Effects of cytosine methylation on pyrimidine dimer formation in DNA

The relative induction of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone photoproducts ([6-4]PD) was quantified in the duplex homopolymers polydeoxyadenosine:polydeoxythymidine, polydeoxyguanosine:polydeoxycytidine and polydeoxyguanosine:polydeoxy-5-methylcytidine irradiated with UVC or UVB radiation. Cytosine methylation significantly increased the yield of cytosine (6-4)PD after irradiation with UVC light and of cytosine CPD and (6-4)PD after irradiation with UVB light. The data suggest that CPD and (6-4)PD are preferentially induced at 5-methylcytosine bases in DNA of cells exposed to sunlight and comprise a major component of the mutation spectrum leading to the initiation of sunlight-induced skin cancer.     

Crystal Structure of the T(6‐4)C Lesion in Complex with a (6‐4) DNA Photolyase and Repair of UV‐Induced (6‐4) and Dewar Photolesions

UV‐light irradiation induces the formation of highly mutagenic lesions in DNA, such as cis‐syn cyclobutane pyrimidine dimers (CPD photoproducts), pyrimidine(6‐4)pyrimidone photoproducts ((6‐4) photoproducts) and their Dewar valence isomers ((Dew) photoproducts). Here we describe the synthesis of defined DNA strands containing these lesions by direct irradiation. We show that all lesions are efficiently repaired except for the T(Dew)T lesion, which cannot be cleaved by the repair enzyme under our conditions. A crystal structure of a T(6‐4)C lesion containing DNA duplex in complex with the (6‐4) photolyase from Drosophila melanogaster provides insight into the molecular recognition event of a cytosine derived photolesion for the first time. In light of the previously postulated repair mechanism, which involves rearrangement of the (6‐4) lesions into strained four‐membered ring repair intermediates, it is surprising that the not rearranged T(6‐4)C lesion is observed in the active site. The structure, therefore, provides additional support for the newly postulated repair mechanism that avoids this rearrangement step and argues for a direct electron injection into the lesion as the first step of the repair reaction performed by (6‐4) DNA photolyases.     

UVB-lnduced DNA Damage and Its Photorepair in Nuclei and Chloroplasts of Spinacia oleracea L.

Ultraviolet-B-induced lesions and their photorepair in nuclear and chloroplast DNA of spinach (Spinacia oleracea L.) leaves were examined with two photoproducts, cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidinone photoproducts (6-4PP). These photoproducts were induced both in nuclear and chloroplast DNA by UVB irradiation and could be detected by enzyme-linked immunosorbent assay using their respective monoclonal antibodies. Formation of CPD was greater in nuclear DNA than in chloroplast DNA (about 10 to 7), whereas 6-4PP formation was comparable in both DNA. On subsequent exposure of leaves to blue/UVA after UVB irradiation, photorepair of CPD and 6-4PP occurred in nuclear DNA but not in chloroplast DNA. When isolated chloroplasts were irradiated with UVB, CPD was also induced in their DNA. But photorepair of CPD did not occur in them by subsequent exposure to blue/UVA, suggesting that no photorepair system operates in chloroplasts.     

Direct Sensing of 5‐Methylcytosine by Polymerase Chain Reaction

The epigenetic control of genes by the methylation of cytosine resulting in 5‐methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3′‐mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation‐specific PCR approach directly from untreated human genomic DNA.     

