Imidazolo‐dC Metal‐Mediated Base Pairs: Purine Nucleosides Capture Two Ag+ Ions and Form a Duplex with the Stability of a Covalent DNA Cross‐Link

8‐Phenylimidazolo‐dC (^phImidC, 2 ) forms metal‐mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent “purine” 2′‐deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6 . Owing to the ease of nucleobase deprotonation, the new Ag⁺‐mediated base pair containing a “purine” skeleton is much stronger than that derived from the pyrrolo‐ [3,4‐d]pyrimidine system (^phPyrdC, 1 ). The silver‐mediated ^phImidC–^phImidC base pair fits well into the DNA double helix and has the stability of a covalent cross‐link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.     

Base Pairing of 8‐Aza‐7‐deazapurine‐2,6‐diamine Linked via the N(8)‐Position to the DNA Backbone: Universal Base‐Pairing Properties and Formation of Highly Stable Duplexes when Alternating with dT

The unusually N⁸‐glycosylated pyrazolo[3,4‐d]pyrimidine‐4,6‐diamine 2′‐deoxyribonucleoside ( 3 ) was synthesized and converted to the phosphoramidite 11 . Oligonucleotides were prepared by solid‐phase synthesis, and the base pairing of compound 3 was studied. In non‐self‐complementary duplexes containing compound 3 located opposite to the four canonical DNA constituents, strong base pairs are formed that show ambiguous pairing properties. The self‐complementary duplex d( 3 ‐T)₆ ( 34 ⋅ 34 ) is significantly more stable than d(A‐T)₆.     

Genomic N(6)-methyladenine determination by MEKC with LIF

2′‐Deoxy‐N⁶‐methyladenosine (N⁶mdA) is frequently found in prokaryotic and unicellular eukaryotic genomes. Although methylated bases represent only a minor fraction of the genome, they, however, exhibit strong biological effects. Here, we report a fast and sensitive method for the quantification of global adenine methylation in DNA. The method is based on a recently developed procedure consisting of fluorescence labeling of deoxyribonucleotides with BODIPY FL EDA and analysis by CE with LIF. An oligodeoxyribonucleotide site specifically modified with N⁶mdA was used for peak assignment, to establish separation conditions and to determine the LOD. The method yielded a LOD for N⁶mdA of 280 pM (1.4 amol), which is equivalent to ～1 N⁶mdA per 10⁴ normal nucleotides (0.01%) using 1 μg of DNA as the matrix. After calibration with completely dam methylated λ DNA, the assay was applied to the analysis of various DNAs.     

Analysis of genomic methylation level using micellar electrokinetic chromatography with UV detection

Analytical methods for quantification of 5′‐methylcytosine in genomes are important tools to investigate epigenetic changes in gene expression during development, differentiation, aging, or cancer. Here, we report a novel genomic methylation content assay based on enzymatic hydrolysis of DNA and MEKC separation of 5′‐deoxyribonucleoside monophosphates (dNMP) using the cationic surfactant CTAB as pseudostationary phase. Calf Thymus DNA was used during method development to determine electrophoretic parameters and electrolyte composition for a complete separation between 2′‐deoxycytosine‐5′‐monophosphate and 2′‐deoxy‐5′‐methylcytosine 5′‐monophosphate (d5mCMP). Methylated and not methylated oligonucleotides were used to confirm the identity of each peak and evaluate analytical parameters of the method. The LOD of the method was found to be 12.5 pmol/μL for d5mCMP.     

Analysis of short‐chain aliphatic amines in food and water samples using a near infrared cyanine 1‐(ε‐succinimydyl‐hexanoate)‐1′‐methyl‐3,3,3′,3′‐tetramethyl‐indocarbocyanine‐5,5′‐disulfonate potassium with CE–LIF detection

Precolumn derivatization of six short‐chain aliphatic amines by a near‐infrared dye, 1‐(ε‐succinimydyl‐hexanoate)‐1′‐methyl‐3,3,3′,3′‐tetramethyl‐indocarbocyanine‐5,5′‐ disulfonate potassium (MeCy5‐OSu), followed by MEKC–CE–LIF detection has been developed as a method for the determination of aliphatic amines in environmental water and food. Optimum derivatization was operated nicely in pH 9.0 borate buffer at 20°C for 30 min. Well separated peaks were observed with a pH 9.5 BGE containing 10 mmol L^?1 phosphoric acid, 20 mmol L^?1 SDS, and 7% methanol buffered with 1.0 mol L^?1 NaOH. The separation procedure was rapidly achieved within 11 min and the matrix interferences could be effectively eliminated. A linear calibration graph was obtained for 5–200 nmol L^?1 analytes with a correlation coefficient in the range 0.9933–0.9995 for amines. This method was successfully utilized to determine aliphatic amines in lake, sewage water, and red wine with recoveries ranging from 96.4 to 105% and the RSDs ranging from 0.9 to 2.9%. Near‐infrared, LIF‐detector‐compatible MeCy5‐OSu was proved suitable for the accurate, sensitive, and rapid separation and determination of aliphatic amines in water and food samples.     

