Site-specific gene modification by PNAs conjugated to psoralen

DNA-binding molecules, including triplex-forming oligonucleotides (TFOs) and peptide nucleic acids (PNAs), can be utilized to introduce site-specific mutations or to promote recombination at selected genomic sites. To further evaluate the utility of PNAs for site-specific gene modification, we tested dimeric bis-PNAs conjugated to psoralen. These PNAs are designed to form a triplex-invasion complex within the supF reporter gene in an episomal shuttle vector and to direct site-specific photoadduct formation by the conjugated psoralen. The psoralen-bis-PNA conjugate was found to direct photoadduct formation to the intended 5'-TpA base step next to the PNA-binding site, and the photoadduct formation efficiency displayed both concentration and UVA irradiation dependence. The effect of PNA-targeted photoadducts in a mammalian system was tested by SV40-based shuttle vector assay. After in vitro binding, we found that photoadducts directed by PNAs conjugated to psoralen-induced mutations at frequencies in the range of 0.46%, 6.5-fold above the background. In a protocol for intracellular gene targeting in the episomal shuttle vector, the psoralen-PNA-induced mutation frequency was 0.13%, 3.5-fold higher than the background. Most of the induced mutations were deletions and single-base-pair substitutions at or adjacent to the targeted PNA-binding and photoadduct-formation sites. When the results are taken together, they demonstrate the ability of bis-PNAs conjugated with psoralen to mediate site-specific gene modification, and they further support the development of PNAs as tools for gene-targeting applications.     

Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine.

Oligodeoxyribonucleotides containing thymidine and 8-oxo-2'-deoxyadenosine can form pyr.pur.pyr type triplexes with double-stranded DNA. Unlike triplexes whose third strands contain thymidine and deoxycytidine, the stability of these triplexes is independent of pH. We have prepared d-ps-TAAATAAATTTTTAT-L [I(A)], where A is 8-oxo-2'-deoxyadenosine, ps is 4'-hydroxymethyl-4,5',8- trimethylpsoralen and L is a 6-amino-2-(hydroxymethyl)hexyl linker. The oligomer is designed to interact with a homopurine sequence in the promoter region of the human gene coding for the 92 kDa form of collagenase type IV. Oligomer I(A) and oligomer I(C), which contains 2'-deoxycytidine in place of 8-oxo-2'-deoxycytidine, both form stable triplexes at pH 6.2, but only I(A) forms a stable triplex with a model duplex DNA target at pH 7.5, as determined by UV melting experiments. Triplex formation is stabilized by the presence of the psoralen group. Upon irradiation both I(A) and I(C) form photoadducts with the DNA target at pH 6.2, but only I(A) forms a photoadduct at pH 7.5. In these photoreactions oligomer I(A) appears to selectively form a photoadduct with a C in the purine-rich strand of the duplex target. Although a T residue is present in the pyrimidine-rich strand of the target at the duplex/triplex junction, essentially no adduct formation takes place with this strand, nor is interstrand cross-linking observed. The extent of photoadduct formation decreases with increasing temperature, behavior which is consistent with the UV melting curve of the triplex. A tetramethylrhodamine derivative of I(A) was prepared and found to cross-link less extensively than I(A) itself. Oligomer I(A) is completely resistant to hydrolysis when incubated for 24h in the presence of 10% fetal bovine serum at 37 degree C, although it is hydrolyzed by S1 nuclease. The properties of oligomer I(A) suggest that 8-oxo- containing oligomers may find utility as antigene oligonucleotide reagents.     

Endoplasmic reticulum proteins involved in glycosylphosphatidylinositol-anchor attachment: photocrosslinking studies in a cell-free system.

Assembly of glycosylphosphatidylinositol (GPtdIns)-anchored proteins requires translocation of the nascent polypeptide chain across the endoplasmic reticulum (ER) membrane and replacement of the C-terminal signal sequence with a GPtdIns moiety. The anchoring reaction is carried out by an ER enzyme, GPtdIns transamidase. Genetic studies with yeast indicate that the transamidase consists of a dynamic complex of at least two subunits, Gaa1p and Gpi8p. To study the GPtdIns-anchoring reaction, we used a small reporter protein that becomes GPtdIns-anchored when the corresponding mRNA is translated in the presence of microsomes, in conjunction with site-specific photocrosslinking to identify ER membrane components that are proximal to the reporter during its conversion to a GPtdIns-anchored protein. We generated variants of the reporter protein such that upon in vitro translation in the presence of Nepsilon-(5-azido-2-nitrobenzoyl)-lysyl-tRNA, photoreactive lysine residues would be incorporated in the protein specifically near the GPtdIns-attachment site. We analyzed photoadducts resulting from UV irradiation of the samples. We show that proproteins can be crosslinked to the transamidase subunit Gpi8p, as well as to ER proteins of molecular mass approximately 60 kDa, approximately 70 kDa, and approximately 120 kDa. The identification of a photoadduct between a proprotein and Gpi8p provides the first direct evidence of an interaction between a proprotein substrate and one of the genetically identified transamidase subunits. The approximately 70-kDa protein that we identified may correspond to the other subunit Gaa1p, while the other proteins possibly represent additional, hitherto unidentified subunits of the mammalian GPtdIns transamidase complex.     