Novel Photodynamic Effect of a Psoralen‐Conjugated Oligonucleotide for the Discrimination of the Methylation of Cytosine in DNA

DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression significantly. In particular, C‐5‐methylation of cytosine in the CpG islands is important for the epigenetic modification in genes, which plays a key role in regulating gene expression. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis. Here we designed a psoralen‐conjugated oligonucleotide (PS‐oligo) for the discrimination of 5‐methylcytosine (5‐mC) in DNA. The cross‐linking behavior of psoralen derivatives with pyrimidine bases, such as thymine, uracil and cytosine has been well discussed, but there are no reports which have examined whether cross‐linking efficiency of psoralen with cytosine would be changed with or without C‐5 methylation. We found that the cross‐linking efficiency of PS‐oligo with target‐DNA containing 5‐mC was greatly increased compared to the case of target‐DNA without 5‐mC, approximately seven‐fold higher. Here we report a new aspect of the photocross‐linking behavior of psoralen with 5‐mC that is applicable to a simple, sequence‐specific and quantitative analysis for the discrimination of 5‐mC in DNA, which can be applicable to study the epigenetic behavior of gene expressions.     

UVB-induced Cyclobutane Pyrimidine Dimer Frequency Correlates with Skin Cancer Mutational Hotspots in p53

Abstract— Ultraviolet light has been identified as the major carcinogen in skin cancer and the p53 tumor suppressor gene is a major target for UV-induced mutations. The mutations are probably caused by unrepaired UV-induced cyclobutane pyrimidine dimers (CPD) and possibly by the less frequent pyrimidine (6-4) pyrimidone photoproducts. While hot spots for p53 mutations in human nonmela-noma skin tumors correspond quite well to slow spots for CPD repair in cultured cells irradiated with the model mutagen 254 nm UVC (which is not present in terrestrial sunlight), they do not all coincide with sequences that are initially frequently damaged by 254 nm UVC. Using LMPCR (ligation-mediated polymerase chain reaction), we show that environmentally relevant UVB light induces CPD at CC and PyrmC positions much more frequently than does UVC light, and that all eight skin cancer hot spots in p53 are also hot spots for UVB-induced CPD. Our results show that methylation of dipyrimidine sites (PyrmCpG) is associated with an increase rate of CPD formation upon UVB irradiation. Consequently, DNA methylation may increase the mutagenic potential of UVB and explains that several p53 mutation hot spots are found at PyrmCpG. The distribution patterns of CPD formation and the photofootprint patterns found along exons 5 and 6 of p53 gene are suggestive of DNA folding into nucleosomes.     

Pyrimidine (6-4) pyrimidone photoproduct mapping after sublethal UVC doses: nucleotide resolution using terminal transferase-dependent PCR

UVC irradiation of genomic DNA induces two main types of potentially mutagenic base modifications: cyclobutane pyrimidine dimers (CPDs) and the less frequent (15-30% of CPD levels) pyrimidine (6-4) pyrimidone photoproducts (6-4PP). Ligation-mediated PCR (LMPCR), a genomic sequencing technique, allows CPD mapping at nucleotide resolution following irradiation with sublethal doses of UVB or UVC for most cell types. In contrast, a dose of 80 J/m(2) of UVC that is lethal for the majority of cell types is necessary to map 6-4PP by the LMPCR technique. This compromises the use of LMPCR to study the repair of 6-4PP. To date, no other techniques have been developed to study 6-4PP repair at nucleotide resolution. We have therefore adapted a recently developed technique for the mapping of 6-4PP: terminal transferase-dependent PCR (TDPCR). TDPCR is in many ways similar to LMPCR. This technique is more sensitive and allows the mapping of 6-4PP at UVC doses as low as 10 J/m(2) in genomic DNA and in living cells.     

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).     

Cyclobutane Pyrimidine Dimer Density as a Predictive Biomarker of the Biological Effects of Ultraviolet Radiation in Normal Human Fibroblast

This study compared biological responses of normal human fibroblasts (NHF1) to three sources of ultraviolet radiation (UVR), emitting UVC wavelengths, UVB wavelengths, or a combination of UVA and UVB (solar simulator; emission spectrum, 94.3% UVA and 5.7% UVB). The endpoints measured were cytotoxicity, intra‐S checkpoint activation, inhibition of DNA replication and mutagenicity. Results show that the magnitude of each response to the indicated radiation sources was best predicted by the density of DNA cyclobutane pyrimidine dimers (CPD). The density of 6‐4 pyrimidine–pyrimidone photoproducts was highest in DNA from UVC‐irradiated cells (14% of CPD) as compared to those exposed to UVB (11%) or UVA–UVB (7%). The solar simulator source, under the experimental conditions described here, did not induce the formation of 8‐oxo‐7,8‐dihydroguanine in NHF1 above background levels. Taken together, these results suggest that CPD play a dominant role in DNA damage responses and highlight the importance of using endogenous biomarkers to compare and report biological effects induced by different sources of UVR.     

Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N‐Demethylation

TET family enzymes are known for oxidation of the 5‐methyl substituent on 5‐methylcytosine (5mC) in DNA. 5mC oxidation generates the stable base 5‐hydroxymethylcytosine (5hmC), starting an indirect, multi‐step process that ends with reversion of 5mC to unmodified cytosine. While probing the nucleobase determinants of 5mC recognition, we discovered that TET enzymes are also proficient as direct N‐demethylases of cytosine bases. We find that N‐demethylase activity can be readily observed on substrates lacking a 5‐methyl group and, remarkably, TET enzymes can be similarly proficient in either oxidation of 5mC or demethylation of N4‐methyl substituents. Our results indicate that TET enzymes can act as both direct and indirect demethylases, highlight the active‐site plasticity of these Fe^II/α‐ketoglutarate‐dependent dioxygenases, and suggest activity on unexplored substrates that could reveal new TET biology.     

Direct Electrocatalytic Oxidation and Simultaneous Determination of 5‐Methylcytosine and Cytosine at Electrochemically Reduced Graphene Modified Glassy Carbon Electrode

Direct electrocatalytic oxidation and simultaneous determination of 5‐methylcytosine (5‐mC) and cytosine(C) were realized in alkaline solutions by differential pulse voltammetry (DPV) based on an electrochemically reduced graphene oxide (er‐GO) modified glassy carbon electrode (er‐GO/GCE). The as‐prepared er‐GO/GCE exhibited good electrocatalytic activity towards the oxidation of 5‐mC and C. Under optimum conditions, the er‐GO/GCE was applied to the simultaneous determination of 5‐mC and C with a significantly improved peak potential resolution (about 150 mV), and a linear relationship can be obtained in the range of 6–200.0 µmol/L and 8–250.0 µmol/L, respectively. In addition, the proposed method was further successfully applied to the analysis of methylation status in short CpG oligonucleotides with satisfactory results.     

Hydrogen bonding in nitroaniline analogues: hydrogen‐bonded sheets in 2‐amino‐4,6‐dimethoxy‐5‐nitropyrimidine and π‐stacked hydrogen‐bonded sheets in 4‐amino‐2,6‐dimethoxy‐5‐nitropyrimidine

In 2‐amino‐4,6‐di­methoxy‐5‐nitro­pyrimidine, C₆H₈N₄O₄, the mol­ecules are linked by one N—H⋯N and one N—H⋯O hydrogen bond to form sheets built from alternating R(8) and R(32) rings. In isomeric 4‐amino‐2,6‐di­methoxy‐5‐nitro­pyrimidine, C₆H₈N₄O₄, which crystallizes with Z′ = 2 in P, the two independent mol­ecules are linked into a dimer by two independent N—H⋯N hydrogen bonds. These dimers are linked into sheets by a combination of two‐centre C—H⋯O and three‐centre C—H⋯(O)₂ hydrogen bonds, and the sheets are further linked by two independent aromatic π–π‐stacking interactions to form a three‐dimensional structure.     