Quantification of γ-aminobutyric acid in the heads of houseflies (Musca domestica) and diamondback moths (Plutella xylostella (L.)), using capillary electrophoresis with laser-induced fluorescence detection

A novel method was developed for quantifying the levels of γ‐aminobutyric acid (GABA) in the heads of houseflies (Musca domestica) and diamondback moths (Plutella xylostella (L.)), using capillary electrophoresis with laser‐induced fluorescence detection (CE‐LIF). The GABA in sample was derivatized with 4‐chloro‐7‐nitro‐2,1,3‐benzoxadiazole (NBD‐Cl) prior to CE‐LIF analysis. In total, 32 mmol/L borate buffer, at pH 9.2 and containing 5.3 mmol/L β‐cyclodextrin (β‐CD) and 10.4 mmol/L sodium dodecyl sulfate (SDS), was determined to be the optimum CE background electrolyte (BGE) for GABA analysis. The detection limit of GABA was 0.016 μmol/L. The relative standard deviations (RSDs) of the migration time and peak area of GABA were 1.78 and 4.93%, respectively. The average recoveries of 0.97, 3.88, and 5.83 μmol/L of GABA, each added to the head sample of housefly, ranged from 88.9 to 110.5%. This method is simple and applicable to GABA assays of the heads of insects. With this newly developed CE‐LIF method, the amounts of GABA in the heads of houseflies (M. domestica) and diamondback moths (P. xylostella (L.)) were measured. The results are relevant to the understandings of some insecticides and insecticide‐resistance mechanisms in pests.     

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.     

Stabilization of a Bimolecular Triplex by 3′‐S‐Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single‐stranded nucleic acids are also relevant in third‐strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base‐paired DNA duplexes and a Hoogsteen base‐paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA‐like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′‐S‐phosphorothiolate (3′‐SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. ¹H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′‐SP modifications is more compact. The 3′‐SP modification was previously shown to stabilise G‐quadruplex and i‐motif structures and therefore is now proposed as a generic solution to stabilising multi‐stranded DNA structures.     

Oligonucleotides Containing 7‐Deaza‐2′‐deoxyxanthosine: Synthesis,Base Protection,and Base‐Pair Stability

Oligonucleotides incorporating 7‐deaza‐2′‐deoxyxanthosine ( 3 ) and 2′‐deoxyxanthosine ( 1 ) were prepared by solid‐phase synthesis using the phosphoramidites 6 – 9 and 16 which were protected with allyl, diphenylcarbamoyl, or 2‐(4‐nitrophenyl)ethyl groups. Among the various groups, only the 2‐(4‐nitrophenyl)ethyl group was applicable to 7‐deazaxanthine protection being removed with 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) by β‐elimination, while the deprotection of the allyl residue with Pd⁰ catalyst or the diphenylcarbamoyl group with ammonia failed. Contrarily, the allyl group was found to be an excellent protecting group for 2′‐deoxyxanthosine ( 1 ). The base pairing of nucleoside 3 with the four canonical DNA constituents as well as with 3‐bromo‐1‐(2‐deoxy‐β‐D ‐erythro‐pentofuranosyl)‐1H‐pyrazolo[3,4‐d]pyrimidine‐4,6‐diamine ( 4 ) within the 12‐mer duplexes was studied, showing that 7‐deaza‐2′‐deoxyxanthosine ( 3 ) has the same universal base‐pairing properties as 2′‐deoxyxanthosine ( 1 ). Contrary to the latter, it is extremely stable at the N‐glycosylic bond, while compound 1 is easily hydrolyzed under slightly acidic conditions. Due to the pK_a values 5.7 ( 1 ) and 6.7 ( 3 ), both compounds form monoanions under neutral conditions (95% for 1 ; 65% for 3 ). Although both compounds form monoanions at pH 7.0, pH‐dependent T_m measurements showed that the base‐pair stability of 7‐deaza‐2′‐deoxyxanthosine ( 3 ) with dT is pH‐independent. This indicates that the 2‐oxo group is not involved in base‐pair formation.     

