DNA甲基化对子宫内膜异位症（EMs）的作用及其调控机制

表观遗传通过DNA甲基化、组蛋白修饰、染色质重塑、以及microRNA等调控方式来实现对基因表达、DNA复制和基因组稳定性的控制。DNA甲基化是目前研究的最为广泛的表观遗传修饰方式之一,可调控真核生物的基因表达。DNA甲基化在哺乳动物发育、肿瘤发生发展及人类其他疾病中均发挥着至关重要的作用。DNA甲基化状态的改变已被视为人类肿瘤细胞的生物标志之一。EMs虽是一种良性妇科疾病,但伴有细胞增殖、侵袭性及远处种植转移等肿瘤的特点。最新研究发现,DNA甲基化可能与子宫内膜异位症（EMs）的发生存在密切的关系并认为EMs从根本上是一种表观遗传学疾病。由于表观遗传修饰都是可逆的过程,这就为EMs的治疗提供了一种新的途径。本文就DNA甲基化在EMs中的发生发展中的作用及其调控的分子机制,以及在诊断治疗中作用的最新研究进展做一综述。     

DNA甲基化对子宫内膜异位症(EMs)的作用及其调控机制

表观遗传通过DNA甲基化、组蛋白修饰、染色质重塑、以及microRNA等调控方式来实现对基因表达、DNA复制和基因组稳定性的控制。DNA甲基化是目前研究的最为广泛的表观遗传修饰方式之一,可调控真核生物的基因表达。DNA甲基化在哺乳动物发育、肿瘤发生发展及人类其他疾病中均发挥着至关重要的作用。DNA甲基化状态的改变已被视为人类肿瘤细胞的生物标志之一。EMs虽是一种良性妇科疾病,但伴有细胞增殖、侵袭性及远处种植转移等肿瘤的特点。最新研究发现,DNA甲基化可能与子宫内膜异位症(EMs)的发生存在密切的关系并认为EMs从根本上是一种表观遗传学疾病。由于表观遗传修饰都是可逆的过程,这就为EMs的治疗提供了一种新的途径。本文就DNA甲基化在EMs中的发生发展中的作用及其调控的分子机制,以及在诊断治疗中作用的最新研究进展做一综述。     

Non-Watson-Crick base associations in DNA and RNA revealed by single crystal x-ray diffraction methods: Mismatches,modified bases,and nonduplex DNA

Single crystal x-ray diffraction methods have been used to characterize numerous oligonucleotide structures, providing valuable information on the fine structure of DNA, oligonucleotide hydration, interactions with small molecule ligands and proteins. There has been a particular focus on nonstandard base associations and a number of groups have sought to characterize different non-Watson-Crick base pairs to further the understanding of their influence on the structure of duplex DNA and RNA, and to investigate which structural features might be utilized by enzymes in recognition and repair of these errors in DNA. Bases that have been chemically damaged by mutagenic or carcinogenic agents have distinctive modified hydrogen-bonding patterns and these have been investigated. The structure determination of a series of nonduplex DNA structures including examples of a triplex, quadruplexes, and a novel DNA loop have recently been published. In this article we survey the structures of a series of non-Watson-Crick base associations in duplex DNA and RNA. We show how nonstandard base pairs, base triads, and tetrads play an important role in stabilizing nonduplex structures. © 1997 John Wiley & Sons, Inc. Biopoly 44: 91–103, 1997     

Analysis of modified bases in DNA by stable isotope dilution gas chromatography-mass spectrometry: 5-Methylcytosine

A sensitive assay for 5-methylcytosine in DNA has been developed based on stable isotope dilution gas chromatography-mass spectrometry with selected ion monitoring. 5-([²H₃]-Methyl)cytosine and [methyl-²H₃]thymine have been synthesized as internal standards for analysis of DNA following acid digestion, conversion of pyrimidines to volatile t-butyldimethylsilyl derivatives, and separation in 3 min by gas chromatography. Submicrogram amounts of DNA have been analyzed for 5-methylcytosine content in the range 0.02–1.5 mol%. The estimated limit of quantitative measurement is 0.3 pmol of methylated base in a DNA hydrolysate. The method is compared with other techniques for quantitative measurement of methylated bases in DNA, and 5-methylcytosine levels and precision of analysis for calf thymus, pBR322, and ΦX-174 DNAs are reported and compared with literature values. The method can readily be adapted to the accurate high-sensitivity analysis of other methylated bases in DNA.     

