Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA Modifications”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources
PubMed1990

On the chemical nature of DNA and RNA modification by a hemin model system.

In order to model the interaction of hemin with DNA and other polynucleotides, we have studied the degradation of DNA, RNA, and polynucleotides of defined structure by [meso-tetrakis(N-methyl-4-pyridyl)porphinato]manganese(III) (MnTMPP) + KHSO5. The activated porphyrin was shown to release adenine, thymine, and cytosine from DNA; RNA degradation afforded adenine, uracil, and cytosine. The same products were obtained from single- and double-stranded DNA oligonucleotides of defined sequence, and also from single-stranded DNA and RNA homopolymers. The overall yield of bases from the dode-canucleotide d(CGCT3A3GCG) was equal to 14% of the nucleotides present initially, indicating that each porphyrin catalyzed the release of approximately 4 bases. Although no guanine was detected as a product from any of the substrates studied, the ability of MnTMPP + KHSO5 to degrade guanine nucleotides was verified by the destruction of pGp, and by the appearance of bands corresponding to guanosine cleavage following treatment of 32P end labeled DNA restriction fragments with activated MnTMPP. Inspection of a number of sites of MnTMPP-promoted cleavage indicated that the process was sequence-selective, occurring primarily at G residues that were part of 5'-TG-3' or 5'-AG-3' sequences, or at T residues. Also formed in much greater abundance were alkali-labile lesions; these were formed largely at guanosine residues. Also studied was the degradation of a 47-nucleotide RNA molecule containing two hairpins. Degradation of the 5'-32P end labeled RNA substrate afforded no distinct, individual bands, suggesting that multiple modes of degradation may be operative.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1977

[Sensitivity of B- and C-DNA forms to modifications by O-methylhydroxylamine].

Effects of high concentrations of lithium, cesium and ammonium chlorides on the reaction ability of free CMP and cytosine in free DNA of CD phage with respect to O-methylhydroxylamine (OMHA) are studied. CMP reaction in all the cases takes place mainly for 24 hours. Like classical B-form, native DNA, having C-form in high ionic strength solution (as estimated from circular dichroism data), is not modificated. Thus, the access of some cytosine residues in intraphage DNA to OMHA is due not to the decreased DNA hydratation in situ, but to the presence of differently ordered regions in DNA.

Ammonium Chloride↗
PubMedDate not supplied

Nephroblastoma. DNA characteristics and their modifications induced by prenephrectomy chemotherapy: a cytofluorimetric study.

Treatment of nephroblastoma (Wilms' tumor) has presently achieved a 90% survival rate. Stage and grade are considered the most reliable prognostic parameters, but other biological factors are under study in order to improve patient stratification. Deoxyribonucleic acid (DNA) ploidy has been suggested to be useful in this setting. We retrospectively studied 79 patient with nephroblastoma (58 pretreated with chemotherapy and 21 not pretreated) by means of flow cytometry. DNA content and synthetic phase values were correlated with pathologic features and outcome. DNA modifications induced by chemotherapy were investigated. Sixty-nine tumors were diploid and 10 aneuploid. DNA content did not correlate with clinical course and was not modified by pretreatment. Aneuploid tumors were restricted to lower stages. Mean S-phase rate was lower and did not vary according to histology in pretreated tumors, while it was higher and increased with grade (p = 0.007) in previously untreated tumors. The fraction of cells in synthetic activity was related to outcome: Patients whose tumors displayed higher S-phase rates had a more favorable clinical course. Ploidy did not appear to be of prognostic significance. S-phase rate decreased after chemotherapy (p = 0.0002) and was related to survival. The worse outcome of pretreated patients might be attributed to a minor sensitivity to postoperative treatment: Preoperative chemotherapy would decrease the cell proliferation and might select resistant cellular clones of (possible) neoplastic residues.

Adolescent↗
PubMed1996

Anomalous nonidentity between Salmonella genotoxicants and rodent carcinogens: nongenotoxic carcinogens and genotoxic noncarcinogens.

