Determination of DNA Methylation and Hydroxymethylation Levels in Biological Samples by Field-Amplified Sample Injection-Capillary Zone Electrophoresis with UV Detection

In this study, a method of field-amplified sample injection coupled with capillary zone electrophoresis with ultraviolet detection was established for evaluation of DNA methylation and hydroxymethylation levels in biological materials. By modifying an existing method, the separation of cytosine (C), 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) was performed on an uncoated capillary column (40 cm × 75 μm I.D.) using 300 mmol L⁻¹ tris solution (pH 2.90) as running buffer and detected at 280 nm. The detection limits (S/N = 3) of the method were 0.004 ng mL⁻¹ for cytosine (C), 0.01 ng mL⁻¹ for 5-methylcytosine (5-mC), and 0.02 ng mL⁻¹ for 5-hydroxymethylcytosine (5-hmC). The proposed method has been successfully applied to the evaluation of DNA methylation and hydroxymethylation levels of blood samples from 15 hepatocellular carcinoma patients and 5 liver cirrhosis patients and liver tissues from 50 pairs of tumor and matched tumor-adjacent samples.

     

Determination of global DNA methylation level by capillary electrophoresis using octyl-modified quaternized cellulose as an electrolyte additive

A new cellulose derivative, octyl-modified quaternized cellulose (OMQC), was synthesized and used as electrolyte additive for the analysis of 5-methylcytosine by capillary electrophoresis with UV detection. While added in the background electrolyte, OMQC carrying octyl groups and quaternary ammonium groups exhibited dynamic coating ability. Capillary coated with OMQC was able to generate a stable anodal electro-osmotic flow even at pH 12.0. After several running conditions were optimized, a new method for quantification of genomic methylation level was developed on the basis of hydrolysis of DNA by formic acid and separation of nucleic acid bases by capillary electrophoresis. Cytosine and 5-methylcytosine were separated with a resolution near 4.0 in less than 10 min. The detection limits (S/N?=?3) were 1.1 and 1.5 μg/mL for cytosine and 5-methylcytosine, respectively.     

Rapid quantification of DNA methylation by high performance capillary electrophoresis

The actual methods to evaluate total DNA methylation based on high performance liquid chromatography (HPLC) are long and tedious due to the specific running buffers required. In this work, a new open-tube capillary electrophoresis system has been applied to the separation of acid hydrolyzed genomic DNA and so, to the evaluation of genomic DNA methylation. Several running conditions were tested but separation of cytosine and 5-methyl-cytosine was only possible by sodium dodecyl sulfate (SDS) micelle system. The importance of sample dissolution preparation has also been demonstrated. The results of this study open up the possibility of quantification of the relative methylation degree of rapid genomic DNA by a simple method based on high performance capillary electrophoresis (HPCE).     

亲水作用色谱法测定组织中全基因组DNA甲基化水平

建立了亲水作用色谱(HILIC)测定组织中全基因组DNA甲基化水平的方法。采用苯酚-氯仿提取组织中的DNA,提取的DNA用88%甲酸在140 ℃下裂解,经N2吹干后,加乙腈-水(9:1, v/v)溶解,用Waters BEH HILIC柱进行分离,在277 nm波长下检测胞嘧啶(Cyt)及5-甲基胞嘧啶(5-mCyt)含量。结果表明,以乙腈-10 mmol/L甲酸铵溶液(94:6, v/v)为流动相,流速为0.5 mL/min, Cyt与5-mCyt分离较好,保留时间分别为2.6与3.1 min。胞嘧啶的线性范围为1～900 μmol/L,相关系数为0.9999; 5-甲基胞嘧啶的线性范围为1～64 μmol/L,相关系数为0.9998。胞嘧啶和5-甲基胞嘧啶的检出限为54 nmol/L(柱中为0.54 pmol),定量限为250 nmol/L(柱中为2.5 pmol);在5～900 μmol/L的添加水平下,胞嘧啶和5-甲基胞嘧啶的平均加标回收率为94.7%～100.5%,相对标准偏差小于1.48%。用该方法检测了结肠癌组织中DNA甲基化水平,结果显示该癌组织中全基因组的DNA甲基化均值为4.0%。该方法快速、简单,稳定性好,灵敏度较高,能满足全基因组DNA甲基化的检测要求。     