Photocytotoxicity and near-IR light DNA cleavage activity of oxovanadium(IV) Schiff base complexes having phenanthroline bases

Oxovanadium(IV) complexes [VO(L)(B)] (1-3), where H₂L is a Schiff base ligand 2-(2-hydroxybenzylideneamino)phenol and B is 1,10-phenanthroline (phen for 1), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq for 2) or dipyrido[3,2-a:2′,3′-c]phenazine (dppz for 3), have been prepared, characterized and their DNA binding property and photo-induced DNA cleavage activity studied. Complex 3 which is structurally characterized by X-ray crystallography shows the presence of an oxovanadium(IV) moiety in a six coordinate VO₃N₃ coordination geometry. The complexes show a d-d band within 800-850 nm in DMF. The complexes display an oxidative response near 0.7 V versus SCE for V(V)-V(IV) and a reductive response within −1.1 to −1.3 V due to V(IV)-V(III) couple in DMF-0.1 M TBAP. The complexes are avid binders to calf thymus DNA giving binding constant values of 4.2 × 10⁴ to 1.2 × 10⁵ M⁻¹. The complexes do not show any “chemical nuclease” activity in dark. The dpq and dppz complexes are photocleavers of plasmid DNA in UV-A light of 365 nm via ¹O₂ pathway and in near-IR light (752.5 to 799.3 nm IR optics) by HO^• pathway. Complex 3 exhibits significant photocytotoxicity in visible light in HeLa cells giving IC₅₀ value of 13 μM, while it is less toxic in dark (IC₅₀ = 97 μM).     

Synthetically modified DNAs as substrates for polymerases

DNA polymerase enzymes process their natural substrates with very high specificity. Yet recent experiments have shown that these enzymes can also process DNA in which the backbone or bases are modified to a surprising degree. Such experiments have important implications in understanding the mechanisms of DNA replication, and suggest important biotechnological uses as well.     

Synthesis, structure, DNA binding and DNA cleavage activity of oxovanadium(IV) N-salicylidene-S-methyldithiocarbazate complexes of phenanthroline bases

Ternary oxovanadium(IV) complexes [VO(salmdtc)(B)] (1-3), where salmdtc is dianionic N-salicylidene-S-methyldithiocarbazate and B is N,N-donor phenanthroline bases like 1,10-phenanthroline (phen, 1), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq, 2) and dipyrido[3,2-a:2′,3′-c]phenazine (dppz, 3), are prepared, characterized and their DNA binding and DNA cleavage activity studied. Complex 3 is structurally characterized by single-crystal X-ray crystallography. The molecular structure shows the presence of a vanadyl group in six-coordinate VN₃O₂S coordination geometry. The S-methyldithiocarbazate Schiff base acts as a tridentate NSO-donor ligand in a meridional binding mode. The N,N-donor heterocyclic base displays a chelating mode of binding with an N-donor site trans to the vanadyl oxo-group. The complexes show a d-d band in the range of 675-707 nm in DMF. They exhibit an irreversible oxidative cyclic voltammetric response near 0.9 V due to the V(V)/V(IV) couple and a quasi-reversible reductive V(IV)/V(III) redox couple near −1.0 V vs. SCE in DMF-0.1 M TBAP. The complexes show good binding propensity to calf thymus DNA giving binding constant values in the range of 7.4 × 10⁴-2.3 × 10⁵ M⁻¹. The thermal denaturation and viscosity binding data suggest DNA surface and/or groove binding nature of the complexes. The complexes show poor chemical nuclease activity in dark in the presence of 3-mercaptopropionic acid (MPA) or hydrogen peroxide. The dpq and dppz complexes show efficient DNA cleavage activity in UV-A light of 365 nm via a type-II mechanistic pathway involving formation of singlet oxygen (¹O₂) as the reactive species.     

