Polybrene/DMSO-assisted gene transfer. Generating stable transfectants with nanogram amounts of DNA

Polybrene/DMSO-assisted gene transfer is a simple and versatile transfection strategy capable of producing high numbers of stable transfectants from adherent monolayer cultures with low (nanogram) quantities of exogenous DNA. The procedure involves two stages: adsorption and internalization. The former is mediated by polybrene (a polycation polymer) and favors the uniform coating of target cells with polybrene-DNA complexes. Following adsorption, the cells are permeabilized by a brief exposure to dimethyl sulfoxide (DMSO) to facilitate the uptake of DNA complexes. Diverse cell types can be exposed to a wide range of polybrene concentrations without adverse effects. By contrast, the key determinant of success is the DMSO permeabilization regime, which must be configured independently for each cell line. Protocols optimized for gene transfer in murine and human fibroblasts are presented along with a guide for the rapid optimization of the method. The advantages and limitations of the method are also discussed.

Influence of nitrogen, oxygen, and nitroimidazole radiosensitizers on DNA damage induced by ionizing radiation

Oxygen and nitroaromatic compounds are known to enhance the sensitivity of cells to ionizing radiation. Employing calf thymus DNA and oligo(dA)12/poly(dT), we have examined the differences to DNA damage, in particular thymine glycols and the 3'-DNA termini at strand breaks, arising from irradiation under anoxic and oxic conditions and the presence and absence of misonidazole [1-(2-nitro-1-imidazoyl)-3-methoxy-2-propanol]. We show that (i) irradiation under nitrogen generates strand breaks almost exclusively with 3'-phosphate termini; (ii) irradiation under oxic conditions increases the yield of strand breaks 3-fold, and the 3' termini consist of 3'-phosphoglycolate and 3'-phosphate end groups in a ratio of approximately 1.6; (iii) the patterns of base and sugar damage detectable by a postlabeling assay [Weinfield, M., & Soderlind, K.-J. (1991) Biochemistry 30, 1091-1097] differ completely between DNA irradiated under oxic vs anoxic conditions; (iv) the presence of misonidazole under anoxic conditions does not increase the level of strand breakage but, like oxygen, significantly enhances the formation of 3'-phosphoglycolate end groups; (v) the presence of misonidazole during anoxic irradiation does not increase the yield of any other type of 'oxic' damage detectable by the postlabeling assay, such as thymine glycols; and (vi) misonidazole at concentrations greater than 50 microM affords significant protection to naked DNA, probably by OH radical scavenging, and both the nitroaromatic ring and methoxyisopropanol side chain contribute to this protective action.

Influence of nucleic acid base aromaticity on substrate reactivity with enzymes acting on single-stranded DNA

Stacking between aromatic amino acids and nucleic acid bases may play an important role in the interaction of enzymes with nucleic acid substrates. In such circumstances, disruption of base aromaticity would be expected to decrease enzyme activity on the modified substrates. We have examined the requirement for DNA base aromaticity of five enzymes that act on single-stranded DNA, T4 polynucleotide kinase, nucleases P1 and S1, and snake venom and calf spleen phosphodiesterases, by comparing their kinetics of reaction with a series of dinucleoside monophosphates containing thymidine or a ring-saturated derivative. The modified substrates contained either cis-5R,6S-di-hydro-5,6-dihydroxythymidine (thymidine glycol) or a mixture of the 5R and 5S isomers of 5,6-dihydrothymidine. It was observed that for all the enzymes, except snake venom phosphodiesterase, the parent molecules were better substrates than the dihydrothymidine derivatives, while the thymidine glycol compounds were significantly poorer substrates. Snake venom phosphodiesterase acted on the unmodified and dihydrothymidine molecules at almost the same rate. These results imply that for all the remaining enzymes base aromaticity is a factor in enzyme-substrate interaction, but that additional factors must contribute to the poorer substrate capacity of the thymidine glycol compounds. The influence of the stereochemistry of the dihydrothymidine derivatives was also investigated. We observed that nuclease P1 and S1 hydrolysed the molecules containing 5R-dihydrothymidine approximately 50-times faster than those containing the S-isomer. The other enzymes displayed no measurable stereospecificity.

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.