2‐Amino‐4‐(4‐pyridyl)­pyrimidine and the 1:1 adduct with 4‐amino­benzoic acid

The structure of the title compound, C₉H₈N₄, comprises non‐planar mol­ecules that associate via pyrimidine N—H?N dimer R(8) hydrogen‐bonding associations [N?N 3.1870 (17) Å] and form linear hydrogen‐bonded chains via a pyrimidine N—H?N(pyridyl) interaction [N?N 3.0295 (19) Å]. The dihedral angle between the two rings is 24.57 (5)°. The structure of the 1:1 adduct with 4‐amino­benzoic acid, C₉H₈N₄·C₇H₇NO₂, exhibits a hydrogen‐bond­ing network involving COOH?N(pyridyl) [O?N 2.6406 (17) Å], pyrimidine N—H?N [N?N 3.0737 (19) and 3.1755 (18) Å] and acid N—H?O interactions [N?O 3.0609 (17) and 2.981 (2) Å]. The dihedral angle between the two linked rings of the base is 38.49 (6)° and the carboxyl­ic acid group binds to the stronger base group in contrast to the (less basic) complementary hydrogen‐bonding site.     

Design of two series of 1:1 cocrystals involving 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine and carboxylic acids

Two series of a total of ten cocrystals involving 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine with various carboxylic acids have been prepared and characterized by single‐crystal X‐ray diffraction. The pyrimidine unit used for the cocrystals offers two ring N atoms (positions N1 and N3) as proton‐accepting sites. Depending upon the site of protonation, two types of cations are possible [Rajam et al. (2017). Acta Cryst. C 73 , 862–868]. In a parallel arrangement, two series of cocrystals are possible depending upon the hydrogen bonding of the carboxyl group with position N1 or N3. In one series of cocrystals, i.e. 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–3‐bromothiophene‐2‐carboxylic acid (1/1), 1 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–5‐chlorothiophene‐2‐carboxylic acid (1/1), 2 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–2,4‐dichlorobenzoic acid (1/1), 3 , and 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–2‐aminobenzoic acid (1/1), 4 , the carboxyl hydroxy group (–OH) is hydrogen bonded to position N1 (O—H…N1) of the corresponding pyrimidine unit (single point supramolecular synthon). The inversion‐related stacked pyrimidines are doubly bridged by the carboxyl groups via N—H…O and O—H…N hydrogen bonds to form a large cage‐like tetrameric unit with an R₄²(20) graph‐set ring motif. These tetrameric units are further connected via base pairing through a pair of N—H…N hydrogen bonds, generating R₂²(8) motifs (supramolecular homosynthon). In the other series of cocrystals, i.e. 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–5‐methylthiophene‐2‐carboxylic acid (1/1), 5 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–benzoic acid (1/1), 6 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–2‐methylbenzoic acid (1/1), 7 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–3‐methylbenzoic acid (1/1), 8 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–4‐methylbenzoic acid (1/1), 9 , and 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–4‐aminobenzoic acid (1/1), 10 , the carboxyl group interacts with position N3 and the adjacent 4‐amino group of the corresponding pyrimidine ring via O—H…N and N—H…O hydrogen bonds to generate the robust R₂²(8) supramolecular heterosynthon. These heterosynthons are further connected by N—H…N hydrogen‐bond interactions in a linear fashion to form a chain‐like arrangement. In cocrystal 1 , a Br…Br halogen bond is present, in cocrystals 2 and 3 , Cl…Cl halogen bonds are present, and in cocrystals 5 , 6 and 7 , Cl…O halogen bonds are present. In all of the ten cocrystals, π–π stacking interactions are observed.     

Radical‐mediated cytosine and 5‐methylcytosine hydrolytic deamination reactions

The mechanisms of cytosine and 5‐methylcytosine hydrolytic deamination reactions in the gas phase have been investigated. The rate‐determining steps of the reactions are found by density functional theory (DFT). The lower barriers of hydrogen and hydroxyl radical‐mediated 5‐methylcytosine deamination make the C‐5 site of 5‐methylcytosine the hot spot for spontaneous mutations. The hydrogen radical inhibits cytosine and 5‐methylcytosine hydrolytic deamination reactions, while the hydroxyl radical clearly leads to an increased risk of genetic mutagenesis. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Synthesis of Some New 1,2,3,4‐Tetrahydropyrimidine‐2‐thione and Their Thiazolo[3,2‐a]pyrimidine,Thiazino and Benzothiazepine Derivatives