Rapid quantification of total genomic DNA methylation degree by short-end injection capillary zone electrophoresis

We propose a new capillary zone electrophoresis method applying short-end injection technique for the fast evaluation of methylcystosine/total cytosine ratio after acidic DNA hydrolysis. By short-end injection and by using a 100 mmol/l Tris solution titrated with 1 mol/l phosphoric acid to pH 3.75 as background electrolyte, cytosine and methylcytosine were separated with a good resolution in less than 1.5 min. Stepwise multiple linear regression with DNA methylation degree as the dependent variable and age, cysteine, homocysteine and methionine as independent variables, showed a negative association with age and that total cysteine is the most important determinant of DNA methylation.     

Electrochemical detection of DNA methylation using a glassy carbon electrode modified with a composite made from carbon nanotubes and β-cyclodextrin

We describe a method for detecting DNA methylation. It is based on direct oxidation of DNA bases at a glassy carbon electrode (GCE) modified with film of a multiwalled carbon nanotube-β-cyclodextrin composite. This nano-structured film causes a strong enhancement on the oxidation current of DNA bases due to its large effective surface area and extraordinary electronic properties. Well-defined peaks were obtained as a result of electro-oxidation of guanine (at 0.67 V), adenine (at 0.92 V), thymine (at 1.11 V), cytosine (at 1.26 V), and 5-methylcytosine (at 1.13 V; all data vs. saturated calomel electrode (SCE)). The potential difference between 5-methylcytosine and cytosine (130 mV) is large enough to enable reliable simultaneous determination and analysis. The interference by thymine can be eliminated by following the principle of complementary pairing between purine and pyrimidine bases in DNA. The modified electrode was successfully applied to the evaluation of 5-methylcytosine in a fish sperm DNA, the methylation level of cytosine was found to be 7.47 %, and the analysis process took less than 1 h.     

A simple colorimetric detection of DNA methylation

In this work, we describe a simple colorimetric method to detect DNA methylation. Adenomatous polyposis coli (APC) with a small CpG region containing methylated cytosine (methylated APC) was synthesized and tested. Methylated APC was first captured and enriched by anti-5-methylcytosine monoclonal antibody conjugated magnetic microspheres (MMPs). Then a probe partly complementary to the APC sequence was added, resulting in the formation of DNA duplexes. The microsphere-captured probe was then released by heat denaturation and added into unmodified gold nanoparticle (AuNP) solution. Colorimetric detection was performed by salt-induced aggregation. The limit of detection is 80 fmol. Semi-quantitative analysis was done with a UV/Vis spectrophotometer by recording the absorbance of AuNP solution at 520 nm. Thus, this method provides a simple, rapid and quantitative tool for DNA methylation detection.     

Trace level determination of substance P using capillary electrophoresis and laser-induced fluorescence

An analytical method was developed to determine the undecapetide substance P (SP) based on capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. SP was derivatized with the fluorogenic reagent 2,3-naphthalenedicarboxaldehyde (NDA) prior to injection into the CE-LIF system. The pre-column derivatization scheme combined with injection enhancement techniques extends the detectability of SP to the subnanomolar level. Limit of detection (LOD) of 100 pM was achieved without pre-concentrating the sample prior to injection. The reproducibility for six different preparations of a standard sample containing 5 nM of SP was 6.8% RSD and that of the CE migration time was 0.08% RSD. The method was used to determine SP in a saliva sample.     

Determination of 5-methyl-cytosine and cytosine in tumor DNA of cancer patients

The determination of the relative methylation in DNA tumor samples, in order to evaluate the activity of some anti-cancer drugs, has become a very important issue in the clinical field. Capillary electrophoresis (CE) applications in this area have been done previously but no good separation for model samples or tumor samples has been reported. In this work, the CE conditions have been optimized in order to obtain baseline separation and efficient peaks for cytosine and 5-methylcytosine in both, standard mixtures and actual tumor samples; other bases (adenine, uracil, guanine, and thymine) have also been integrated in the optimization studies. More efficient peaks and shorter analysis time compared with the already reported conditions have been obtained employing a fused-silica capillary (75 microm inner diameter) of 44.5 cm effective length, 20 mM carbonate buffer (pH 9.6) plus 80 mM sodium dodecyl sulfate, a separation voltage of 20 kV, and detection at 223 nm.     

