Sequence Specificity Of DNA Damage Research Articles

Accurate DNA Fragment Sizing by Capillary Electrophoresis with Laser-Induced Fluorescence Array for Detection of Sequence Specificity of DNA Damage

Cancer has been linked to mutations within specific codons in genes that code for critical biomolecules such as tumor suppressor proteins (e.g., p53). Activated metabolites like benzo[a]pyrenediol epoxide act on preferred nucleotide sequences of DNA, and such mutations have been identified in cancers. DNA reaction site identification depends on accurate analysis of oligonucleotide fragment sizes produced by strand breakage at the damaged sites. Herein, we report a new method for DNA fragment sizing using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF). Absolute sizing accuracy and speed are achieved by utilizing a CE-LIF array with two-color fluorescence detection. Accuracy depends on correcting results with commercial standards by referring them to primary standards with the same sequences and identical labels as sample fragments. The method is demonstrated by detection of a [...GGCGCGCAG...] G reaction site for styrene oxide on an oligonucleotide representing the CYP1B1 gene. This approach avoids the need for radioactive isotopes and is less labor intensive and faster than the alternative PAGE with (32)P end labeling.

Guanine-specific DNA damage photosensitized by the dihydroxo(tetraphenylporphyrinato)antimony(V) complex

The dihydroxo(tetraphenylporphyrinato)antimony(V) complex (SbTPP) demonstrates bactericidal activity under visible-light irradiation. This phototoxic effect could be caused by photodamage to biomolecules, but the mechanism has not been well understood. In this study, to clarify the mechanism of phototoxicity by SbTPP, DNA damage photosensitized by SbTPP was examined using [ 32P]-5′-end-labeled DNA fragments. SbTPP induced markedly severe photodamage to single-stranded rather than to double-stranded DNA. Photo-irradiated SbTPP frequently caused DNA cleavage at the guanine residue of single-stranded DNA after Escherichia coli formamidopyrimidine-DNA glycosylase or piperidine treatment. HPLC measurement confirmed the formation of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG), an oxidation product of 2′-deoxyguanosine, and showed that the content of 8-oxodG in single-stranded DNA is larger than that in double-stranded DNA. The effects of scavengers of reactive oxygen species on DNA damage suggested the involvement of singlet oxygen. These results have shown that the mechanism via singlet oxygen formation mainly contributes to the phototoxicity of SbTPP. On the other hand, SbTPP induced DNA damage specifically at the underlined G of 5′- GG, 5′- GGG, and 5′- GGGG in double-stranded DNA. The sequence-specificity of DNA damage is quite similar to that induced by the type I photosensitizers, suggesting that photo-induced electron transfer slightly participates in the phototoxicity of SbTPP. In conclusion, SbTPP induces DNA photodamage via singlet oxygen formation and photo-induced electron transfer. A similar mechanism can damage other biomacromolecules, such as protein and the phospholipid membrane. The damage to biomacromolecules via these mechanisms may participate in the phototoxicity of SbTPP.

Hydroxylation of Deoxyguanosine at 5′ Site of GG and GGG Sequences in Double-stranded DNA Induced by Carbamoyl Radicals

Free radicals generated by chemicals can cause sequence-specific DNA damage and play important roles in mutagenesis and carcinogenesis. Carbamoyl group (CONH 2 ) and its derived groups (CONR 2 ) occur as natural products and synthetic chemical compounds. We have investigated the DNA damage by carbamoyl radicals · (CONH 2 ), one of carbon-centered radicals. Electron spin resonance (ESR) spectroscopic study has demonstrated that carbamoyl radicals were generated from formamide by treatment with H 2 O 2 plus Cu(II), and from azodicarbonamide by treatment with Cu(II). We have investigated sequence specificity of DNA damage induced by carbamoyl radicals using 32 P-labeled DNA fragments obtained from the human c-Ha- ras -1 and p 53 genes. Treatment of double-stranded DNA with carbamoyl radicals induced an alteration of guanine residues, and subsequent treatment with piperidine or Fpg protein led to chain cleavages at 5'-G of GG and GGG sequences. Carbamoyl radicals enhanced Cu(II)/H 2 O 2 -mediated formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in double-stranded DNA more efficiently than that in single-stranded DNA. These results shows that carbamoyl radicals specifically induce hydroxylation of deoxyguanosine at 5' site of GG and GGG sequences in double-stranded DNA.