Human HeLa cell enzymes that remove phosphoglycolate 3'-end groups from DNA

We have purified three chromatographically distinct human enzyme activities from HeLa cells, that are capable of converting bleomycin-treated DNA into a substrate for E. coli DNA polymerase I. The bleomycin-treated DNA substrate used in this study has been characterized via a 32P-postlabeling assay and shown to contain strand breaks with 3'-phosphoglycolate termini as greater than 95% of the detectable dose-dependent lesions. The purified HeLa cell enzymes were shown to be capable of removing 3'-phosphoglycolates from this substrate. Also 3'-phosphoglycolate removal and nucleotide incorporation were enzyme dependent. In addition, all three Hela cell enzymes have been determined to possess Class II AP endonuclease activity. The enzymes lack 3'----5' exonuclease activity and are, therefore, dissimilar to exonuclease III--an E. coli enzyme that can remove 3'-phosphoglycolate.

Specification and implementation of a digital Hopfield-type associative memory with on-chip training

The definition of the requirements for the design of a neural network associative memory, with on-chip training, in standard digital CMOS technology is addressed. Various learning rules that can be integrated in silicon and the associative memory properties of the resulting networks are investigated. The relationships between the architecture of the circuit and the learning rule are studied in order to minimize the extra circuitry required for the implementation of training. A 64-neuron associative memory with on-chip training has been manufactured, and its future extensions are outlined. Beyond the application to the specific circuit described, the general methodology for determining the accuracy requirements can be applied to other circuits and to other autoassociative memory architectures.

32P-postlabeling detection of radiation-induced DNA damage: identification and estimation of thymine glycols and phosphoglycolate termini

A 32-P-postlabeling assay has been developed that permits detection of several radiogenic base and sugar lesions of DNA at the femtomole level. The technique is based on the inability of DNase I and snake venom phosphodiesterase to cleave the internucleotide phosphodiester bond immediately 5' to the site of damage so that complete digestion of irradiated DNA with these nucleases and alkaline phosphatase yields lesion-bearing "dinucleoside" monophosphates. Because these fragments contain an unmodified nucleoside at the 5'-end of each molecule, they can be readily phosphorylated by T4 polynucleotide kinase and [gamma-32P]ATP and analyzed by polyacrylamide gel electrophoresis and reverse-phase HPLC. We observed a linear induction of total damage in DNA irradiated with 5-50 Gy. Virtually no damage was detected when the DNA was irradiated in solution containing 1 M DMSO, implicating hydroxyl radicals in the formation of these lesions. Evidence for the presence of thymine glycols and phosphoglycolate groups came from (i) a comparison of the radiation-induced products with those produced by OsO4 and KMnO4 and (ii) incubation of irradiated DNA with Escherichia coli endonuclease III and exonuclease III before analysis by the postlabeling procedure. This was confirmed by comigration of the radiogenic products with chemically synthesized markers. G values of 0.0022 and 0.0105 mumol J-1 were obtained for thymine glycol and phosphoglycolate production, respectively. The identity of the 5'-nucleotide of each isolated compound was obtained by nuclease P1 digestion. This analysis of nearest-neighbor bases to thymine glycols and phosphoglycolates indicated a nonrandom interaction between radiation-induced hydroxyl radicals and DNA.

Preparation of Recombinant Plasmid DNA for DNA-Mediated Gene Transfer

Recombinant plasmid constructs are frequently employed in transfection experiments. With the availability of a wide spectrum of specialized and versatile eucaryotic cloning/expression vectors, investigators have been given powerful tools to expedite the elucidation of mechanisms governing gene expression, and to facilitate the identification of genes participating in diverse cellular processes (namely, metabolism, the immune response, differentiation and development, the repair of DNA damage, and malignant transformation).

Effect of membrane fatty acyl composition on LDL metabolism in Hep G2 hepatocytes

The mechanism by which dietary cis-unsaturated fatty acids lower plasma levels of low-density lipoprotein (LDL) cholesterol is unknown. Since plasma membrane incorporation of dietary cis-unsaturated fatty acids is known to alter the function of plasma membrane associated proteins, perhaps by increasing membrane fluidity, we examined LDL receptor function in Hep G2 hepatocytes that were unmodified, enriched with the cis-unsaturated fatty acids oleate or linoleate, or enriched with the saturated fatty acids stearate or palmitate. Hepatocytes enriched in cis-unsaturated fatty acids exhibited augmented LDL binding, uptake, and degradation in comparison to unmodified cells. In contrast, Hep G2 hepatocytes enriched in saturated fatty acids had decreased LDL binding, uptake, and degradation. Enrichment with oleate or linoleate resulted in a decrease in the calculated fatty acyl mole-weighted melting point of the plasma membrane and an increase in plasma membrane fluidity, as measured by the steady-state fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene incorporated into the plasma membrane. Conversely, stearate or palmitate enrichment resulted in an increased plasma membrane fatty acyl mole-weighted melting point and decreased plasma membrane fluidity. LDL binding, uptake, and degradation varied with plasma membrane fluidity in a highly correlated manner. Thus, one mechanism by which dietary cis-unsaturated fatty acids lower LDL cholesterol may possibly involve an alteration in membrane lipid composition or membrane fluidity that promotes enhanced LDL receptor function, thereby leading to increased hepatic clearance of LDL.