Rapid and sensitive determination of free thiols by capillary zone electrophoresis with near‐infrared laser‐induced fluorescence detection using a new BODIPY‐based probe as labeling reagent

A CZE with near‐infrared (NIR) LIF detection method has been developed for the analysis of six low molecular weight thiols including glutathione, homocysteine, cysteine, γ‐glutamylcysteine, cysteinylglycine, and N‐acetylcysteine. For this purpose, a new NIR fluorescent probe, 1,7‐dimethyl‐3,5‐distyryl‐8‐phenyl‐(4'‐iodoacetamido)difluoroboradiaza‐s‐indacene was utilized as the labeling reagent, whose excitation wavelength matches the commercially available NIR laser line of 635 nm. The optimum procedure included a derivatization step of the free thiols at 45°C for 25 min and CZE analysis conducted within 14 min in the running buffer containing 16 mmol/L pH 7.0 sodium citrate and 60% v/v ACN. The LODs (S/N = 3) ranged from 0.11 nmol/L for N‐acetylcysteine to 0.31 nmol/L for γ‐glutamylcysteine, which are better than or comparable to those reported with other derivatization‐based CE‐LIF methods. As the first trial of NIR CE‐LIF method for thiol determination, the practical application of the proposed method has been validated by detecting thiols in cucumber and tomato samples with recoveries of 96.5–104.3%.     

The crystal structure of the CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC)

Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon–carbon double bond replacing the O4′‐oxygen atom of the natural D ‐2′‐deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activity and their hybridisation is RNA selective. Additionally, CeNA has been shown to induce an enhanced biological activity when incorporated in siRNA. This makes CeNA a good candidate for siRNA and synthetic aptamer applications. The crystal structure of the synthetic CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC) has been solved with a resolution of 2.50 Å. The CeNA:RNA duplex adopts an anti‐parallel, right‐handed double helix with standard Watson–Crick base pairing. Analyses of the helical parameters revealed the octamer to form an A‐like double helix. The cyclohexenyl rings mainly adopt the ³H₂ conformation, which resembles the C3′‐endo conformation of RNA ribose ring. This C3′‐endo ring puckering was found in most of the RNA residues and is typical for A‐family helices. The crystal structure is stabilised by the presence of hexahydrated magnesium ions. The fact that the CeNA:RNA hybrid adopts an A‐type double helical conformation confirms the high potential of CeNAs for the construction of efficient siRNAs which can be used for therapeutical applications.     

7‐Iodo‐5‐aza‐7‐deazaguanine ribonucleoside: crystal structure,physical properties,base‐pair stability and functionalization

The positional change of nitrogen‐7 of the RNA constituent guanosine to the bridgehead position‐5 leads to the base‐modified nucleoside 5‐aza‐7‐deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton‐acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all‐purine' DNA and DNA with silver‐mediated base pairs. The present work reports the single‐crystal X‐ray structure of 7‐iodo‐5‐aza‐7‐deazaguanosine, C<sub>10</sub>H<sub>12</sub>IN<sub>5</sub>O<sub>5</sub> ( 1 ). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′‐endo) for the ribose moiety, with an antiperiplanar orientation of the 5′‐hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7‐iodo substituent forms a contact to oxygen‐2′ of the ribose moiety. Self‐pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H…O and N—H…O). The concept of pK‐value differences to evaluate base‐pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all‐purine' RNA. Furthermore, the 7‐iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.     

Portable capillary electrophoresis system for identification of cattle breeds based on DNA mobility

A portable CE system was developed for the identification of cattle breeds. The system had a width of 44 cm, depth of 27 cm, height of 13 cm, and a weight of only ∼8 kg and included an LIF detector, with everything integrated into a small box. The specific sizes of genes were quickly separated and detected with a high sensitivity based on the difference in the DNA mobility using a diode‐pumped solid‐state LIF detector. Using this system, the 100‐bp DNA ladder was analyzed under a 1.0% PVP (M_r=300 000) sieving gel matrix in a fused silica capillary with LODs of 4.4–13.0 pg/μL (S/N=3) for 100–3000 bp DNAs, which indicates ten times improved value than other commercialized portable CE system. The migration times and the peak areas showed good reproducibilities with relative standard deviations that were less than 0.49 and 1.3% (n=5), respectively. Based on the difference in the DNA mobility of the microsatellite and SNP markers, Korean cattle and Holstein were exactly identified as the model cattle breeds within 32 and 3.5 min, respectively.     