The interaction of DNA-targeted 9-aminoacridine-4-carboxamide platinum complexes with DNA in intact human cells

As part of an ongoing drug development programme, this paper describes the sequence specificity and time course of DNA adduct formation for a series of novel DNA-targeted analogues of cis-diaminedichloroplatinum(II) (cisplatin) (9-aminoacridine-4-carboxamide Pt complexes) in intact HeLa cells. The sequence specificity of DNA damage caused by cisplatin and analogues in human (HeLa) cells was studied using Taq DNA polymerase and a linear amplification/polymerase stop assay. Primer extension is inhibited by a Pt–DNA adduct, and hence the sites of these lesions can be analysed on DNA sequencing gels. The repetitive alphoid DNA sequence was used as the target DNA in human cells. The 9-aminoacridine-4-carboxamide Pt complexes exhibited a markedly different sequence specificity relative to cisplatin and other analogues. The sequence specificity of the 9-aminoacridine-4-carboxamide Pt complexes is shifted away from a preference for runs of guanines. The 9-aminoacridine-4-carboxamide Pt complexes have an enhanced preference for GA dinucleotides. This is the first occasion that an altered DNA sequence specificity has been demonstrated for a cisplatin analogue in human cells. A time course of DNA damage revealed that the DNA-targeted Pt complexes, consisting of four 9-aminoacridine-4-carboxamide Pt complexes and one acridine-4-carboxamide Pt complex, damaged DNA more rapidly compared to cisplatin and non-targeted analogues. A comparison of the time taken to reach half the maximum relative intensity indicated that the DNA-targeted Pt complexes reacted approximately 4-fold faster than cisplatin and the non-targeted analogues.

Mechanism of guanine-specific DNA damage by oxidative stress and its role in carcinogenesis and aging.

Reactive species generated by chemicals and UV radiation can cause sequence-specific DNA damage and play important roles in mutagenesis, carcinogenesis and aging. We have investigated sequence specificity of oxidative stress-mediated DNA damage by using 32P-labeled DNA fragments obtained from the human c-Ha-ras-1 and p53 genes. Free hydroxyl radical causes DNA damage with no marked site specificity. Reactive nitrogen species, sulfate radicals, nitrogen-centered radicals, benzoyloxyl radical and alkoxyl radical show different sequence specificity. Benzoyloxyl radical specifically causes damage to the 5'-G in GG sequence. UVA radiation also causes DNA damage at this site through electron transfer in the presence of certain photosensitizers. The 5'-G in GG sequence is easily oxidized because a large part of the highest occupied molecular orbital is distributed on this site. On the basis of these findings, the sequence specificity of DNA damage is presumably determined by (a) redox potential of reactive species; (b) ionization potential of DNA bases; and (c) site-specific binding of metal ion to DNA. Here we discuss the mechanisms of sequence-specific DNA damage in relation to carcinogenesis and aging.

Distinct mechanisms of site-specific DNA damage induced by endogenous reductants in the presence of iron(III) and copper(II)

The ability of Cu(II) and Fe(III) to promote site-specific DNA damage in the presence of endogenous reductants was investigated by using 32P-5′-end-labeled DNA fragments obtained from the human p53 tumor suppressor gene and the c-Ha- ras-1 protooncogene. Ascorbate induced metal-dependent DNA damage most efficiently (ascorbate>GSH>NADH). Cu(II) induced endogenous reductants-dependent DNA damage more efficiently than Fe(III). Endogenous reductants plus Fe(III) caused DNA cleavage at every nucleotide, without marked site preference. DNA damage by Fe(III) was inhibited by hydroxyl free radical ( ⋅OH) scavengers and catalase. These results suggest that endogenous reductants plus Fe(III) generate free or extremely near free ⋅OH via H 2O 2 formation, and that ⋅OH causes DNA damage. In the presence of 50 μM Cu(II) in bicarbonate buffer, ascorbate caused DNA cleavage frequently at sites of two or more adjacent guanine residues. In contrast, in the presence of 20 μM Cu(II), ascorbate caused DNA cleavage frequently at thymine residues. Catalase and a Cu(I)-specific chelator inhibited DNA damage by Cu(II), whereas ⋅OH scavengers did not. Fe(III)-dependent 8-oxo-7,8-dihydro-2′-deoxyguanosine formation was inhibited by ⋅OH scavengers, whereas no inhibition by ⋅OH scavengers was observed with Cu(II). These results suggest that ⋅OH is the main active species formed with Fe(III), whereas copper-peroxide complexes with a reactivity similar to ⋅OH participate in Cu(II)-dependent DNA damage. The polyguanosine sequence specificity of DNA damage in the presence of high concentrations of Cu(II) can be explained by the preferential binding of Cu(II) to guanine residues.