Lipoprotein(a), fibrin binding, and plasminogen activation

Lipoprotein(a) (Lp[a]) is a complex plasma lipoprotein in which apolipoprotein (apo) B-100 is covalently linked by a disulfide bridge to a unique apolipoprotein, apo(a). The cDNA of apo(a) has recently been isolated and sequenced, and a remarkable homology to human plasminogen has been noted. In this report, we demonstrate that, like plasminogen, Lp(a) binds to fibrin. In addition, Lp(a) competes with plasminogen and tissue-type plasminogen activator for fibrin binding. As a functional consequence of these binding properties, we show that Lp(a) attenuates the fibrin-dependent enhancement of tissue-type plasminogen activator activity against the native substrate, and does so as an uncompetitive inhibitor (Ki = 15 nM). Finally, we show that in a plasma milieu, Lp(a) attenuates clot lysis induced by tissue-type plasminogen activator. None of these effects was noted with low density lipoprotein free of apo(a). These data suggest that Lp(a) influences the fibrinolytic system and probably does so by virtue of the fibrin binding properties conferred by the kringle repeats of apo(a).

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.

Plasma membrane enrichment with cis-unsaturated fatty acids enhances LDL metabolism in U937 monocytes

The mechanism by which dietary cis-unsaturated fatty acids lower low density lipoprotein (LDL) cholesterol is unknown. Because cis-unsaturated fatty acids incorporated into cell membranes increase membrane fluidity and, as a result, can alter membrane-dependent cell functions, we examined LDL binding, uptake, and degradation in upregulated U937 monocytes enriched in membrane oleate, a monounsaturated fatty acid, and membrane linoleate, a polyunsaturated fatty acid. The same parameters were also examined in upregulated U937 monocytes enriched in membrane stearate, a saturated fatty acid, and in upregulated, unmodified U937 monocytes. Monocytes enriched in cis-unsaturated fatty acids exhibited augmented LDL binding, internalization, and degradation compared with both stearate-enriched monocytes and unmodified monocytes. The molar potency of linoleate in augmenting LDL metabolism was 50% greater than that of oleate. Enrichment with oleate and linoleate resulted in a decrease in the fatty acyl mole-weighted melting point of the plasma membrane and an increase in plasma membrane fluidity, as indicated by a reduction in the steady-state fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene incorporated into the membrane. Stearate-enriched monocytes exhibited a slight increase in the plasma membrane fatty acyl mole-weighted melting point and essentially no change in plasma membrane fluidity. Thus, one mechanism by which cis-unsaturated fatty acids lower LDL cholesterol may involve alteration in membrane lipid composition and physical properties, thereby leading to an increase in cellular clearance of this atherogenic lipoprotein.

Selective hydrolysis by exo- and endonucleases of phosphodiester bonds adjacent to an apurinic site

Partial depurination of d-ApA produced two UV260nm-absorbing isomers, d-SpA and d-ApS (where S represents the depurinated deoxyribose sugar), that provided simple model compounds with which to examine, by HPLC, the response of nucleases to phosphodiester bonds flanked 3' or 5' by an apurinic site. The structural identity of each compound was established by (i) reaction with methoxyamine to confirm the presence of an abasic deoxyribose group, and (ii) degradation of d-SpA under mild alkaline conditions to distinguish it from d-ApS. At an enzyme concentration which led to complete hydrolysis of d-ApA, snake venom phosphodiesterase readily cleaved d-SpA to 5'-dAMP but had no discernible effect on d-ApS. Calf spleen phosphodiesterase also failed to act on one isomer, in this instance d-SpA, but additionally reacted at a much slower rate (approximately 100 fold) with d-ApS than with d-ApA. Three single-strand specific endonucleases, nuclease P1, nuclease S1 and mung bean nuclease, all responded in an identical manner, hydrolysing d-ApS but not d-SpA. The possibility that the aldehyde group at the AP sites might be responsible for some of these observations was rejected after repeating the enzyme digestions with the methoxyamine-capped molecules and observing no differences from the reactions with d-SpA and d-ApS.