Different roles of bases within the integration signal sequence of human immunodeficiency virus type 1 in vitro.

To investigate the roles of bases near the tips of each strand of the long terminal repeat of the human immunodeficiency virus type 1 in the integration reaction, we examined the efficiencies of both binding and integration activities of staggered-ended substrates and mismatched mutant substrates by the integration assay and the UV cross-linking assay. Our results suggest that some bases of the human immunodeficiency virus type 1 long terminal repeat are required primarily for binding, whereas others are more critical for later reaction steps in vitro.     

Repairing the Sickle Cell mutation. II. Effect of psoralen linker length on specificity of formation and yield of third strand-directed photoproducts with the mutant target sequence

Three identical deoxyoligonucleotide third strands with a 3′-terminal psoralen moiety attached by linkers that differ in length (N = 16, 6 and 4 atoms) and structure were examined for their ability to form triplex-directed psoralen photoproducts with both the mutant T residue of the Sickle Cell β-globin gene and the comparable wild-type sequence in linear duplex targets. Specificity and yield of UVA (365 nm) and visible (419 nm) light-induced photoadducts were studied. The total photoproduct yield varies with the linker and includes both monoadducts and crosslinks at various available pyrimidine sites. The specificity of photoadduct formation at the desired mutant T residue site was greatly improved by shortening the psoralen linker. In particular, using the N-4 linker, psoralen interaction with the residues of the non-coding duplex strand was essentially eliminated, while modification of the Sickle Cell mutant T residue was maximized. At the same time, the proportion of crosslink formation at the mutant T residue upon UV irradiation was much greater for the N-4 linker. The photoproducts formed with the wild-type target were fully consistent with its single base pair difference. The third strand with the N-4 linker was also shown to bind to a supercoiled plasmid containing the Sickle Cell mutation site, giving photoproduct yields comparable with those observed in the linear mutant target.     

DNA polymerase eta reduces the gamma-H2AX response to psoralen interstrand crosslinks in human cells

DNA interstrand crosslinks are processed by multiple mechanisms whose relationships to each other are unclear. Xeroderma pigmentosum-variant (XP-V) cells lacking DNA polymerase eta are sensitive to psoralen photoadducts created under conditions favoring crosslink formation, suggesting a role for translesion synthesis in crosslink repair. Because crosslinks can lead to double-strand breaks, we monitored phosphorylated H2AX (gamma-H2AX), which is typically generated near double-strand breaks but also in response to single-stranded DNA, following psoralen photoadduct formation in XP-V fibroblasts to assess whether polymerase eta is involved in processing crosslinks. In contrast to conditions favoring monoadducts, conditions favoring psoralen crosslinks induced gamma-H2AX levels in both XP-V and nucleotide excision repair-deficient XP-A cells relative to control repair-proficient cells; ectopic expression of polymerase eta in XP-V cells normalized the gamma-H2AX response. In response to psoralen crosslinking, gamma-H2AX as well as 53BP1 formed coincident foci that were more numerous and intense in XP-V and XP-A cells than in controls. Psoralen photoadducts induced gamma-H2AX throughout the cell cycle in XP-V cells. These results indicate that polymerase eta is important in responding to psoralen crosslinks, and are consistent with a model in which nucleotide excision repair and polymerase eta are involved in processing crosslinks and avoiding gamma-H2AX associated with double-strand breaks and single-stranded DNA in human cells.     