Mutagenic role of Watson-Crick protons in alkylated DNA bases: A theoretical study

Loss of Watson-Crick protons following DNA base alkylation has been proposed as a key event which confers mutation-inducing properties on to alkylated DNA bases. In this theoretical study, the promutagenic O⁶-guanine and O⁴-thymine sites are clearly distinguished from the nonmutagenic N⁷-guanine site on the basis of calculated values of mechanistic indicators for Watson-Crick proton acidity following alkylation at these respective sites. The degree of acidity predicted for these protons for each type of alkylated base accords well with the presence or absence of mutagenicity observed experimentally in each case.     

Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding

Summary Sixty-four eucaryotic nuclear DNA sequences, half of them coding and half noncoding, have been examined as expressions of first-, second-, or third-order Markov chains. Standard statistical tests found that most of the sequences required at least second-order Markov chains for their representation, and some required chains of third order. For all 64 sequences the observed one-step second-order transition count matrices were effective in predicting the two-step transition count matrices, and 56 of 64 were effective in predicting the three-step transition count matrices. The departure from random expectation of the observed first- and second-order transition count matrices meant that a considerable sample of eucaryotic nuclear DNA sequences, both protein coding and noncoding, have significant local structure over subsequences of three to five contiguous bases, and that this structure occurs throughout the total length of the sequence. These results suggested that present DNA sequences may have arisen from the duplication, concatenation, and gradual modification of very early short sequences.     

Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA·DNA duplexes

The effects of incorporation of the modified nucleobases, 2,6-diaminopurine (D) (substituting for adenine) and 7-chloro-1,8-naphthyridin-2-(1H)-one (bicyclic thymine, bT) (substituting for thymine), that stabilize PNA·DNA duplex formation by increasing hydrogen bonding and/or base pair stacking interactions have been studied by thermal denaturation in terms of thermodynamics. Although the stabilizing effect of the bT base (in contrast to that of D base) is abolished upon addition of dimethyl formamide, thereby indicating that the stabilization is predominantly due to hydrophobic stacking forces, duplex stabilization was found to be enthalpic for both nucleobases. Increased stabilization (although not fully linearly) was observed with increasing numbers of modified bases, and single base sequence discrimination was only slightly compromised, but showed significant dependence on the sequence context.     

New phthalimide‐appended Schiff bases: Studies of DNA binding,molecular docking and antioxidant activities

Herein, we investigated new phthalimide‐based Schiff base molecules as promising DNA‐binding and free radical scavenging agents. Physicochemical properties of these molecules were demonstrated on the basis of elemental analysis, ultraviolet–visible (UV–Vis), infra‐red (IR), ¹H and ¹³C nuclear magnetic resonance (NMR) spectroscopy. All spectral data are agreed well with the proposed Schiff base framework. The DNA‐binding potential of synthesized compounds were investigated by means of UV–visible, fluorescence, iodide quenching, circular dichroism, viscosity and thermal denaturation studies. The intrinsic binding constants (K _b) were calculated from absorption studies were found to be 1.1 × 10⁴ and 1.0 × 10⁴ M^?1 for compounds 2a and 2b suggesting that compound 2a binding abilities with DNA were stronger than the compound 2b. Our studies showed that the presented compounds interact with DNA through groove binding. Molecular docking studies were carried out to predict the binding between Ct‐DNA and test compounds. Interestingly, in silico predictions were corroborated with in vitro DNA‐binding conclusions. Furthermore, the title compounds displayed remarkable antioxidant activity compared with reference standard.     

Synthesis,characterization, redox behavior,DNA and protein binding and antibacterial activity studies of ruthenium(II) complexes of bidentate schiff bases

