Enzymatic Analysis of Isomeric Trithymidylates Containing Ultraviolet Light-induced Cyclobutane Pyrimidine Dimers

Post- and Pre-Radiolabeling Assays for anti Thymidine Cyclobutane Dimers as Intrinsic Photoprobes of Various Types of G-Quadruplexes, Reverse Hoogsteen Hairpins, and Other Non-B DNA Structures

G-quadruplexes are thought to play an important role in gene regulation and telomere maintenance, but developing probes for their presence and location is challenging due to their transitory and highly dynamic nature. The majority of probes for G-quadruplexes have relied on antibody or small-molecule binding agents, many of which can also alter the dynamics and relative populations of G-quadruplexes. Recently, it was discovered that ultraviolet B (UVB) irradiation of human telomeric DNA and various G-quadruplex forming sequences found in human promoters, as well as reverse Hoogsteen hairpins, produces a unique class of non-adjacent anti cyclobutane pyrimidine dimers (CPDs). Therefore, one can envision using a pulse of UVB light to irreversibly trap these non-B DNA structures via anti CPD formation without perturbing their dynamics, after which the anti CPDs can be identified and mapped. As a first step toward this goal, we report radioactive post- and pre-labeling assays for the detection of non-adjacent CPDs and illustrate their use in detecting trans,anti T=(T) CPD formation in a human telomeric DNA sequence. Both assays make use of snake venom phosphodiesterase (SVP) to degrade the trans,anti T=(T) CPD-containing DNA to the tetranucleotide pTT=(pTT) corresponding to CPD formation between the underlined T's of two separate dinucleotides while degrading the adjacent syn TT CPDs to the trinucleotide pGT=T. In the post-labeling assay, calf intestinal phosphodiesterase is used to dephosphorylate the tetranucleotides, which are then rephosphorylated with kinase and [32P]-ATP to produce radiolabeled mono- and diphosphorylated tetranucleotides. The tetranucleotides are confirmed to be non-adjacent CPDs by 254 nm photoreversion to the dinucleotide p*TT. In the pre-labeling assay, radiolabeled phosphates are introduced into non-adjacent CPD-forming sites by ligation prior to irradiation, thereby eliminating the dephosphorylation and rephosphorylation steps. The assays are also demonstrated to detect the stereoisomeric cis,anti T=(T) CPD.

On the origins and development of the (32)P-postlabelling assay for carcinogen-DNA adducts

The (32)P-postlabelling method for the analysis of carcinogen-DNA adducts originated 30years ago from Baylor College of Medicine in Houston and was the work of a team comprised of Kurt and Erica Randerath, Ramesh Gupta and Vijay Reddy. With subsequent modifications and developments, it has become a highly sensitive and versatile method for the detection of DNA adducts that has been applied in a wide range of human, animal and in vitro studies. These include monitoring human exposure to environmental and occupational carcinogens, investigating genotoxicity of chemicals, elucidating pathways of metabolic activation of carcinogens, mechanistic studies of DNA repair, analysing the genotoxicity of complex mixtures and in ecotoxicology studies. Its use has been instrumental in providing new clues to the aetiology of some cancers and in identifying a new human carcinogen.

A selective, inexpensive probe for UV-induced damage in nucleic acids

Absorption of UV light by nucleic acids can result in the formation of molecular lesions in DNA and RNA, leading to mutagenesis, carcinogenesis, and cell death. In this work, hairpin oligonucleotide probes, which have previously been shown to be selective for DNA damage, are used. The hypochromic effect, which arises from the formation of the target–hairpin hybrid when there is no damage, is used to measure the amount of UV damage by measuring the amount of single-stranded DNA oligonucleotides. With accumulated UV exposure, the target–hairpin hybrid concentration decreases and the absorbance increases, enabling detection of UV-induced DNA damage. Our results show that the selectivity for DNA damage of the hypochromism probe is comparable with the molecular beacon probes, detecting between one and three lesions in an oligonucleotide. In addition, this probe is more than 10 times cheaper than molecular beacon probes. However, it shows lower sensitivity to DNA damage. This makes its use recommended for high-throughput, qualitative analysis of DNA damage. This introduces a simple, fast, mix-and-read assay for the detection of DNA damage.