Capillary electrophoresis‐laser‐induced fluorescence detection of rat brain catecholamines with microwave‐assisted derivatization

In this study, a rapid and sensitive method is described for the catecholamines detection in rat brain. CE with LIF detection for the determination of FITC derivatized catecholamines (dopamine, epinephrine, and norepinephrine) was demonstrated. Conventional water bath and microwave‐assisted derivatization methods were employed and a significant reduction in the derivatization time from 2 h for the conventional water bath at room temperature (ca. 25°C) to 2 min for the microwave‐assisted derivatization was achieved. Online sample concentration of field‐amplified sample stacking (FASS) method was employed to achieve higher sensitivities (the detection limits obtained in the normal injection mode ranged from 2.6 to 4.5 ng L^?1 and in the FASS mode ranged from 22 to 34 pg L^?1). Furthermore, this microwave‐assisted derivatization CE–LIF method successfully determined catecholamines in rat brain with as low as 100 ng L^?1 (FASS mode) to 10 μg L^?1 (normal injection mode). This CE–LIF method provided better detection ability when compared to the best reports on catecholamines analyses.     

Base‐Pairing Properties of 8‐Aza‐7‐deazaadenine Linked via the 8‐Position to the DNA Backbone

The base‐pairing properties of oligonucleotides containing the unusual N⁸‐linked 8‐aza‐7‐deazaadenine 2′‐deoxyribonucleoside ( 2a ) as well as its 7‐bromo derivative 2b are described. The oligonucleotides were prepared by solid‐phase synthesis employing phosphoramidite chemistry. Compound 2a forms a strong base pair with T_d for which a reverse Watson‐Crick pair is suggested (Fig. 9). Compound 2a displays a lower N‐glycosylic‐bond stability than its N⁹‐nucleoside and shows strong stacking interactions when incorporated into oligonucleotides. The replacement of 2′‐deoxyadenosine by 2a does not significantly influence the duplex stability. However, this behavior depends on the position of the incorporation.     

Major‐Groove‐Halogenated DNA: The Effects of Bromo and Iodo Substituents Replacing H−C(7) of 8‐Aza‐7‐deazapurine‐2,6‐diamine or H−C(5) of Uracil Residues

Oligonucleotides containing halogenated `purine' and pyrimidine bases were synthesized. Bromo and iodo substituents were introduced at the 7‐position of 8‐aza‐7‐deazapurine‐2,6‐diamine (see 2b , c ) or at the 5‐position of uracil residues (see 3b , c ). Phosphoramidites were synthesized after protection of 2b with the isobutyryl residue and of 2c with the benzoyl group. Duplexes containing the residues 2b or 2c gave always higher T<sub>m</sub> values than those of the nonmodified counterparts containing 2′‐deoxyadenosine, the purine‐2,6‐diamine 2′‐deoxyribonucleoside ( 1 ), or 2a at the same positions. Six 2b residues replacing dA in the duplex 5′‐d(TAGGTCAATACT)‐3′ ( 11 )⋅5′‐d(AGTATTGACCTA)‐3′ ( 12 ) raised the T<sub>m</sub> value from 48 to 75° (4.5° per modification (Table 3)). Contrary to this, incorporation of the 5‐halogenated 2′‐deoxyuridines 3b or 3c into oligonucleotide duplexes showed very little influence on the thermal stability, regardless of which `purine' nucleoside was located opposite to them (Tables 4 and 5). The positive effects on the thermal stability of duplexes observed in DNA were also found in DNA⋅RNA hybrids or in DNA with parallel chain orientation (Tables 8 and 9, resp.).     

Analysis of DNA complexes with small solutes by CE with LIF detection

In this article, we describe the analysis of aptamers for Hg²⁺ ions through CE with LIF (CE‐LIF) detection using 2% poly(ethylene oxide) solutions containing OliGreen (fluorophore). In the presence of an EOF, DNA strands migrating against the EOF were detected at the cathode end. Four DNA strands – T₃₃, T₅C₂₈, T₅C₅T₂₃, and T₁₅C₅T₁₃ – could not be separated through CE‐LIF in the absence of Hg²⁺. At 0.3 mM Hg²⁺, however, all four were partially separated within 20 min, with SDs of the migration times all being less than 2.5%. From the CE, fluorescence, and ellipticity data, we concluded that the conformations of these four DNA strands all changed from random‐coil to folded structures as a result of T–Hg²⁺–T bonding. In addition, we found that this CE approach provided different electropherograms patterns for T₇, T₁₅, and T₃₃ in the absence and presence of Hg²⁺, indicating various interactions of the DNA strands with Hg²⁺. Using this simple, high‐resolution CE approach, we also demonstrated that adenosine triphosphate has a stronger interaction with the adenosine triphosphate aptamer than with either the platelet‐derived growth factor aptamer or T₃₃. This CE approach holds great potential for screening aptamers for small solutes, studying the catalytic activity of DNAzymes, and evaluating the biological functions of microRNA.     