Two new ruthenium(II) complexes of Schiff base ligands (L) derived from cinnamaldehyde and ethylenediamine formulated as [Ru(L)(bpy)₂](ClO₄)₂, where L¹ = N,N’-bis(4-nitrocinnamald-ehyde)ethylenediamine and L² = N,N’-bis(2-nitrocinnamaldehyde)-ethylenediamine for complex 1 and 2, respectively, were isolated in pure form. The complexes were characterized by physicochemical and spectroscopic methods. The electrochemical behavior of the complexes showed the Ru(III)/Ru(II) couple at different potentials with quasi-reversible voltammograms. The interaction of the complexes with calf thymus DNA (CT-DNA) using absorption, emission spectral studies and electrochemical techniques have been used to determine the binding constant, K_b and the linear Stern–Volmer quenching constant, K_SV. The results indicate that the ruthenium(II) complexes interact with CT-DNA strongly in a groove binding mode. The interactions of bovine serum albumin (BSA) with the complexes were also investigated with the help of absorption and fluorescence spectroscopy tools. Absorption spectroscopy proved the formation of a ground state BSA-[Ru(L)(bpy)₂](ClO₄)₂ complex. The antibacterial study showed that the Ru(II) complexes (1 and 2) have better activity than the standard antibiotics but weak activity than the ligands.     

Letters to the editor

A decrease in salinity and temperature over the past 3000 years has presented the marine algae of the Baltic Sea with very considerable problems in adaptation. The effects of salinity upon a number of Baltic algae have been measured. The results showed cell mortality to be severe in 0, 68 and 102‰, and minimal in 6 and 11‰: there was most variation in tolerance to 34 and 51‰. The salt tolerances of Baltic marine algae have proved more hyposaline than those of British intertidal algae. Water uptake and loss in tissues of Chorda filum and Fucus vesiculosus from Baltic and British populations have been measured in response to salinity changes. The results revealed significant population differences in both live and killed tissues. Receptacle development and oogonial maturation have been observed in Baltic and British F. vesiculosus, and found to differ in seasonality. Some observations were associated with local sea temperatures but differences in the timing of receptacle initiation and in oogonial size were not. Th depauperate thallus, commonly ascribed to the effects of low salinity, was found to be a complicated phenomenon, comprising numerous attributes which are combined differently in different taxa. The morphological differences between Baltic and British marine algae were usually striking.

The marine algae of the Baltic Sea have therefore diverged in a number of ways from their N. Atlantic counterparts. The naturally high variability of these taxa has enabled them to survive the period of increasingly strong selection pressure which followed the Littorina Sea episode. Divergence seems not to have advanced to the point where speciation may be said to have occurred. The Baltic may therefore be contrasted with the much older Mediterranean Sea, which contains a large number of endemic species. Nevertheless, the Baltic is a site of very considerable evolutionary importance.     

Carbon-14 decay as a source of non-canonical bases in DNA

Background

Significant experimental effort has been applied to study radioactive beta-decay in biological systems. Atomic-scale knowledge of this transmutation process is lacking due to the absence of computer simulations. Carbon-14 is an important beta-emitter, being ubiquitous in the environment and an intrinsic part of the genetic code. Over a lifetime, around 50 billion ¹⁴C decays occur within human DNA.

Methods

We apply ab initio molecular dynamics to quantify ¹⁴C-induced bond rupture in a variety of organic molecules, including DNA base pairs.

Results

We show that double bonds and ring structures confer radiation resistance. These features, present in the canonical bases of the DNA, enhance their resistance to ¹⁴C-induced bond-breaking. In contrast, the sugar group of the DNA and RNA backbone is vulnerable to single-strand breaking. We also show that Carbon-14 decay provides a mechanism for creating mutagenic wobble-type mispairs.

Conclusions

The observation that DNA has a resistance to natural radioactivity has not previously been recognized. We show that ¹⁴C decay can be a source for generating non-canonical bases.

General significance

Our findings raise questions such as how the genetic apparatus deals with the appearance of an extra nitrogen in the canonical bases. It is not obvious whether or not the DNA repair mechanism detects this modification nor how DNA replication is affected by a non-canonical nucleobase. Accordingly, ¹⁴C may prove to be a source of genetic alteration that is impossible to avoid due to the universal presence of radiocarbon in the environment.     