Enzymatic analysis of isomeric trithymidylates containing ultraviolet light-induced cyclobutane pyrimidine dimers. II. Phosphorylation by phage T4 polynucleotide kinase

Phage T4 polynucleotide kinase (EC 2.7.1.78) proved incapable of catalyzing the phosphorylation of thymidylyl-(3'----5')-thymidine containing either a cis-syn-cyclobutane pyrimidine dimer (d-T less than p greater than T) or a 6-4'-[pyrimidin-2'-one]pyrimidine photoproduct (d-T[p]-T), and similarly the UV-modified compounds of (dT)3 bearing either photoproduct at their 5'-end (d-T less than p greater than TpT and d-T[p]TpT). In contrast, the 3'-structural isomers of these trinucleotides (d-TpT less than p greater than T and d-TpT[p]T) were phosphorylated at the same rate as the parent compound. These phosphorylatable lesion-containing oligonucleotides are quantitatively released from UV-irradiated poly(dA):poly(dT) by enzymatic hydrolysis with snake venom phosphodiesterase and alkaline phosphatase (Liuzzi, M., Weinfeld, M., and Paterson, M. C. (1989) J. Biol. Chem. 264, 6355-6363). By combining this digestion regimen with phosphorylation by polynucleotide kinase and [gamma-32P]ATP, pyrimidine dimers were quantitated at the fmol level following exposure of poly(dA):poly(dT) and herring sperm DNA to biologically relevant UV fluences. The rate of dimer induction in the synthetic polymer, approximately 10 dimers/10(6) nucleotides/Jm-2, was in close agreement with that obtained by conventional methods. Dimers were induced at one-fourth of this rate in the natural DNA. Further treatment of the phosphorylated oligonucleotides derived from irradiated herring sperm DNA with nuclease P1 released the labeled 5'-nucleotide, thus permitting analysis of the nearest-neighbor bases 5' to the lesions. We observed a ratio for pyrimidine-to-purine bases of almost 6:1, implicating tripyrimidine stretches as hotspots for UV-induced DNA damage.

Enzymatic analysis of isomeric trithymidylates containing ultraviolet light-induced cyclobutane pyrimidine dimers. I. Nuclease P1-mediated hydrolysis of the intradimer phosphodiester linkage

Our recent findings suggest that enzymatic hydrolysis of the intradimer phosphodiester bond may constitute the initial step in the repair of UV light-induced cyclobutane pyrimidine dimers in human cells. To examine the susceptibility of this phosphodiester linkage to enzyme-mediated hydrolysis, the trinucleotide d-Tp-TpT was UV-irradiated and the two isomeric compounds containing a cis-syn-cyclobutane dimer were isolated by high performance liquid chromatography and treated with various deoxyribonucleases. Snake venom phosphodiesterase hydrolyzed only the 3'-phosphodiester group in the 5'-isomer (d-T less than p greater than TpT) but was totally inactive toward the 3'-isomer (d-TpT less than p greater than T). In contrast, calf spleen phosphodiesterase only operated on the 3'-isomer by cleaving the 5'-internucleotide bond. Kinetic analysis revealed that (i) the activity of snake venom phosphodiesterase was unaffected by a dimer 5' to a phosphodiester linkage, (ii) the action of calf spleen phosphodiesterase was partially inhibited by a dimer 3' to a phosphodiester bond, and (iii) Escherichia coli phr B-encoded DNA photolyase reacted twice as fast with d-T less than p greater than TpT as with d-TpT less than p greater than T. Mung bean nuclease, nuclease S1, and nuclease P1 all cleaved the 5'-internucleotide linkage, but not the intradimer phosphodiester bond, in d-TpT less than p greater than T. Both phosphate groups in d-T less than p greater than TpT were refractory to mung bean nuclease or nuclease S1. Incubation of d-T less than p greater than TpT with nuclease P1, however, generated the novel compound dT less than greater than d-pTpT containing a severed intradimer phosphodiester linkage. Accordingly, nuclease P1 represents the first purified enzyme known to hydrolyze an intradimer phosphodiester linkage.