³²P-postlabelling for the sensitive detection of DNA adducts

32P-postlabelling is a technique originally described by Kurt Randerath and colleagues for the sensitive detection of damage produced in DNA by reactive chemicals or genotoxins. The procedure essentially entails the enzymatic digestion of DNA to nucleoside 3'-monophosphates which are then radioactively labelled using T4 polynucleotide kinase and [γ(32)P]-adenosine triphosphate. Adducted nucleoside-3'-5'-bisphosphates are then separated from their normal counterparts by thin layer chromatography. Prior to the development of the assay, quantification of DNA adducts was confined to studies that utilised compounds synthesised to be isotopically labelled with tritium or carbon-14. As such, these studies were limited to specific and recognised genotoxins that could be administered only in the laboratory to cultures or animals. With (32)P-postlabelling it was possible not only to determine DNA adduct induction by a relatively uncharacterised suspected carcinogen, but also following exposure to complex mixtures containing a multitude of known and unknown potential genotoxins. The small amount of DNA required to perform the (32)P-postlabelling assay also meant that human biomonitoring studies using readily obtainable tissues, such as lymphocytes, were possible. Using the standard (32)P-postlabelling method, it is possible to detect a single DNA adduct in 10(7) to 10(8) normal nucleotides. The subsequent development of several enhancement methods improved this detection rate to one adduct in 10(10) nucleotides. For these reasons, the (32)-postlabelling assay represents an extremely versatile and extremely sensitive method to detect and monitor DNA damage.

A novel single-stranded DNA-specific 3'-5' exonuclease, Thermus thermophilus exonuclease I, is involved in several DNA repair pathways

Single-stranded DNA (ssDNA)-specific exonucleases (ssExos) are expected to be involved in a variety of DNA repair pathways corresponding to their cleavage polarities; however, the relationship between the cleavage polarity and the respective DNA repair pathways is only partially understood. To understand the cellular function of ssExos in DNA repair better, genes encoding ssExos were disrupted in Thermus thermophilus HB8 that seems to have only a single set of 5'-3' and 3'-5' ssExos unlike other model organisms. Disruption of the tthb178 gene, which was expected to encode a 3'-5' ssExo, resulted in significant increase in the sensitivity to H(2)O(2) and frequency of the spontaneous mutation rate, but scarcely affected the sensitivity to ultraviolet (UV) irradiation. In contrast, disruption of the recJ gene, which encodes a 5'-3' ssExo, showed little effect on the sensitivity to H(2)O(2), but caused increased sensitivity to UV irradiation. In vitro characterization revealed that TTHB178 possessed 3'-5' ssExo activity that degraded ssDNAs containing deaminated and methylated bases, but not those containing oxidized bases or abasic sites. Consequently, we concluded that TTHB178 is a novel 3'-5' ssExo that functions in various DNA repair systems in cooperation with or independently of RecJ. We named TTHB178 as T. thermophilus exonuclease I.

The 32P-postlabeling assay for DNA adducts

32P-postlabeling analysis is an ultrasensitive method for the detection and quantitation of carcinogen-DNA adducts. It consists of four principal steps: (i) enzymatic digestion of DNA to nucleoside 3'-monophosphates; (ii) enrichment of the adduct fraction of the DNA digest; (iii) 5'-labeling of the adducts by transfer of 32P-orthophosphate from [gamma-32P]ATP mediated by polynucleotide kinase (PNK); (iv) chromatographic or electrophoretic separation of the labeled adducts or modified nucleotides and quantitation by measurement of their radioactive decay. The assay requires only microgram quantities of DNA and is capable of detecting adducts at frequencies as low as 1 in 10(10) nt, making it applicable to the detection of events resulting from environmental exposures, or experiments using physiological concentrations of agents. It has a wide range of applications in human, animal and in vitro studies, and can be used for a wide variety of classes of compound and for the detection of adducts formed by complex mixtures. This protocol can be completed in 3 d.

Urinary thymidine dimer as a marker of total body burden of UV-inflicted DNA damage in humans

High levels of DNA damage are induced in human skin following exposure to UV radiation. Cyclobutane thymidine dimer (T = T) is the most common of these lesions, which are enzymatically removed as oligonucleotides from DNA and further degraded before excretion in urine. Analysis of such repair products in the urine could serve as a biomarker of total body burden of UV exposure. The aim of this study was to examine the kinetics of T = T excretion following a single tanning session in a commercial solarium and to validate the method by delivering different doses. Ten individuals used the solarium for a total of 35 sessions of body tanning. Urine was collected before UV exposure and daily thereafter (up to 5 or 11 days) and T = T was analyzed using a very sensitive and quantitative (32)P-postlabeling technique combined with high-performance liquid chromatography. Following exposure, T = T levels increased dramatically and reached a peak 3 days later; afterwards, the T = T levels gradually decreased. The total amount of T = T excreted differed about 5-fold among subjects given an equal dose. A 50% excretion time was calculated using the excretion data for the first 5 days and it was found to be between 55 and 76 hours for different individuals. There was a good correlation between the amount of T = T excreted during days 1 to 5 and the delivered UV dose. Reducing exposure time to 50% lowered the amount of T = T to 47%; if half of the lamps were covered, T = T decreased to 44%. Our data show that urinary T = T could be a suitable noninvasive biomarker for UV exposure; a finding which could also be applicable to studies in children.