Photoaddition of chlorpromazine to DNA

Chlorpromazine, 2-chloro-N-(3-dimethylaminopropyl)phenothiazine (CPZ), is a frequently prescribed antipsychotic drug that causes cutaneous photosensitivity in man. CPZ is also phototoxic and photomutagenic in vitro. We have investigated the photoaddition of CPZ to DNA as a possible mechanism for these photobiologic effects. Prior to irradiation, CPZ binds non-covalently to double-stranded calf thymus DNA. At high nucleotide to CPZ ratios, the CPZ absorption maximum shifts from 305 nm to 340 nm with an isosbestic point at 323 nm and 90% of the CPZ fluorescence at 455 nm is quenched. The excitation and emission spectra for the unquenchable fluorescence are the same as those for unbound CPZ. The absorption and fluorescence spectra of unbound CPZ are restored at 0.1 mM magnesium acetate or 100 mM sodium acetate. Non-covalent binding of CPZ to heat-denatured DNA does not shift the CPZ absorption spectrum but quenches 65% of the CPZ fluorescence. Photolytic decomposition of CPZ was inhibited by binding to DNA. In the presence of high concentrations of double-stranded DNA or denatured DNA the photolysis rates were reduced by greater than 98% and 65%, respectively, compared to free CPZ. Formation of covalent photoadducts between CPZ and denatured DNA was 10-fold more efficient than photoadduct formation with double-stranded DNA. Approximately 10% of the CPZ which photodecomposed upon irradiation at 323 nm photoadded to denatured DNA. These results indicate that formation of a complex between CPZ and double-stranded DNA absorbing at 340 nm protects CPZ from photodecomposition and inhibits covalent photoadduct formation.     

The photoreactivity of T-A sequences in oligodeoxyribonucleotides and DNA.

Photoaddition between adjacent adenine and thymine bases occurs, with a quantum yield of approximately 5 X 10(-4) mol einstein-1, when d(T-A), dT-A, d(pT-A), d(T-A-T), d(T-A-T-A) and poly(dA-dT) are irradiated, at 254 nm, in aqueous solution. The photoadduct thus formed is specifically degraded by acid to the fluorescent heterocyclic base 6-methylimidazo[4,5-b]pyridin-5-one (6-MIP) with retention of C(8) of adenine and the methyl group of thymine. This reaction, coupled with either spectrofluorimetric or radiochemical assay of 6-MIP isolated by high voltage paper electrophoresis, has been used to demonstrate formation of the adenine-thymine photoadduct on UV irradiation of poly(dA-dT).poly(dA-dT) and both native and denatured DNA from calf thymus and E. coli. Estimated quantum yields for this new type of photoreaction in DNA show that it is substantially quenched by base pairing. Possible biological implications of the photoreaction are discussed.     

In vivo persistence of DNA triple helices containing psoralen-conjugated oligodeoxyribonucleotides.

Triple helices represent an attractive method for modulating specific gene expression. In particular, cross-linking between a triplex-forming oligonucleotide (TFO) and its duplex DNA target, typically through the formation of psoralen photoadducts, allows efficient blocking of elongation by RNA polymerases in vitro. However, in vivo, this approach is limited by DNA repair of the photoadduct. Here we describe the use of an oligodeoxyribonucleotide 19mer psoralen-modified TFO to form covalent linkages between an oligonucleotide and both strands of the targeted duplex DNA, thereby efficiently blocking expression of a luciferase reporter gene. Most importantly, we demonstrate that both the psoralen cross-link and the purine-motif triplex remained intact for at least 72 h post-transfection, indicating that such species can persist for an extended period of time in vivo. These findings support the feasibility of an antigene approach for the therapeutic regulation of specific gene expression.     

Site-specific targeting of psoralen photoadducts with a triple helix-forming oligonucleotide: characterization of psoralen monoadduct and crosslink formation.

A polypurine tract in the supF gene of bacteriophage lambda (base pairs 167-176) was selected as the target for triple helix formation and targeted mutagenesis by an oligopurine (5'-AGGAAGGGGG-3') containing a chemically linked psoralen derivative (4'-hydroxymethyl-4,5',8-trimethylpsoralen) at its 5' terminus (psoAG10). The thymines at base pairs 166 and 167, a 5'ApT site, were targeted for photomodification. Exposure of the triple helical complex to long wavelength ultraviolet radiation led to the covalent binding of psoAG10 to the targeted region in the supF gene and to the induction of site-specific mutations. We report here experiments to characterize the photomodification of the targeted region of the supF gene in the context of triple helix formation. An electrophoretic mobility-shift assay showed that, at low radiation doses, monoadducts at base pair 166 were the major photoadducts. At higher doses the monoadducts were converted to crosslinks between base pairs 166 and 167. HPLC analysis of enzymatically hydrolyzed photoreaction mixtures was used to confirm the electrophoresis results. A strong strand preference for specific photoadduct formation was also detected.     

