cys-13alpha and Cys-125beta. Cys-13alpha was bound to DMA (III) in the Hb of rats fed with arsenic, and this binding was responsible for arsenic accumulation in rat blood, while Cys-125beta was found to bind to glutathione in rat blood. This study revealed the relative reactivity of the cysteines in rat Hb in the following decreasing order: Cys-13alpha >> Cys-111alpha > Cys-104alpha and Cys-13alpha >> Cys-125beta > Cys-93beta. Arsenic-labeling is easy and fast for identification of active binding sites without enzymatic digestion and acid hydrolysis, and useful for characterization and identification of metal binding sites in other proteins.

Focusing and stabilization of bis-intercalating dye-DNA complexes for high-sensitive CE-LIF DNA analysis

Multiple labeling of nucleic acids by intercalative dyes is a promising method for ultrasensitive nucleic acid assays. The properties of the fast dissociation and instability of dye–DNA complexes may prevent from their wide applications in CE‐LIF nucleic acid analysis. Here, we describe an optimum CE focusing method by using appropriately paired sample and separation buffers, Tris‐glycine buffer and Tris‐glycine‐acetic acid buffer. The developed method was applied in both uncoated and polyacrylamide coated fused‐silica capillary‐based CE‐LIF analysis while the sample and separation buffers were conversely used. The complexes of intercalative dye benzoxazolium‐4‐pyridinium dimer and dsDNA were greatly focused (separation efficiency: 1.8 million theoretical plates per meter) by transient isotachophoresis mechanism in uncoated capillary, and moderately focused by transient isotachophoresis in combination of field amplified sample stacking and further stabilized by the paired buffer in polyacrylamide coated capillary. Based on the developed focusing strategy, an ultrasensitive DNA assay was developed for quantitation of calf thymus dsDNA (from 0.02 to 2.14 pM). By the use of an excitation laser power as low as 1 mW, the detection limits of calf thymus dsDNA (3.5 kb) are 7.9 fM in concentration and 2.4×10−22 mol (150 molecules) in mass. We further demonstrate that the non‐gel sieving CE‐LIF analysis of DNA fragments can be enhanced by the same strategy. Since the presented strategy can be applied to uncoated and coated capillaries and does not require special device, it is also reasonable to extend to the applications in chip‐based CE DNA analysis.

Microdialysis sampling method for evaluation of binding kinetics of small molecules to macromolecules

Here we present an application of microdialysis sampling for evaluation of the binding kinetics of small molecules to macromolecules. It is label-free, and no immobilization of any interaction partner is required. The method was established by the coupling of a binding reaction with a membrane transport in a miniature and dynamic microdialysis sampling system. A theoretical model was established to describe the quantitative relationship between the binding kinetics of small ligands to macromolecules and the enhanced mass transport of small ligands and was applied to estimate the binding kinetics. To demonstrate the proof-of-principle, we examined the binding kinetics of an abundant plasma protein human serum albumin (HSA) and a representative drug ketoprofen as an example. The primary binding constant of ketoprofen to HSA was estimated as 1.63 (+/-0.12) x 10(6) M(-1). The estimated association and dissociation rate constants (k1 and k(-1)) were about 3.71 x 10(5) M(-1) s(-1) and 0.227 s(-1), respectively. The results suggest a fast binding of ketoprofen to HSA and a fast dissociation of the formed complex, which are consistent with the reversible binding property of drug and HSA (k(-1) in the order of s(-1)). This is the first report on binding-kinetics measurement using microdialysis sampling.

Identification and characterization of cysteinyl exposure in proteins by selective mercury labeling and nano‐electrospray ionization quadrupole time‐of‐flight mass spectrometry

We describe a method for probing surface-exposed cysteines in proteins by selective labeling with p-hydroxymercuribenzoate (PMB) combined with nano-electrospray ionization mass spectrometric analysis (nanoESI-MS). The rapid, stoichiometric, and specific labeling by PMB of surface-exposed cysteines allows for characterization of the accessibility of the cysteines using a single MS analysis. Moreover, by taking advantage of the large mass shift of 321 Da, unique isotopic pattern, and enhanced MS signal of PMB-labeled cysteine-containing peptide fragments, the surface-exposed cysteines in proteins can be accurately identified by peptide mapping. The number and sites of reactive cysteines on the surface of human and rat hemoglobins (hHb and rHb) were identified as examples. Collision-induced dissociation tandem mass spectrometric (MS/MS) analysis of specific peptides further confirmed the selective labeling of PMB in hHb. The subtle difference between the different cysteine residues in rHb was also evaluated by multiple PMB titrations. The difference between the two cysteines in their environment may partially explain their reaction specificity. Cysteine 125 in the beta unit of rHb is exposed on the surface, explaining its reactivity with glutathione. Cysteine 13 in the alpha subunit of rHb is much less exposed, and is located in a hydrophobic pocket, a conclusion that is consistent with the previous observation of its selective binding with dimethylarsinous acid, a reactive arsenic metabolite. The method is potentially useful for probing cysteines in other biologically important proteins and for studying proteins that are associated with conformational or structural changes induced by denaturing processes, protein modifications, protein-protein interactions and protein assemblies.

Metal cation mediated-capillary electrophoresis of nucleic acids.

Nucleic acid electrophoresis separation heavily depends upon gel or nongel sieving matrix. Here we propose a metal ion mediated-capillary electrophoresis (MCE-CE) by utilizing the nonspecific interactions of Mg(2+) and Ca(2+) and demonstrate the size, conformation, or sequence based separation and characterization of versatile nucleic acid molecules in free solution. Mg(2+) and Ca(2+) can induce DNA separation at the concentrations as low as 100 and 50 muM, respectively. Noteworthy, the two naturally occurring polymorphisms of one base substitution that may change the secondary folding structure or base stacking can be discriminated by MCM-CE, showing its unique capability of resolving length-identical but conformation-different ssDNA. Benefiting from the achieved separation, we further demonstrate that the folding conformation of oligomers and its change caused by single base substitution can be promptly sensed by online coupled fluorescence polarization. We anticipate that this method will be applicable in length polymorphism analysis, single-strand polymorphism analysis, hybridization analysis, microRNA analysis, and study of protein-nucleic acid interactions and the conformation-function relationship.