Pressure-tuning infrared and Raman microscopy study of the DNA bases: adenine,guanine, cytosine,and thymine

Diamond-anvil cell, pressure-tuning infrared (IR), and Raman microspectroscopic measurements have been undertaken to examine the effects of high pressures up to about 45?kbar on the vibrational spectra of the four DNA bases, adenine, cytosine, guanine, and thymine. Small structural changes were evident for all the four bases, viz., for adenine and cytosine at 28–31?kbar; for guanine at 16–19?kbar; and for thymine at 25–26?kbar. These changes are most likely associated with alterations in the intermolecular hydrogen-bonding interactions. The pressure dependences of the main peaks observed in the IR spectra of the two phases of guanine lie in the ?0.07–0.66 (low-pressure phase) and 0.06–0.91 (high-pressure phase) cm^?1/kbar ranges. Also, in the Raman spectra of this nucleoside base, the dν/dP values range from ?0.07–0.31 (low-pressure phase) to 0.08–0.50 (high-pressure phase) cm^?1/kbar. Similar ranges of dν/dP values were obtained for the other three nucleoside bases.     

Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.

The repair of T:G mismatches in DNA is key for maintaining bacterial restriction/modification systems and gene silencing in higher eukaryotes. T:G mismatch repair can be initiated by a specific mismatch glycosylase (MIG) that is homologous to the helix-hairpin-helix (HhH) DNA repair enzymes. Here, we present a 2.0 A resolution crystal structure and complementary mutagenesis results for this thermophilic HhH MIG enzyme. The results suggest that MIG distorts the target thymine nucleotide by twisting the thymine base approximately 90 degrees away from its normal anti position within DNA. We propose that functionally significant differences exist in DNA repair enzyme extrahelical nucleotide binding and catalysis that are characteristic of whether the target base is damaged or is a normal base within a mispair. These results explain why pure HhH DNA glycosylases and combined glycosylase/AP lyases cannot be interconverted by simply altering their functional group chemistry, and how broad-specificity DNA glycosylase enzymes may weaken the glycosylic linkage to allow a variety of damaged DNA bases to be excised.     

The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study

In the present work, the influence of Cu⁺ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine–guanine, hypoxanthine–adenine, hypoxanthine–cytosine, hypoxanthine–thymine and hypoxanthine–hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu⁺ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu⁺ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu⁺ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses.

Communicated by Ramaswamy H. Sarma     

Synthesis, crystal structure and photo-induced DNA cleavage activity of ternary copper(II)-thiosemicarbazone complexes having heterocyclic bases

New ternary copper(II) complexes of formulations [Cu(Ph-tsc)B] (B=1,10-phenanthroline, phen (1); dipyridoquinoxaline, dpq (2); dipyridophenazine, dppz (3); Ph-H₂tsc, salicylaldehyde-N(4)-phenylthiosemicarbazone) and [Cu(Me-tsc)(phen)] (4, Me-H₂tsc, salicylaldehyde-N(4)-methylthiosemicarbazone) are prepared, and their DNA binding and cleavage properties studied. Complex 1 has been characterized by single crystal X-ray crystallography. The molecular structure shows a distorted square pyramidal (4 + 1) geometry of the complex with the dianionic NSO-donor N(4)-phenyl-substituted thiosemicarbazone binding at the basal plane and the NN-donor planar heterocyclic base (phen) displaying axial-equatorial coordination. The one-electron paramagnetic complexes exhibit axial EPR spectra and show a d-d band near 580 nm for the phen and near 720 nm for the dpq, dppz complexes in their electronic spectra in DMF. The complexes show quasireversible cyclic voltammetric response near 0.08 V vs. SCE in DMF-0.1 M TBAP assignable to the Cu(II)/Cu(I) couple. The Ph-tsc complexes display good binding propensity to calf thymus (CT) DNA. They also show oxidative cleavage of supercoiled (SC) pUC19 DNA in dark under aerobic condition in the presence of mercaptopropionic acid. The complexes exhibit light-induced DNA cleavage activity at 312 and 532 nm. Mechanistic investigations reveal DNA minor groove binding for the phen and dpq complexes, and major groove binding for the dppz species. The complexes are cleavage inactive under argon atmosphere. In the ternary structure, the thiosemicarbazones, dpq and dppz act as photosensitizers, while the planar heterocyclic bases are binder to DNA. The mechanistic pathways involved and the role of metal in the DNA cleavage reactions are discussed.