Isolation and characterization of the diastereoisomers of a series of phosphate-ethylated dinucleoside monophosphates

Internucleotide phosphate esterification is a common reaction of many potent carcinogenic alkylating agents. It can give rise to two stereochemically distinct molecules about a triesterified phosphorus atom. The eight individual diastereoisomers derived from phosphate ethylation of d-ApT, d-CpT, d-GpT, and d-TpT were prepared from o-chlorophenyl phosphotriester intermediates and isolated by reverse-phase HPLC. Each pair of isomers, together with its parent analog, was examined by variable temperature circular dichroism. The results are interpreted in terms of secondary structure changes from which the absolute configurations of the ethylated phosphate groups can be inferred. These configurational assignments were confirmed by 31P NMR.

DNA cyclobutane pyrimidine dimers with a cleaved internal phosphodiester bond can be photoenzymatically reversed by Escherichia coli PhrB photolyase

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Factors influencing efficiency and reproducibility of polybrene-assisted gene transfer

A systematic investigation of factors influencing the efficiency of polybrene-assisted gene transfer for both transient and stable foreign gene expression was carried out utilizing NIH 3T3 fibroblasts as prototypic recipients for the plasmid expression vectors pSV2cat and pSV2neo. While transfection cocktail composition and cell density, in addition to polybrene exposure conditions and exogenous DNA concentration, each played an important role, the key determinant to achieving excellent transfection efficiency proved to be the DMSO treatment regimen. Under optimal conditions, the yield of colonies resistant to the neomycin analog, G418, increased linearly at the rate of 10 clones/ng of input (native form I pSV2neo) DNA up to a plasmid concentration of 50 ng, whereupon the dose-response for colony recovery became semilogarithmic. The incidence of stable transformants was doubled by linearization of the vector DNA, whereas the addition of carrier DNA to the transfection cocktail was without effect until present at concentrations above 10-fold molar excess, at which point the efficacy of gene transfer declined rapidly. Combined Southern and dot-blot analyses of transformed cell DNA demonstrated that the polybrene-DMSO procedure led to the stable integration of relatively few copies of the marker gene in each transformant; the actual number varied from 1-3 to 10-15 per host genome, depending on the concentration of pSV2neo DNA added. The potential for the adaptation of this DNA transfection procedure for general use with other mammalian cell types, as well as its technical strengths and weaknesses, is discussed.

Rapid radiolabel-sparing thin-layer chromatography method for the visual assessment of chloramphenicol acetyltransferase gene expression

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Mutual involvement and alienation in families of Holocaust survivors

Clinical studies suggest that children of Holocaust survivors remain enmeshed with their families or alienated from them. To examine the applicability of these observations to a nonclinic population, questionnaire responses of a randomly selected community sample of adult children (ages 19-36) of Holocaust survivors (COS) were compared to those of children of other immigrants (COI), and of children of native-born parents (CON). The clinical findings were not supported in most of the wide range of possible manifestations of ties to or distance from the family. COS did, however, report more dissatisfaction with some aspects of the cross-sexed parents' disciplinary habits in the past. Male COS continued to feel that way in the present, wishing their mothers would be more permissive. Documented negative consequences of prolonged, severe victimization may affect only small segments of the second generation.

Selective inhibition by methoxyamine of the apurinic/apyrimidinic endonuclease activity associated with pyrimidine dimer-DNA glycosylases from Micrococcus luteus and bacteriophage T4

The UV endonucleases [endodeoxyribonuclease (pyrimidine dimer), EC 3.1.25.1] from Micrococcus luteus and bacteriophage T4 possess two catalytic activities specific for the site of cyclobutane pyrimidine dimers in UV-irradiated DNA: a DNA glycosylase that cleaves the 5'-glycosyl bond of the dimerized pyrimidines and an apurinic/apyrimidinic (AP) endonuclease that thereupon incises the phosphodiester bond 3' to the resulting apyrimidinic site. We have explored the potential use of methoxyamine, a chemical that reacts at neutral pH with AP sites in DNA, as a selective inhibitor of the AP endonuclease activities residing in the M. luteus and T4 enzymes. The presence of 50 mM methoxyamine during incubation of UV- (4 kJ/m2, 254 nm) treated, [3H]thymine-labeled poly(dA).poly(dT) with either enzyme preparation was found to protect completely the irradiated copolymer from endonucleolytic attack at dimer sites, as assayed by yield of acid-soluble radioactivity. In contrast, the dimer-DNA glycosylase activity of each enzyme remained fully functional, as monitored retrospectively by release of free thymine after either photochemical- (5 kJ/m2, 254 nm) or photoenzymic- (Escherichia coli photolyase plus visible light) induced reversal of pyrimidine dimers in the UV-damaged substrate. Our data demonstrate that the inhibition of the strand-incision reaction arises because of chemical modification of the AP sites and is not due to inactivation of the enzyme by methoxyamine. Our results, combined with earlier findings for 5'-acting AP endonucleases, strongly suggest that methoxyamine is a highly specific inhibitor of virtually all AP endonucleases, irrespective of their modes of action, and may therefore prove useful in a wide variety of DNA repair studies.