Interactions between different solar UVB/UVA filters contained in commercial suncreams and consequent loss of UV protection.

A systematic investigation of two well-known and popular commercial suncreams reveals significant degradation when exposed to simulated UV sunlight at an irradiance corresponding to natural sunlight. We have examined the photochemistry of two widely used sunscreen active agents in pure solvents separately and together (in solution), and in neat form, as well as their photochemistry when present in the actual suncream emulsion (as thin films on a glass substrate) since their combination typically produces suncreams with high sun protection factors (SPF): (1a) octyl methoxycinnamate (OMC; octinoxate) and (2a) 4-tert-butyl-4'-methoxydibenzoylmethane (also known as avobenzone and Parsol 1789), present in the two suncream formulations in combination with others (one also contained TiO2). Intermediates and/or photoproducts were identified by UV/visible spectroscopy, HPLC and liquid chromatographic/mass spectral methods, and by both 1H and 13C-NMR techniques. Structural assignments of the substrates produced were aided by examining model systems {viz. ethyl cinnamate (1b) and dibenzoylmethane (2b)} of the two sunscreen active agents. Irradiation of the cinnamates and the diketones together led to a [2 + 2] photocycloaddition process yielding cinnamate dimers and cyclobutylketone photoadducts that subsequently fragmented into substituted oxopentanoates and oxobutanoates. Similar findings were observed when the two active agents were simultaneously present in the same suncream emulsion.     

Triplex staples: DNA double-strand cross-linking at internal and terminal sites using psoralen-containing triplex-forming oligonucleotides

A method has been developed to attach 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen to the 5 position of thymine bases during solid-phase oligonucleotide synthesis. UV irradiation of triplex-forming oligonucleotides (TFOs) containing internally attached psoralens produces photoadducts at TpA steps within target duplexes, thus relaxing the constraints on selection of psoralen target sequences. Photoreaction of TFOs containing two psoralens, located at the 5'- and 3'-ends, has been used to create double-strand cross-links (triplex staples) at both termini of the TFO. Such complexes have no free single-stranded ends. TFOs containing 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen, 3-methyl-2-aminopyridine, and 5-(3-aminoprop-2-ynyl)deoxyuridine formed photoadducts with target duplexes under near-physiological conditions.     

The photochemistry of d(T-A) in aqueous solution and in ice.

When d(T-A) is irradiated at 254 nm in aqueous solution an internal photoadduct is formed between its constituent adenine and thymine bases. The resultant photoproduct, designated TA*, arises from a singlet excited state precursor; a similar photoreaction is not observed with d(C-A) or d(T-G). In contradistinction, irradiation of d(T-A) in frozen aqueous solution yields a dimeric photoproduct in which two d(T-A) molecules are coupled together by a (6-4) photoadduct linkage between their respective thymine bases. Both photoproducts have been extensively characterised by a combination of electron impact and fast atom bombardment mass spectrometry, UV, CD, 1H NMR and fluorescence spectroscopy. Acid treatment of TA* gives 6-methylimidazo[4,5-b]pyridin-5-one whose identity was established by an independent chemical synthesis involving photorearrangement of 6-methyl-imidazo[4,5-b]pyridine N(4)-oxide. A tentative mechanism is presented to account for the acid degradation of TA*. The structure of the dimeric ice photoproduct follows from its cleavage, by snake venom phosphodiesterase, to 5'-dAMP and the (6-4) bimolecular photoadduct of thymidine; on acid hydrolysis it gives adenine and 6-(5'-methyl-2'-oxopyrimidin-4'-yl) thymine.     

Peroxidase catalyzed oxidation of naturally-occurring phenols and hardwood lignins

Horseradish peroxidase and hydrogen peroxide form phenoxy radicals from 4-substituted-2,6-dimethoxyphenols, milled wood lignin and alkali lignins. A number of factors governing this reaction are examined. Side chain cleavage to quinones is the principal disproportionation reaction of these radicals. Catalysis by UV light and inhibition by quinones is observed. Aerobic oxidation of phenols is catalyzed by small amounts of hydrogen peroxide. Lignin substrates are degraded by the same oxidation mechanism as are the simple phenolic substrates.     