According to current data, the capacity to cause nonprogrammed or unscheduled cell proliferation in target tissues, a common characteristic of chemical carcinogens, may play a more important role in the development of tumors than does genotoxicity. This paper provides strong support for the validity of this conclusion. Ames-negative nongenotoxicants may be considered to be carcinogenic primarily because of their ability to induce cell proliferation in animal tissues and organs. In addition, such nongenotoxic carcinogens may also provide latent and modest DNA (equivocal) modifications that never lead to Ames-positive events. Conversely, noncarcinogenesis by Ames-positive agents is likely to be linked to a lack of stimulation of cell division. Nongenotoxic and genotoxic carcinogens rely on both cell proliferation and equivocal DNA modification for their full carcinogenicity. Such equivocal DNA modifications do not appear to be formed by tumor promoters. The role of cell proliferation may provide a favorable milieu for the occurrence of genetic instability, give rise to selective "apoptosis-resistant abnormal cells," and then affect clonal expansion of these cells. Therefore, understanding the influence of nongenotoxic and genotoxic carcinogens on cell proliferation capability is a key point in determining the mechanisms of chemical carcinogenesis. Considering the contradictory and common features of genotoxicants and carcinogens, early detection of nonprogrammed cell proliferation is the most effective approach to predict human and rodent carcinogenicity.

Animals↗
PubMed1986

Detection of single base-pair mismatches in DNA by chemical modification followed by electrophoresis in 15% polyacrylamide gel.

We have developed a method for distinguishing fragments of DNA that contain single-base mismatches from their perfectly paired homologues. Single-stranded regions within a duplex fragment are accessible to 1-cyclohexyl-3-(2-[4-(4-methyl)morpholinyl]ethyl)carbodiimide, which reacts with unpaired guanidylate and thymidylate residues in DNA. Intact linear duplex DNA molecules do not react with carbodiimide, whereas DNA molecules containing single-base mismatches react quantitatively. After carbodiimide reaction, the DNA molecules are electrophoresed in high-percentage polyacrylamide gels so that modified and unmodified fragments can be resolved. Application of this technique should make it possible to locate and purify DNA fragments that exhibit sequence differences from those that do not; these might be used to signal phenotypic variation as well as to diagnose inherited disease.

Base Composition↗
PubMed2005

DNA methylation and histone modifications: teaming up to silence genes.

DNA methylation, histone deacetylation, and methylation of histone H3 at lysine 9 are the three best-characterized covalent modifications associated with a repressed chromatin state. Recent advances highlight an essential, intricate web of interactions among these processes, generating a self-reinforcing, self-perpetuating cycle of epigenetic events that lead to long-term transcriptional repression. Histone deacetylation and methylation at lysine 9 of H3 might also contribute to the establishment of DNA methylation patterns, a long-standing mystery in epigenetics. What's more, recent clues suggest a potential link between CpG methylation and other histone modifications. A complex picture is emerging in which DNA methylation and histone modifications work hand-in-hand as parts of an epigenetic program that integrates gene-silencing networks within the cell.

Animals↗
PubMed2003

Sequence-specific modification of genomic DNA by small DNA fragments.

Small DNA fragments have been used to modify endogenous genomic DNA in both human and mouse cells. This strategy for sequence-specific modification or genomic editing, known as small-fragment homologous replacement (SFHR), has yet to be characterized in terms of its underlying mechanisms. Genotypic and phenotypic analyses following SFHR have shown specific modification of disease-causing genetic loci associated with cystic fibrosis, beta-thalassemia, and Duchenne muscular dystrophy, suggesting that SFHR has potential as a therapeutic modality for the treatment of monogenic inherited disease.

Anemia, Sickle Cell↗
PubMed1996

Nitric oxide inhibits DNA ligase activity: potential mechanisms for NO-mediated DNA damage.

Nitric oxide-induced modifications of DNA occur either by directly altering DNA chemically through reactive nitrogen oxide species (RNOS) or indirectly by inhibiting various repair processes. DNA ligases are enzymes which rejoin single-strand breaks and are critical for DNA integrity during processes such as gene transcription and repair. The eukaryotic and T4 DNA ligases are active in the presence of ATP and act in two steps: the formation of protein-AMP intermediates, then the ligation of DNA breaks. When T4 DNA ligase was exposed to the NO generator DEA/NO (Et2N[NO(NO)]Na), a concentration- and time-dependent inhibition of these two steps, adenylylation of the protein and ligation of the substrate, was observed. This inhibition was abated by the presence of cysteine, suggesting that RNOS, rather than NO, mediated the inhibition of the ligase activity. As mammalian and T4 DNA ligases act by the same mechanism, the inhibition of DNA ligase may explain the increase in single-strand breaks reported for cells exposed to NO and provides a mechanism to increase DNA lesions without direct chemical modification of DNA by NO or RNOS.