Molecular evidence for cleavage of intradimer phosphodiester linkage as a novel step in excision repair of cyclobutyl pyrimidine photodimers in cultured human cells

A re-analysis of the metabolic fate of ultraviolet light (u.v.)-induced cyclobutyl pyrimidine dimers in the DNA of dermal fibroblasts from patients with different genetic forms of xeroderma pigmentosum (XP), a rare cancer-prone skin disorder, has provided new insight into the mode of dimer repair in normal human cells. When DNA isolated from post-u.v. incubated cultures was subjected to enzymic photoreactivation (PR) to probe dimer authenticity, single-strand scissions were produced in the damaged DNA of incubated XP group A and D cells, but not in DNA from XP group C cells or normal controls. Since enzymic PR treatment ruptures only the cyclobutane ring, these results suggested that in dimer excision-defective XP group A and D strains, the intradimer phosphodiester bond may have been cleaved without site restoration. Such a cleavage event had not previously been detected; the possibility that this reaction may be an early step in the normal excision-repair process is supported by the observed release of free thymidine (dThd) and its monophosphate (TMP), but not of thymine, upon photochemical reversal of the dimer-containing excision fragments isolated from post-u.v. incubated normal cells. The combined number of dThd and TMP molecules released was equal to approximately equal to 80% of the number of dimers photoreversed; for such release to occur, the dimer must both be at one end of an excised fragment and contain an internal phosphodiester break. Taken together, these data lead us to propose a novel model for dimer repair in human cells in which hydrolysis of the intradimer phosphodiester linkage precedes the concerted action of a generalized 'bulky lesion-repair complex' involving conventional strand incision/lesion excision/repair resynthesis/strand ligation reactions.

Synthesis and properties of oligodeoxyribonucleotides containing an ethylated internucleotide phosphate

Internucleotide phosphotriesters comprise an important class of DNA lesions produced by carcinogenic alkylating agents. To avoid confusion resulting from the presence of other DNA lesions, synthetically prepared oligonucleotides containing ethylated internucleotide phosphates as the sole form of damage were employed to investigate several chemical and biochemical properties of DNA alkyl phosphotriesters. A total of four oligonucleotides were synthesised for this study, the dimers Tp(Et)T and pTp(Et)T and the decamer d-TpTpTp(Et)TpCpTpApTpTpT together with its unmodified analogue. The dimers were characterized by UV and phosphorus NMR spectroscopy and the decamers by two-dimensional homochromatography, alkali hydrolysis, and variable-temperature circular dichroism (CD). Alkali hydrolysis of the ethylated decamer produced strand breaks in approximately 75% of the molecules. This is in close agreement with data previously obtained for dinucleoside ethyl phosphotriesters and triesters in alkylated cellular DNA. Results from the CD study suggest that the ethyl substituent does not disrupt base stacking within the oligomer. The interactions of two enzymes with the alkylated oligonucleotides were examined. First, it was found that ethylation of the internucleotide phosphate renders TpT inactive as a substrate for T4 polynucleotide kinase, implying that a negative charge is required on the 3'-phosphate group of the nucleotide to be phosphorylated. Hence, postlabeling assays of DNA damage that depend upon enzymatic phosphorylation of modified 3'-nucleotides cannot be applied to dinucleoside alkyl phosphotriesters. Second, both decamers, when annealed to a single-stranded plasmid template, were able to prime DNA synthesis, catalyzed by Escherichia coli DNA polymerase I, with equal effectiveness. The use of this reaction as a means of site-specifically incorporating phosphotriesters into viral vectors is recognized.