Interaction of 11 cisplatin analogues with DNA: characteristic pattern of damage with monofunctional analogues

In this paper the sequence specificity of DNA damage has been determined for 11 cisplatin analogues. A number of the analogues used in this study have been included in clinical trials. A Taq DNA polymerase linear amplification technique was utilised to ascertain the sequence selectivity of cisplatin analogues damage to DNA. The analogues differed in their ability to damage DNA with cisplatin being the most effective DNA damaging agent followed by (in decreasing order): tetraplatin (tetrachloro(1,2-diaminocyclohexane)platinum(IV) (RR isomer)), cis-dichlorobis(isopropylamine)platinum(II), dichloro(1,2-diaminocyclohexane)platinum(II) (SS isomer), dichloro(1,2-diaminocyclohexane)platinum(II) (RR isomer), cis-bis(cyclohexylamine)dichloroplatinum(II), carboplatin, cis-dichlorobis(isopentylamine)platinum(II), and CHIP ( cis-dichloro- trans-dihydroxybis(isopropylamine)platinum(IV)). However, the sequence specificity of these analogues was similar in position and relative intensity of damage. We also provide evidence that platinum(IV) complexes can damage DNA without being reduced to platinum(II). It was found that a 10-fold higher concentration of cisplatin was required to damage DNA in Tris–HCl compared to Hepes buffers. In this paper we have detected a characteristic pattern of damage with monofunctional analogues that could be used to determine the mode of binding of a cisplatin analogue with DNA. The monofunctional analogues tested were chloro(diethylenetriamine)platinum(II) and cis-diamminechloro(1-octylamine)platinum(II) as well as transplatin.

Use of an automated sequencer to determine the sequence specificity of DNA damage.

An automated sequencer was used to determine the sequence specificity of DNA damage caused by hedamycin in the plasmid pUC19 using a linear amplification/Taq DNA polymerase method. Previously, manual DNA sequencers have been in widespread use to investigate the sequence specificity of a DNA damaging agent. Manual DNA sequencers are restricted in the length of DNA sequence that can be read at base pair resolution for densitometry. An automated sequencer can greatly expand on the length of analysable DNA sequence. An additional important capability of the automated sequencer, is the ability to quantitate the intensity of damage at each base pair site. Thus we have used the automated sequencer to elucidate the sequence specificity of DNA damage for 300 bp. We have carried out an extended analysis of the sequence specificity of hedamycin DNA damage and found that the sequence 5'-cGt-3', tGt and cGg are preferentially damaged. The sequence specificity of cisplatin was also investigated.

The influence of linker chain length on the sequence specificity of DNA damage by n-bromoalkylphenanthridinium bromides in plasmid DNA and in intact human cells