Chemical structure of 3-carbethoxypsoralen-DNA photoadducts

The enzymatic digest from salmon sperm DNA photochemically modified by the monofunctional 3-carbethoxypsoralen was analyzed by high-performance liquid chromatography. The modified nucleosides extracted from DNA were compared with model compounds obtained from irradiation in the dry state of mixtures of 3-carbethoxypsoralen with 2'-deoxyribonucleosides whose chemical structures had previously been characterized. The main photoadducts formed in DNA are two cis-syn diastereoisomers formed via a C4-cycloaddition reaction involving the 4', 5' double bond of 3-carbethoxypsoralen and the 5,6 double bond of 2'-deoxythymidine. Among them, the most polar one accounts for 72%. Under the same conditions, photoadducts formed between 3-carbethoxypsoralen and 2'deoxycytidine account for less than 1%.     

DNA substrate requirements for different activities of the human immunodeficiency virus type 1 integrase protein.

The integrase protein (IN) of human immunodeficiency virus type 1 removes two nucleotides from both 3' ends of the viral DNA (donor cleavage) and subsequently couples the newly generated 3' OH groups to phosphates in the target DNA (integration). The sequence requirements of IN for cleavage as well as for integration of viral DNA substrates have previously been studied by mutational analyses and by adduct interference assays. We extended these studies by analysis of heteroduplex oligonucleotide substrates and by missing-base analysis. We found for some base pairs that mutation of only one of the two bases and not the other affected IN activity. These base pairs center around the cleavage site. Besides donor cleavage and integration, IN can also perform "intermolecular disintegration," which has been described as the reversal of the integration reaction. We found that this reaction is independent of viral DNA sequences. In addition, the optimum spacing between the integration sites in intermolecular disintegration does not reflect the spacing found in vivo. These results indicate that this reaction is not the exact reversal of integration but rather is a sequence-independent phosphoryl transfer reaction between gapped DNA duplex molecules.     

Analysis of Human DNA-Arginine Photoadduct Modified with Peroxynitrite

The aim of the study is the biochemical characterization of human DNA modified with arginine and peroxynitrite. In the present study, DNA was isolated from human blood cells and its adduct was formed with one of the amino acid, arginine. The DNA-arginine adduct was then modified with peroxynitrite, a reactive nitrogen species. The modified DNA adduct was characterized by ultraviolet (UV) absorption spectroscopy, thermal melting profile, and electrophoresis studies. UV spectroscopic analysis of the photoadduct showed hyperchromicity, indicating the formation of single-strand breaks and photomodification. Thermal denaturation studies of DNA-arginine adduct and peroxynitrite-modified adduct showed a decrease in the temperature (T _m) value by 4.5°C and an increase in the T _m of 8°C, respectively. Peroxynitrite modification is evident by an increase in the T _m value and a change in the migration pattern of native and modified photoadducts on agarose gel electrophoresis. The DNA-arginine and peroxynitrite-modified photoadducts could have important implications in various pathophysiological and immunopathological conditions.     

Solution structure of a nucleic acid photoproduct of deoxyfluorouridylyl-(3'-5')-thymidine monophosphate (d-FpT) determined by NMR and restrained molecular dynamics: structural comparison of two sequence isomer photoadducts (d-U5p5T and d-T5p5U).

Acetone-sensitized irradiation using UV-B (sun lamp, lambda max = 313 nm) of deoxyfluorouridylyl-(3'-5')-thymidine monophosphate (d-FpT, F = fluorouracil), produces two major photoproducts, the cis-syn cyclobutane-type photodimer and a defluorinated (5-5) photoadduct, d-U5p5T. Product distribution is dependent on the pH of the irradiation solution, as was the case of irradiated d-TpF. At high pH (8-10) the (5-5) photoadduct is the major photoproduct. Irradiation of d-FpT shows a much faster photodegradation rate than the sequence isomer d-TpF. Multinuclear NMR experiments establish the formation of (5-5) covalent bonding between the C5 (d-U5p-, where the fluorine had been) and the C5 (-p5T) and the C6 (-p5T) acquires an OH group. NOE interproton distances and dihedral angles derived from J coupling analysis are constrained to refine model structures of d-U5p5T in restrained molecular dynamics calculations. The resultant structures obtained show 5S-6S as the most chiralities of the C5 and C6 atoms of the thymine, which is the opposite chirality to the corresponding atoms in the sequence isomer d-T5p5U. The orientation of the C5 substituents (-p5T fragment), the CH3 and the uracil are pseudo-axial and pseudo-equatorial respectively. Glycosidic angles are in the anti regions for both the d-U5p- and -p5T residues. Averaged backbone conformations of the two photoadducts, d-U5p5T and d-T5p5U, are similar, although the overall structure of d-U5p5T appears much more flexible than that of d-T5p5U. In particular, the sugar conformations of the 5'-end residues show a remarkable difference in flexibility.