Adenine↗
PubMed1988

Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutants.

This paper presents the nucleotide sequence of the mod-res operon of phage P1, which encodes the two structural genes for the EcoP1 type III restriction and modification system. We have also sequenced the mod gene of the allelic EcoP15 system. The mod gene product is responsible for binding the system-specific DNA recognition sequences in both restriction and modification; it also catalyses the modification reaction. A comparison of the two mod gene product sequences shows that they have conserved amino and carboxyl ends but have completely different sequences in the middle of the molecules. Two alleles of the EcoP1 mod gene that are defective in modification but not in restriction were also sequenced. The mutations in both alleles lie within the non-conserved regions.

Amino Acid Sequence↗
PubMed1989

[Reactivity of oligonucleotide derivatives, containing a methylphosphate group. Affinity modification of target DNA by 4-N-(methyl-N-2-chlorethylamino)benzyl 3'- and 5'-phosphamide derivatives of octathymidylate containing methylphosphonate residues].

Modification of 5'-32P-labelled octadecadeoxyribonucleotide d(pC5A8C5) (III) with octathymidylate methylphosphonate derivatives bearing both 3'- and 5'-terminal alkylating 4-(N-2-chloroethyl-N-methylamino)benzylphosphoamide residue has been investigated. Yield in the modification depends on configuration of methylphosphonate fragment, in case of Rp-isomer it may amount to 90%. Specificity of alkylation of nucleic acide target (III) by reagents based on the oligonucleotide methylphosphonates is almost the same as by reagents based on the oligonucleotides having phosphodiester internucleotide bonds.

Affinity Labels↗
PubMed1992

Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85.

Fibrobacter succinogenes is an important cellulolytic bacterium found in the rumen and cecum of herbivores. Numerous attempts to introduce foreign DNA into F. succinogenes S85 have failed, suggesting the presence of genetic barriers in this organism. Results from this study clearly demonstrate that F. succinogenes S85 possesses a type II restriction endonuclease, FsuI, which recognizes the sequence 5'-GG(A/T)CC-3'. Analysis of the restriction products on sequencing gels showed that FsuI cleaves between the two deoxyguanosine residues, yielding a 3-base 5' protruding end. These data demonstrate that FsuI is an isoschizomer of AvaII. A methyltransferase activity has been identified in the cell extract of F. succinogenes S85. This activity modified DNA in vitro and protected the DNA from the restriction by FsuI and AvaII. DNA modified in vivo by a cloned methylase gene, which codes for M.Eco47II, also protected the DNA from restriction by FsuI, suggesting that FsuI is inhibited by methylation at one or both deoxycytosine residues of the recognition sequence. The methyltransferase activity in F. succinogenes S85 is likely modifying the same deoxycytosine residues, but the exact site(s) is unknown. A highly active DNase (DNase A) was also isolated from the cell extract of this organism. DNase A is an endonuclease which showed high activity on all forms of DNA (single stranded, double-stranded, linear, and circular) but no activity on RNA. In vitro, the DNase A hydrolyzed F. succinogenes S85 DNA extensively, indicating the lack of protection against hydrolysis by this enzyme. In the presence of Mg2+, DNA was hydrolyzed to fragments of 8 to 10 nucleotides in length. The presence of DNase A and the type II restriction-modification system of F. succinogenes S85 may be the barriers preventing the introduction of foreign DNA into this bacterium.

Base Sequence↗
PubMed1981

Partial NH2- and cooh-terminal sequence analyses of Eco RI DNA restriction and modification enzymes.

NH2- and COOH-terminal amino acid sequences of the Eco RI restriction and modification enzymes have been determined. The results allow localization of the coding regions within the DNA segment which controls activity of both enzymes. Processing of the endonuclease is limited to removal of NH2-terminal formylmethionine whereas, in the case of the methylase, formylMet-Ala is removed.

Amino Acid Sequence↗
PubMed1998

Role of oxidative DNA damage in cancer initiation and promotion.