The starting N‐(2‐pyridyl)‐6‐methyl‐4‐phenyl‐2‐thioxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carboxamide ( 4 ) was used as a key intermediate for the synthesis of new 1,2,3,4‐tetrahydropyrimidine‐2‐thione and their thiazolo[3,2‐a]pyrimidine, thiazino and benzothiazipen derivatives. The reaction of 4 with haloketones in ethanol catalyzed by base afforded the corresponding thiophenopyrimidine and pyrimidothiazipine derivatives 5 , 6 , 7 , 8 , 9 , 10 . Methylation and formylation of 4 led to the pyrimidine derivatives 15 and 16 , respectively. The preventative compounds were established on the basis of elemental and spectral data.     

5‐Ethyl‐2′‐deoxy‐4′‐thiouridine (R)‐S‐oxide monohydrate

The pyrimidine ring of the title compound, C₁₁H₁₆N₂O₅S·H₂O, is planar to within 0.026 (1) Å and makes an angle of 77.73 (8)° with the mean plane of the thiosugar ring. In terms of standard nucleoside nomenclature, this ring has a C1′‐exo,C2′‐endo conformation. The O5′—C5′—C4′—C3′ torsion angle is ?167.4 (2)° and the glycosidic S4′—C1′—N1—C2 torsion angle is ?101.8 (2)° (anti).     

Prototropic tautomers of 5‐methylcytosine and enthalpy changes of their protonation,deprotonation, and deamination: Hybrid density functional B3LYP study

Molecular and thermodynamic properties such as geometric parameters, dipole moments, vibrational frequencies, the first ionization potentials, relative tautomerization energies, and tautomeric equilibrium constants of all prototropic tautomers of 5‐methylcytosine have been studied at the hybrid density functional level B3LYP/6‐31+G(d,p). The methylation on the C5 atom does not lead to significant geometric deformation of the pyrimidine structures of the corresponding tautomers of cytosine, which maintains the similar stability order. The tautomeric species 2‐oxo‐4‐amino [T(0)], 2‐hydroxy‐4‐amino [T(1‐2s) and T(1‐2t)], and trans‐2‐oxo‐4‐imino [T(3‐4t)] are predominated in the gas phase. The zwitterionic conformers of tautomerism [T(1‐4)] and protonation [P(4), P(1‐2s‐4), P(1‐2t‐4), and P(1‐3‐4)] are investigated for the first time due to their close relationship with deamination during genetic repair. Enthalpy changes (Δ_rH) of protonation, deprotonation, and deamination are calculated for these tautomeric species at room temperature; it is noted that the relative enthalpies [δ(ΔH)] of the tautomers are rationalized well in terms of a second‐order polynomial of the sum of the mean Δ_rH values of protonation and deprotonation processes. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

The 7‐bromo derivative of 2‐amino‐2′‐deoxytubercidin fluorinated at the sugar moiety

The title compound, 2,4‐diamino‐5‐bromo‐7‐(2‐deoxy‐2‐fluoro‐β‐d ‐arabinofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine, C₁₁H₁₃BrFN₅O₃, shows two conformations of the exocyclic C4′—C5′ bond, with the torsion angle γ (O5′—C5′—C4′—C3′) being 170.1 (3)° for conformer 1 (occupancy 0.69) and 60.7 (7)° for conformer 2 (occupancy 0.31). The N‐glycosylic bond exhibits an anti conformation, with χ = −114.8 (4)°. The sugar pucker is N‐type (C3′‐endo; ³T₄), with P = 23.3 (4)° and τ_m = 36.5 (2)°. The compound forms a three‐dimensional network that is stabilized by several intermolecular hydrogen bonds (N—H...O, O—H...N and N—H...Br).