Paper‐based solid‐phase microextraction for analysis of 8‐hydroxy‐2’‐deoxyguanosine in urine sample by CE‐LIF

An easy‐to‐do paper‐based solid‐phase microextraction (p‐SPME) was developed for determination of 8‐hydroxy‐2’‐deoxyguanosine (8‐OHdG) in urine sample by CE‐LIF. Small piece of filter paper was used as a solid phase to extract 8‐OHdG from urine sample. Its primary mechanism is based on the hydrogen‐bonding interaction between 8‐OHdG and cellulose molecules. The effects of the pH of the sample solution, extraction time, and temperature on the peak area of the analyte were investigated in order to obtain the optimal p‐SPME conditions. Comparing with the untreated sample, the p‐SPME can significantly reduce the interference to the separation of 8‐OHdG by CE‐LIF. Meanwhile, the p‐SPEM can provide more than three times concentrated effect. The developed method was evaluated according to an FDA guideline for biological analysis. The precisions (RSD%, n = 5) of the peak area and migration time of the analyte at three different concentrations were within 3.02–5.82% and 0.92–1.58%, respectively. The limit of identification of the method is about 5 nM according to the significant difference between two sets of the samples with and without spiking the standard (Student's t ‐test, p < 0.05). Good linearity was obtained in the range of 10–1000 nM (R ²>0.99) based on the standard addition. The recoveries at three different concentrations were within 99.8–103.5%. The results of the real sample analysis are consistent with those reported in our previous paper (Electrophoresis 2014, 35, 1873–1879).     

Synthesis of Selectively 15N‐Labeled 2′‐O‐{[(Triisopropylsilyl)oxy]methyl}(=tom)‐Protected Ribonucleoside Phosphoramidites and Their Incorporation into a Bistable 32Mer RNA Sequence

We present optimized reaction conditions for the conversion of 2′‐O‐{[(triisopropylsilyl)oxy]methyl}(=tom) protected uridine and adenosine nucleosides into the corresponding protected (3‐¹⁵N)‐labeled uridine and cytidine and (1‐¹⁵N)‐labeled adenosine and guanosine nucleosides 4, 6, 12 , and 18 , respectively (Schemes 1–4). On a DNA synthesizer, the resulting ¹⁵N‐labeled 2′‐O‐tom‐protected phosphoramidite building blocks 19 – 22 were efficiently incorporated into five selected positions of a bistable 32mer RNA sequence 23 (known to adopt two different structures) (Fig. 1). By 2D‐HSQC and HNN‐COSY experiments in H₂O/D₂O 9 : 1, the ¹⁵N‐signals of all base‐paired ¹⁵N‐labeled nucleotides could be identified and attributed to one of the two coexisting structures of 23 .     

Determination of genomic N3‐methylthymidine in human cancer cells treated with nitrosamines using capillary electrophoresis with laser‐induced fluorescence

Methylating substances alter DNA by forming N3‐methylthymidine (N3mT), a mutagenic base modification. To develop a sensitive analytical method for the detection of N3mT in DNA based on capillary electrophoresis with laser‐induced fluorescence detection (CE‐LIF), we synthesized the N3mT‐3’‐phosphate as a chemical standard. The limit of detection was 1.9 amol of N3mT, which corresponds to one molecule of N3mT per 1000 normal nucleotides or 0.1%. With this method, we demonstrated that the carcinogenic nitrosamine N’‐nitrosonornicotine (NNN) induced N3mT in the human lung cancer cell line A549. Treatment with NNN also caused an elevated degree of 5‐hydroxymethylcytidine (5hmdC) in DNA, while the methylation degree (i.e. 5‐methylcytidine; 5mdC) stayed constant. According to our data, NNN could, via yet unknown mechanisms, play a role in the formation of N3mT as well as 5hmdC. In this study we have developed a new sensitive analytical method using CE‐LIF for the simultaneous detection of the three DNA modifications, 5mdC, 5hmdC and N3mT.