The sequence specificity of DNA damage of n-bromoalkylphenanthridinium bromides, with linker chain lengths ( n) of 4,6,8 and 10 methylene groups, was investigated in the plasmid pUC8 and in intact human cells. A linear amplification assay was used to elucidate the DNA sequence specificity of the alkylating agents. In this assay Taq DNA polymerase extends from an oligonucleotide primer up to the damage site and the products run on a DNA sequencing gel to reveal the precise sites of DNA damage. For both the plasmid and cellular experiments, the compound that caused the most damage to DNA was the n = 6 compound, followed by (in decreasing order) the n = 4, n = 8, and n = 10 compounds. There were significant differences in the sequence specificity of DNA damage between n-bromoalkylphenanthridinium bromides of different linker chain length: (1) the main sites of damage were at guanines for the n = 4,6 and 8 compounds but at guanines and adenines for the n = 10 compound; (2) a consensus sequence of 5′-c(a/t)Ggg-3′ was obtained for the n = 4,6 and 8 compounds but 5′-c(a/c)(G/A)(g/a)-3′ for the n = 10 compound; (3) runs of consecutive Gs were the major site of damage for the n = 4,6 and 8 compounds, but consecutive Gs or consecutive As for the n = 10 compound; (4) for damage at single isolated guanines, the most damaged sequences were at 5′-Ga-3′ for the n = 4 compound but at 5′-Gt-3′ for the n = 6,8 and 10 compounds. The tandemly repeated alpha RI DNA sequence was the DNA target in intact human K562 cells. In intact human cells, the compounds produced damage with similar DNA sequence selectivity to that found in plasmid DNA. The n = 4 and 6 compounds possess marginal anti-tumour activity and these compounds produced the most damage in intact human cells. The n = 8 and 10 compounds do not demonstrate significant anti-tumour activity and these compounds resulted in the least damage in cells.

An investigation of the sequence-specific interaction of cis-diamminedichloroplatinum(II) and four analogues, including two acridine-tethered complexes, with DNA inside human cells.

The sequence specificity of DNA damage caused by cis-diamminedichloroplatinum(II) (cisplatin) and four analogues in human (HeLa) cells was studied using Taq DNA polymerase and a linear amplification system. The primer extension is inhibited by the drug-DNA adducts, and hence the sites of these lesions can be analyzed on DNA sequencing gels. The repetitive alphoid DNA was used as the target DNA in human cells. A comparison was made between adduct formation in human cells and in purified DNA. The sequence-specific position and relative intensity of damage was similar in both systems for cisplatin, dichloro(ethylenediammine)platinum(II) (PtenCl2), and N-[3-N-(ethylenediamino)propyl]acridine-4-carboxamidedichloropl atinum(II) (4AcC3PtenCl2). However, no DNA damage could be detected in cells for trans-diamminedichloroplatinum(II) (transPt) or N-[3-N-(ethylenediamino)propyl]acridine-2-carboxamide-dichloroplat inum(II) (2AcC3PtenCl2) despite the ability of these latter analogues to damage purified DNA. Cisplatin, PtenCl2, and 4AcC3PtenCl2, which significantly damaged DNA inside cells, also show antitumor activity in mouse models. However, transPt and 2AcC3PtenCl2, which did not detectably damage DNA inside cells, did not show such antitumor activity. This correlation between intracellular DNA damaging ability and in vivo antitumor activity indicates the potential use of the human cells/Taq DNA polymerase/linear amplification technique as a convenient method for screening new cisplatin analogues for useful chemotherapeutic activity.

The use of Taq DNA polymerase to determine the sequence specificity of DNA damage caused by cis-diamminedichloroplatinum(II), acridine-tethered platinum(II) diammine complexes or two analogues.

cis-Diamminedichloroplatinum(II) (cisplatin) forms adducts with DNA. The sequence specificity of formation of cisplatin adducts with plasmid DNA was investigated using Taq DNA polymerase. This procedure involved the extension of an oligonucleotide primer by Taq DNA polymerase up to the cisplatin adduct. Using thermal cycling, this process is repeated many times in order to amplify the signal. The products of this linear amplification can then be examined on DNA sequencing gels, and the sequence specificity of cisplatin adduct formation can be determined to the exact base pair. In the pUC8 plasmid, the sequences that produced the most intense damage sites (as determined by densitometry) were runs of two or more Gs. Adducts could also be detected at GA, AG, and GC dinucleotides. Four other cisplatin analogues were also tested in the system. Two of these analogues contained an attached intercalating chromophore, and the strong damage with these compounds was similar to that found for cisplatin, but the medium and weak damage tended to be different. Weak damage was also detected with trans-diamminedichloroplatinum(II). With this compound, a large number of the damage sites were at the CG dinucleotide. This technique represents a simple, accurate, and quick method for determining the sequence specificity of damage for a cisplatin analogue in any DNA sequence.