Separation of purine and pyrimidine bases by ion chromatography with direct conductivity detection

A simple, rapid and accurate method for the simultaneous determination of four purine and pyrimidine bases (cytosine, 5-methylcytosine, adenine and N6-methyladenine) has been developed. The quantitative determination of these bases was accomplished by ion chromatography (IC) with direct conductivity detection (CD) based on their ionization in acidic medium without chemical suppression. The recovery of cytosine, 5-methylcytosine, and adenine in calf thymus DNA was more than 98% (n=3) and the relative standard deviation (RSD, n=5) less than 2.4%. In a single chromatographic run, the four bases could be separated and determined in less than 10 min. The detection limits were found to be 0.05 microg/mL for cytosine, 0.08 microg/mL for 5-methylcytosine, 0.07 microg/mL for adenine, and 0.07 microg/mL for N6-methyladenine. Linear ranges were 0.2-95.1 microg/mL for cytosine (r2=0.9996), 0.3-196.6 microg/mL for 5-methylcytosine (r2=0.9994), 0.3-105.5 microg/mL for adenine (r2=0.9998), and 0.3-159.1 microg/mL for N6-methyladenine (r2=0.9999). With the proposed method, purine and pyrimidine bases could be successfully detected in calf thymus DNA. We also determined these bases in calf thymus DNA using RP-HPLC. Compared to RP-HPLC, the IC method offers advantages such as high selectivity and simple mobile phase.     

5-Hydroxymethylcytosine-selective oxidation with peroxotungstate

Tungsten oxidation worked as a simple chemical reaction for the effective detection of 5-hydroxymethylcytosine in DNA, distinguishing it from its epigenetic precursors, 5-methylcytosine and unmethylated cytosine. The tungsten-oxidation product obtained from 5-hydroxymethylcytosine was trihydroxylated thymine and was detected as a cleavage band in gel electrophoresis after treatment with hot piperidine.     

液相色谱-串联质谱分析组织中基因组脱氧核糖核酸羟甲基胞嘧啶水平

5-羟甲基胞嘧啶通过阻止脱氧核糖核酸(DNA)甲基化转移酶1(DMNT1)甲基化胞嘧啶来影响DNA甲基化的程度。本文建立了液相色谱-串联质谱(LC-MS/MS)测定组织中全基因组5-羟甲基胞嘧啶水平的方法。采用苯酚-氯仿提取组织DNA,提取的DNA用88%甲酸在140 ℃下裂解,DNA裂解液加入同位素胞嘧啶作内标,经N2吹干后,加乙腈-水(9:1, v/v)溶解,用LC-MS/MS检测5-羟甲基胞嘧啶的含量,并计算全基因组中5-羟甲基胞嘧啶的水平。结果表明,5-羟甲基胞嘧啶的线性范围为0.1～30 ng/mL,相关系数为0.9969,检出限(信噪比为3计)和定量限(信噪比为10计)分别为0.057 ng/mL和0.090 ng/mL;日内相对标准偏差和日间相对标准偏差分别为5.13%和6.24%;加标回收率为90.24%～97.53%。用该方法检测了大鼠大脑组织DNA羟甲基化水平,平均结果为0.66%。该方法简便,重现性好,灵敏度较高,能满足全基因组5-羟甲基胞嘧啶定量检测的要求。     

Measurement of carnosine, homocarnosine and anserine by FASI capillary electrophoresis UV detection: applications on biological samples

A field amplified sample injection (FASI) capillary electrophoresis method with UV detection was developed for the separation and detection of carnosine-related peptides carnosine (Car), anserine (Ans) and homocarnosine (Hcar). The imidazole dipeptides were baseline-separated within 10 min by using 50 mmol/L Tris phosphate pH 2.2 as running buffer. The samples were diluted in water and directly injected on the capillary without complex cleanup and/or sample derivatization procedures. Using the electrokinetic injection, a sensitivity improvement of about 500-fold was achieved without any loss of separation efficiency if compared to the conventional sample injection. The detection limits for carnosine, anserine, and homocarnosine were between 0.4 and 0.5 nmol/L, thus improving of 10-100-fold the LOD of previous described methods based on laser induced fluorescence or chemiluminescence detection. This method has been applied to the analysis of homogenized rat tissue (heart, muscle and brain) and human cerebrospinal fluid (CSF).     