Normal aerobic metabolism produces huge amounts of potentially dangerous oxidants, controlled by a variety of antioxidant systems. An imbalance between the generated and exogenously inflicted oxidants and the oxidant system is termed oxidative stress. Even without oxidative stress, i.e. under normal physiological conditions, the damage to vital cellular micromolecules, such as DNA, is extensive, amounting to hundreds of hits per cell per day. More than one hundred different oxidative modifications in DNA have been described. The hydroxylation of guanine in the 8-position is the most frequent and most mutagenic lesion described. The 8-hydroxylation of guanine leads to lack of base pairing specifically and misreading of the modified base and adjacent residues. The modifications to DNA are so frequent that extensive and specific repair is needed for survival. Indeed, multiple repair enzyme systems to mediate and remove/repair oxidative DNA modification are described. Within DNA, hot-spots of oxidative modification and subsequent mutation have been described, and some specificity appears as compared to other agents that can lead to modification of DNA, i.e. aflatoxin and benzo[a]pyrene. Numerous publications from epidemiology and intervention studies with antioxidants point at oxidative modification as an important factor in cancer development at certain sites. Yet, direct evidence linking oxidative DNA modification to cancer has not been published. With regard to antoxidant prevention of cancer no effective single substance has so far been identified.

DNA Damage↗
PubMed1983

Structural perturbation in supercoiled DNA: hypersensitivity to modification by a single-strand-selective chemical reagent conferred by inverted repeat sequences.

Bromoacetaldehyde, a reagent which modifies unpaired adenine residues, selectively modifies supercoiled DNA in the region of inverted repeats which are known targets for single-strand-specific nucleases. The reaction is dependent upon the topological state of the molecule, and the absolute importance of the inverted repeat has been demonstrated. Finer mapping of the distribution of the modification pattern reveals significant and interesting differences from the S1 nuclease target positions. Bromoacetaldehyde modification is distributed over a wider region covering the whole inverted repeat, with greatest extent of reaction in the regions which flank the inverted repeat. It is suggested that an altered conformation may be propagated into these sequences. These results further support the contention that inverted repeats adopt an altered conformation when negatively supercoiled, for which the principal suggestion remains the cruciform structure.

Acetaldehyde↗
PubMed1989

The FokI restriction-modification system. II. Presence of two domains in FokI methylase responsible for modification of different DNA strands.

Based on the previous findings that the FokI methylase (MFokI) consists of 647 amino acid residues and contains two copies of the segment specific for adenine methylase, Asp-Pro-Pro-Tyr, at amino acid positions 218-221 and 548-551, the role of these copies in the methylation reaction was investigated by introduction of a mutation into each segment. The MFokI gene was inserted into M13 vectors, and the Asp residues in the two segments were converted to Gly and Ala by oligonucleotide-directed mutagenesis. The wild-type and mutant genes were recloned into an expression vector, from which gene products were purified. A short DNA fragment carrying the FokI recognition site was treated with each of these enzymes, and after separation of the two strands by duplex formation with M13 viral DNAs carrying the respective strands, the presence or absence of modification was judged from susceptibility to FokI endonuclease. The results of analysis showed that different strands were modified in an asymmetric way by the introduction of mutations into one of the two segments, and that the segments at the N-terminal and C-terminal moieties participated in modification of the strands carrying 5'-GGATG-3' and 3'-CCTAC-5', respectively. We concluded that MFokI contained two functional domains each of which was responsible for modification of different strands in the target DNA.

Deoxyribonucleases, Type II Site-Specific↗
PubMed1993

2-Nitropropane-induced liver DNA and RNA base modifications: differences between Sprague-Dawley rats and New Zealand white rabbits.

2-Nitropropane (2-NP), a hepatocarcinogen in male Sprague-Dawley rats but not, under the same conditions, in male New Zealand White rabbits, induces characteristic base modifications in rat liver DNA and RNA including increases in 8-oxoguanine and the formation of 8-aminoguanine. We compared the levels of these modifications in the two animal species at 6, 18 and 42 h after a single i.p. treatment with 1.12 mmol/kg 2-NP. Significantly less nucleic acid base modifications were found to be produced in rabbit liver than in rat liver. Thus, the relative resistance of the rabbit to the hepatocarcinogenicity of 2-NP correlates with decreased levels of 2-NP-induced liver DNA and RNA base damage.

Animals↗