Determination of photomodified oligodeoxynucleotides by exonuclease digestion, matrix-assisted laser desorption/ionization and post-source decay mass spectrometry

A fast method to detect and sequence photomodified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is reported. Upon treatment of modified ODNs with both phosphodiesterase I and phosphodiesterase II, the digestion stops at the sites of photomodification. Post-source decay (PSD) of MALDI-produced ions from two enzymatic digestion end products distinguishes isomers such as 5'-d(T[cis-syn]TAAGC) and 5'-d(CGAAT[cis-syn]T), which have symmetrical or identical compositions at the 3' and 5' ends, respectively. Studies have also been done to follow the kinetics for enzyme degradation of photomodified ODNs. The calculated rate constants from a mathematical treatment of the time-dependent MALDI data clearly show that the enzymatic digestion rate slows as the enzyme approaches the modified site.

Nuclease P1 digestion combined with tandem mass spectrometry for the structure determination of DNA photoproducts

UV irradiation of oligodeoxynucleotides at 254 nm generates several different types of DNA photoproducts, such as cis-syn cyclobutane pyrimidine dimers, pyrimidine[6-4]pyrimidone photoproducts and their Dewar valence isomers, and thymine-adenine photoproducts (TA). Nuclease P1 degrades the oligodeoxynucleotide photoproducts to small photoproduct-containing trinucleotides which are more amenable to tandem mass spectrometry (MS/MS) and HPLC. Product-ion mass spectra of these digestion products give characteristic fragmentations, allowing us to identify quickly the types of photomodifications. The results also show that mass spectrometry will be a tool for studying enzyme reaction mechanisms because it can determine rapidly and with high sensitivity the structures of the products that are generated.

Sensitive 32P-HPLC technique shows base sequence dependent differences in photolesion repair in human keratinocytes

Understanding the basis for individual susceptibility to skin cancer requires an understanding of the factors contributing to tumorigenesis. One such factor is the ability of the cell to repair DNA lesions induced following insult to the genome. Currently, research in this field is hampered by the lack of a suitably sensitive and specific method for the detection of DNA lesions. Developed previously 32P-HPLC in vitro analysis is applied in this study to measure UVB-induced dipyrimidine photolesions in human keratinocyte cultures. The high sensitivity of this method permitted the detection of individual cyclobutane pyrimidine dimers and 6-4 photoproducts in cells irradiated with UVB at doses below one minimal erythema dose. Using this technique one could detect approximately a 2-fold difference in a base sequence repair of photolesions. The rates of repair in the chromosomally unstable HaCaT keratinocyte cell line and in cultured primary human keratinocytes were compared. The presented data indicate the potential of the 32P-HPLC method for the study of DNA repair in cultured cells as well as for biomonitoring studies in humans.

Far-UV-induced dimeric photoproducts in short oligonucleotides: sequence effects

Cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone adducts represent the two major classes of far-UV-induced DNA photoproducts. Because of the lack of appropriate detection methods for each individual photoproduct, little is known about the effect of the sequence on their formation. In the present work, the photoproduct distribution obtained upon exposure of a series of dinucleoside monophosphates to 254 nm light was determined. In the latter model compounds, the presence of a cytosine, located at either the 5'- or the 3'-side of a thymine moiety, led to the preferential formation of (6-4) adducts, whereas the cis-syn cyclobutane dimer was the main thymine-thymine photoproduct. In contrast, the yield of dimeric photoproducts, and particularly of (6-4) photoadducts, was very low upon irradiation of the cytosine-cytosine dinucleoside monophosphate. However, substitution of cytosine by uracil led to an increase in the yield of (6-4) photoproduct. It was also shown that the presence of a phosphate group at the 5'- end of a thymine-thymine dinucleoside monophosphate does not modify the photoproduct distribution. As an extension of the studies on dinucleoside monophosphates, the trinucleotide TpdCpT was used as a more relevant DNA model. The yields of formation of the thymine-cytosine and cytosine-thymine (6-4) photoproducts were in a 5:1 ratio, very close to the value obtained upon photolysis of the related dinucleoside monophosphates. The characterization of the two TpdCpT (6-4) adducts was based on 1H NMR, UV and mass spectroscopy analyses. Additional evidence for the structures was inferred from the analysis of the enzymatic digestion products of the (6-4) adducts of TpdCpT with phosphodiesterases. The latter enzymes were shown to induce the quantitative release of the photoproduct as a modified dinucleoside monophosphate in a highly sequence-specific manner.