Preparation of a Hyper‐cross‐linked Polymer Monolithic Column and Its Application to the Sensitive Determination of Genomic DNA Methylation

A hyper‐cross‐linked polymer monolithic column, poly(methacrylatoethyl trimethyl ammonium‐co‐vinylbenzene chloride‐co‐divinylbenzene) (MATE‐co‐VBC‐co‐DVB) with phenyl and quaternary ammonium groups was successfully prepared in the current study. The prepared monolith possesses large specific surface area, narrow mesopore size distribution and high column efficiency. The poly(MATE‐co‐VBC‐co‐DVB) monolithic column was demonstrated to have strong anion exchange/reversed‐phase (SAX/RP) mixed‐mode retention for analytes on capillary liquid chromatography (cLC). By using this monolithic column, we developed a rapid and sensitive method for the detection of DNA methylation. Our results showed that six nucleobases (adenine, guanine, cytosine, thymine, uracil, and 5‐methylcytosine (5‐mC)) can be baseline separated within 15 min by electrostatic repulsion and hydrophobic interactions between nucleobases and the monolithic stationary phase. The limit of detection (LOD, signal/noise=3) of 5‐mC is 0.014 pmol and endogenous 5‐mC can be distinctly detected by using only 10 ng genomic DNA, which is comparable to that obtained by mass spectrometry analysis. Furthermore, by using the method developed here, we found that DNA methylation inhibitor 5‐azacytidine (5‐aza‐C) and 5‐aza‐2′‐deoxycytidine (5‐aza‐CdR) could induce a significant decrease of genome‐wide DNA methylation in human lung carcinoma cells (A549) and cervical carcinoma cells (HeLa).     

Photocurrent response after enzymatic treatment of DNA duplexes immobilized on gold electrodes: electrochemical discrimination of 5-methylcytosine modification in DNA

We demonstrate a photoelectrochemical approach to the detection of the methylation status of cytosine bases in DNA. We prepared anthraquinone (AQ) photosensitizer-tethered oligodeoxynucleotide (ODN) duplexes bearing 5-methylcytosine (mC) or the corresponding cytosine (C) at a restriction site of the ODN strand immobilized on gold electrodes, and measured their photocurrent responses arising from hole transport after enzymatic digestion. Treatment with HapII or HhaI of the duplexes bearing normal C led to strand cleavage, and the photosensitizer unit was eliminated from the ODN strand immobilized on the gold electrode, exclusively reducing the photocurrent density. With a similar treatment, the duplexes bearing mC showed higher photocurrent responses arising from hole transport through the duplex. This significant difference in the photocurrent response between mC and normal C residues in DNA on the gold electrodes is potentially applicable to the detection of mC modification in DNA.     

On-line stacking techniques for the nonaqueous capillary electrophoretic determination of acrylamide in processed food

In the present study, field amplified sample stacking (FASS) techniques in the nonaqueous capillary electrophoresis method (NACE) were introduced for the on-line concentration of the acrylamide to improve acrylamide detection at 210 nm by diode-array detection. Acetonitrile (ACN) as a nonaqueous solvent permits acrylamide to be protonated through the change of its acid-base chemistry, allowing capillary electrophoretic separation of this compound. Choosing 30 mmol L(-1) HClO(4), 20 mmol L(-1) NaClO(4), 218 mmol L(-1) CH(3)COOH in ACN as the separation electrolyte and employing sample stacking methods, the LOD value of acrylamide was decreased to 2.6 ng mL(-1) with electrokinetic injection and 4.4 ng mL(-1) with hydrodynamic injection. Optimized stacking conditions were applied to the determination of acrylamide in several foodstuffs. The method is simple, rapid, inexpensive, and widely applicable for the determination of acrylamide in food samples.     