Detection of DNA modifications by the 32P-postlabelling assay

The 32P-postlabelling assay is widely used for detection of carcinogen-DNA adducts and other types of modified nucleotides in DNA. The principle of the method is the enzymatic digestion of DNA to nucleotides, 5'-labelling of these nucleotides with an isotopically labelled phosphate group, and the resolution and detection of the labelled products. Since the development of the original procedure in the early 1980s, many methods have been developed to increase the sensitivity of the method by selection of the modified nucleotides prior to labelling. In favourable circumstances, the method can achieve a level of detection as low as 1 modification in 10(10) nucleotides and requires relatively small quantities of DNA (less than 10 microg). It has been used to detect and characterise DNA adducts formed by numerous genotoxic carcinogens in bacterial and mammalian cells, in animals and, in some cases, in human tissues. Most classes of carcinogen have been subjected to 32P-postlabelling analysis, ranging from bulky and/or aromatic compounds to small and/or aliphatic compounds; it has also been used, with modifications, to detect apurinic sites in DNA, oxidative damage to DNA, UV-induced photodimers and, to a lesser extent, DNA damage caused by cytotoxic drugs. It has provided the first clear evidence for the DNA-damaging properties of several synthetic carcinogenic hormones. It has revealed the DNA-damaging potential of complex mixtures such as coal-tar and tobacco smoke. It has been used in human biomonitoring studies to detect DNA damage from occupational exposure to carcinogens, and also from environmental (i.e. non-occupational) exposures. It has also led to the discovery of the presence of numerous modifications in DNA arising from endogenous processes. The rapid expansion in the use of the assay has resulted in some divergence of procedures and there is a case to be made for the use of more standardised protocols, particularly where human exposure to carcinogens is being measured and where such results may be required for risk assessment. While the procedure is quantifiable, the efficiency of adduct labelling is, in many cases, not quantitative, and the lack of adduct standards has, in many cases, limited the interpretation of data to a demonstration of higher adduct levels in exposed groups compared with unexposed groups. Future developments are expected in automation, standardisation and, in combination with other analytical methods, elucidation of the structures of the many DNA lesions whose existence has been revealed by the 32P-postlabelling technique.

Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity

The putative blue-light photoreceptor genes of Arabidopsis thaliana and Sinapis alba (mustard) are highly homologous to the DNA repair genes encoding DNA photolyases. The photoreceptors from both organisms were overexpressed in Escherichia coli, purified, and characterized. The photoreceptors contain two chromophores which were identified as flavin adenine dinucleotide and methenyltetrahydrofolate. This chromophore composition suggests that the blue light photoreceptor may initiate signal transduction by a novel pathway which involves electron transfer. Despite the high degree of sequence identity to and identical chromophore composition with photolyases, neither photoreceptor has any photoreactivating activity.

A 32P-postlabelling assay for DNA adducts induced by cis-diamminedichloroplatinum(II)

A 32P-postlabelling method was developed to measure cisplatin-DNA adducts. Platinated oligonucleotides with different chain lengths were enzymatically digested with deoxyribonuclease I, snake venom phosphodiesterase (SVPD) and prostatic acid phosphatase. We found that SVPD was not able to cut the phosphodiester bond immediately 5' to the platinated nucleotide. As a result the adducts had an attached 5' unmodified nucleotide, while the unmodified nucleotides were digested to nucleosides. This is a facile enrichment procedure for the adducts, because the normal nucleosides lacking the 3'-phosphate are not substrates for T4 polynucleotide kinase. Instead, the adduct fragments containing an unmodified nucleotide at their 5' end can be phosphorylated by T4 polynucleotide kinase and [-32P]ATP. This method was also shown to be suitable for the detection of cisplatin-adducts in platinated calf thymus DNA.

Characterization of gamma-radiation induced decomposition products of thymidine-containing dinucleoside monophosphates by nuclear magnetic resonance spectroscopy

To study the chemical and biochemical influence of loss of base aromaticity, dinucleoside monophosphates containing cis-5R,6S-thymidine glycol (Tg) and 5R and 5S 5,6-dihydrothymidine (Th) were prepared from d-ApT and d-TpA by KMnO4 oxidation and rhodium-catalysed hydrogenation, respectively. One and two dimensional 1H NMR techniques were used to characterize the solution conformation of each of the modified dinucleoside monophosphates for comparison with the unmodified compounds. Coupling constant data show that all sugar moieties adopt a predominantly 2'-endo conformation. Estimates of proton-proton distances from two-dimensional NOE experiments reveal that most of the glycosidic bonds prefer the anti conformation. Analysis of the C5'-C4' (gamma) torsion angle of the hydroxymethyl group using 3JH4'H5' and 3JH4'H5" data indicate that these modifications to thymine have little effect on the gamma conformer populations. Although, in general, additions at C5 and C6 of thymine in d-ApT and d-TpA profoundly distort the pyrimidine, they do not otherwise significantly alter the conformation of these compounds relative to the unsubstituted dinucleoside monophosphates. The one exception is the thymine glycol of d-TgpA, which appears to have a higher syn population than the parent compound.

Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase

Photolyases reverse the effects of UV light on cells by converting cyclobutane dipyrimidine photoproducts (pyrimidine dimers, Pyr mean value of Pyr) into pyrimidine monomers in a light-dependent reaction. Previous work has suggested that, based on substrate preference, there are two classes of photolyase: DNA photolyase as exemplified by the Escherichia coli enzyme, and RNA photolyases found in plants such as Nicotiana tabacum and Phaseolus vulgaris. In experiments aimed at identifying substrate determinants, including the pentose ring, for binding and catalysis by E. coli DNA photolyase we tested several Pyr mean value of Pyr. We found that the enzyme has relative affinities for photodimers of T mean value of T greater than or equal to U mean value of T greater than U mean value of U much greater than C mean value of C and that the E-FADH2 form of the enzyme repairs these dimers at 366 nm with absolute quantum yields of 0.9 (T mean value of T), 0.8 (U mean value of T), 0.6 (U mean value of U), and 0.05 (C mean value of C). The enzyme also repairs an isolated thymine dimer and the synthetic substrate, 1,1'-trimethylene-bis (thymine) cyclobutane dimer. Unexpectedly, we found that this enzyme, previously thought to be specific for DNA, repairs uracil cyclobutane dimers in poly(rU). The affinity of photolyase for a uracil dimer in RNA is about 10(4)-fold lower than that for a U mean value of U in DNA; however, once bound, the enzyme repairs the photodimer with the same quantum yield whether the dimer is in ribonucleoside or deoxyribonucleoside form.

Response of phage T4 polynucleotide kinase toward dinucleotides containing apurinic sites: design of a 32P-postlabeling assay for apurinic sites in DNA

We have examined the capacity of bacteriophage T4 polynucleotide kinase (EC 2.7.1.78) to phosphorylate the partially depurinated products of d-ApA, namely, d-SpA and d-ApS (where S represents an apurinic deoxyribose group). It was observed that the enzyme acted only on the latter isomer. Since molecules of this type (d-NpS) are the sole apurinic site containing products resulting from the combined digestion of lightly depurinated DNA by snake venom phosphodiesterase and calf alkaline phosphatase [Weinfeld, M., Liuzzi, M., & Paterson, M. C. (1989) Nucleic Acids Res. 17, 3735-3745], we were able to devise a postlabeling assay for these biologically important DNA lesions. The method offers several advantages, including (a) elimination of the need for prelabeled DNA, (b) high (femtomole range) sensitivity, and (c) nearest-neighbor analysis of bases 5' to apurinic/apyrimidinic sites. Using this assay, we obtained a value for the rate of depurination of form I pRSVneo plasmid DNA, incubated at pH 5.2 at 70 degrees C, of approximately 3.3 apurinic sites per plasmid molecule per hour. This value compares favorably with previously published data of others, acquired by alternative approaches. The rate of depurination of poly(dA), treated in a similar fashion, was found to be approximately 1 base per 10(3) nucleotides per hour.

Monovalent cation-induced structure of telomeric DNA: the G-quartet model

We have investigated the structures formed by oligonucleotides composed of two or four repeats of the telomeric sequences from Oxytricha and Tetrahymena. The Oxytricha four-repeat molecule (d(T4G4)4 = Oxy-4) forms structures with increased electrophoretic mobility in nondenaturing gels containing Na+, K+, or Cs+, but not in gels containing Li+ or no added salt. Formation of the folded structure results in protection of a set of dG's from methylation by dimethyl sulfate. Efficient UV-induced cross-links are observed in Oxy-4 and the related sequence from Tetrahymena (d(T2G4)4 = Tet-4), and join thymidine residues in different repeats. Models proposed to account for these data involve G-quartets, hydrogen-bonded structures formed from four guanosine residues in a square-planar array. We propose that the G-quartet structure must be dealt with in vivo by the telomere replication machinery.