Determination of purine and pyrimidine bases in DNA by micellar electrokinetic capillary chromatography with electrochemical detection

A method based on micellar electrokinetic capillary chromatography with electrochemical detection was developed for the determination of cytosine, 5-methylcytosine (5-MC), thymine, adenine, and guanine in the hydrolysates of DNA. The working electrode was fabricated in a novel self-positioning carbon disc electrode system that can align the capillary outlet with the working electrode without a three-dimensional micromanipulator. The five analytes could be well separated within 10 min in a 40 cm length capillary at a separation voltage of 9 kV in a 40 mmol/l borate buffer (pH 10.0) containing 100 mmol/l sodium dodecyl sulfate. Good linearity was observed between peak current and concentration of bases over three orders of magnitude with the detection limits (SIN=3) ranging from 1.28 x 10(-6) to 5.02 x 10(-6) mol/l. This proposed method demonstrated long-term stability and reproducibility with relative standard deviations of less than 5% for both migration time and peak current (n=7). It has been successfully applied to determine bases including 5-MC in the hydrolysates of fish sperm DNA, calf thymus DNA, and DNA isolated from spleen cells of female mice.     

液相色谱-串联质谱法同时测定生物组织全基因组DNA甲基化和羟甲基化水平

测定全基因组DNA甲基化和羟甲基化水平对于研究环境污染物暴露的影响及致病机理具有重要的作用。本文建立了液相色谱-串联质谱（LC-MS/MS）同时测定动物组织中全基因组DNA甲基化和羟甲基化水平的方法。从动物组织样品中提取DNA,并将其酶解成单核苷,利用液相色谱-串联质谱法测定5-甲基胞嘧啶核苷、5-羟甲基胞嘧啶核苷和鸟嘌呤核苷的含量,计算全基因组DNA甲基化率和羟甲基化率。利用该方法研究了砷暴露对大鼠肝脏和小脑全基因组DNA甲基化和羟甲基化水平的影响,得到了砷影响DNA甲基化及羟甲基化的初步数据。该方法具有良好的重现性、灵敏度和稳定性,可以同时检测差异较大的DNA甲基化和羟甲基化水平。为同时研究DNA甲基化和羟甲基化水平提供了有力的支持。     

Quantitative analysis of DNA methylation in chronic lymphocytic leukemia patients

Changes in the genomic DNA methylation level have been found to be closely associated with tumorigenesis. In order to analyze the relation of aberrant DNA methylation to clinical and biological risk factors, we have determined the cytosine methylation level of 81 patients diagnosed with chronic lymphocytic leukemia (CLL). The analysis was based on DNA hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with BODIPY FL EDA. Derivatives were separated by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. We analyzed potential correlations between DNA methylation levels and numerous patient parameters, including clinical observations and biological data. As a result, we observed a significant correlation with the immunoglobulin variable heavy chain gene (VH) mutation status. This factor has been repeatedly proposed as a reliable prognostic marker for CLL, which suggests that the methylation level might be a valuable factor in determining the prognostic outcome of CLL. We are now in the process of refining our method to broaden its application potential. In this context, we show here that the oxidation of the fluorescence marker in the samples and the evaporation of methanol in the electrolytes can be prevented by a film of paraffin oil. In summary, our results thus establish capillary electrophoresis as a valuable tool for analyzing the DNA methylation status of clinical samples.     

Stacking and quantitative analysis of lovastatin in urine samples by the transient moving chemical reaction boundary method in capillary electrophoresis

A simple, sensitive, and useful concentration method for lovastatin (Lvt) in urine has been developed based on the transient moving chemical reaction boundary method (tMCRBM) in capillary electrophoresis. The MCRB is formed with acidic sample buffer (Gly-HCl) and alkaline running buffer (Gly-NaOH). The following optimal conditions were determined for stacking and separation: electrophoretic buffer of 100 mM Gly- NaOH (pH 11.52), sample buffer of 20 mM Gly-HCl (pH 4.93), fused-silica capillary of 76 cm × 75-μm i.d (67 cm from detector), sample injection at 14 mbar for 3 min. A 21- to 26-fold increase in peak height was achieved for detection of Lvt in urine under the optimal conditions compared with normal capillary zone electrophoresis. By combining the sample pretreatment procedure with the stacking method, the sensitivity of Lvt in urine was increased by 105- to 130-fold. The limits of detection (LOD) and quantification (LOQ) for Lvt in urine were decreased to 8.8 ng/mL and 29.2 ng/mL, respectively. The intra-day and inter-day precision values (expressed as RSD) were 2.23–3.61% and 4.03–5.05%, respectively. The recoveries of the analyte at three concentration levels changed from 82.65 to 100.49%.