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Johnstephen Taylor - One of the best experts on this subject based on the ideXlab platform.
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synthesis and characterization of a 3 15n labeled cis syn Thymine dimer containing dna duplex
Journal of Organic Chemistry, 2006Co-Authors: H M Bdour, Johnstephen TaylorAbstract:Cis-syn Thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight. To better understand the nature of base pairing with cis-syn Thymine dimers, we have synthesized a decamer oligodeoxynucleotide (ODN) containing a cis-syn Thymine dimer labeled at the N3 of both T's with 15N by two efficient routes from [3-15N]-thymidine phosphoramidite. In the postsynthetic irradiation route, an ODN containing an adjacent pair of [3-15N]-labeled T's was irradiated and the cis-syn dimer-containing ODN isolated by HPLC. In the mixed building block route, a mixture of cis-syn and trans-syn dimer-containing ODNs was synthesized from a mixture of [3-15N]-labeled Thymine dimer phosphoramidites after which the cis-syn dimer-containing ODN was isolated by HPLC. The N3-nitrogen and imino proton signals of an 15N-labeled Thymine dimer-containing decamer duplex were assigned by 2D 1H−15N heterocorrelated HSQC NMR spectroscopy, and the 15N−1H coupling constant was found to be 1.8 H...
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the trans syn i Thymine dimer bends dna by approximately 22 degrees and unwinds dna by approximately 15 degrees
Chemical Research in Toxicology, 1993Co-Authors: Chengi Wang, Johnstephen TaylorAbstract:: Irradiation of DNA with ultraviolet light leads to the formation of two classes of cyclobutane dimers at adjacent Thymines sites, of which the cis-syn is the major class and the trans-syn is the minor class. While the structure and properties of DNA containing cis-syn Thymine dimers have been extensively studied, virtually nothing is known about DNA containing trans-syn Thymine dimers. To investigate the bending and unwinding of DNA induced by the trans-syn-I Thymine dimer, the electrophoretic properties of oligomers of trans-syn-I dimer-containing DNA duplexes were studied. Oligonucleotides 10, 11, and 12 bp in length containing a centrally located trans-syn-I Thymine dimer were synthesized, polymerized, and analyzed by polyacrylamide gel electrophoresis. In contrast to the small bending angle (approximately 7 degrees) induced by the cis-syn Thymine dimer, we found that trans-syn-I Thymine dimer bends DNA significantly (approximately 22 degrees). Both dimers, however, are found to unwind DNA by the same amount (approximately 15 degrees). On the basis of previous NMR studies, it appears that the bend of the trans-syn-I dimer is localized at the 5'-side of the dimer. Gel electrophoretic analysis of multimers of two 11-mers containing a cis-syn Thymine dimer at the 5'-end and at the center of a dT6.dA6 tract confirmed our previous estimates for the bending angles of Thymine dimer-containing T6 tracts. The substrates reported may be useful in determining how general repair enzymes recognize DNA damage.
Harri Lonnberg - One of the best experts on this subject based on the ideXlab platform.
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synthesis and properties of 3 deoxypsiconucleosides anomeric 1 3 deoxy d erythro 2 hexulofuranosyl Thymines and 9 3 deoxy d erythro 2 hexulofuranosyl adenines
Synthesis, 1994Co-Authors: Alex Azhayev, Andrei Guzaev, Jari Hovinen, Jorma Mattinen, Reijo Sillanpaa, Harri LonnbergAbstract:Anomeric 1-(3-deoxy-D-erythro-2-hexulofuranosyl)Thymines and 9-(3-deoxy-D-erythro-2-hexulofuranosyl)adenines were prepared by tin(IV) chloride catalyzed N-glycosylation of trimethylsilylated Thymine and N 6 -benzoyladenine with methyl 3-deoxy-D-erythro-2-hexulofuranoside triacetate or tribenzoate, respectively. These O-glycosides used as starting materials were obtained by deoxygenation of 1,2:4,5-di-O-isopropylidene-β-D-fructopyranose and subsequent acid-catalyzed methanolysis of the resulting 3-deoxy derivative. The anomeric configuration of the nucleosides prepared was assigned by a combination of X-ray crystallography and 2D 1 H NMR spectroscopy. The conformation and hydrolytic stability of these new nucleoside analogous are discussed
Josef Jiricny - One of the best experts on this subject based on the ideXlab platform.
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human Thymine dna glycosylase binds to apurinic sites in dna but is displaced by human apurinic endonuclease 1
Journal of Biological Chemistry, 1999Co-Authors: Timothy R. Waters, Josef Jiricny, Paola Gallinari, Peter F SwannAbstract:Abstract In vitro, following the removal of Thymine from a G·T mismatch, Thymine DNA glycosylase binds tightly to the apurinic site it has formed. It can also bind to an apurinic site opposite S 6-methylthioguanine (SMeG) or opposite any of the remaining natural DNA bases. It will therefore bind to apurinic sites formed by spontaneous depurination, chemical attack, or other glycosylases. In the absence of magnesium, the rate of dissociation of the glycosylase from such complexes is so slow (k off 1.8 − 3.6 × 10−5 s−1; i.e. half-life between 5 and 10 h) that each molecule of glycosylase removes essentially only one molecule of Thymine. In the presence of magnesium, the dissociation rates of the complexes with C·AP andSMeG·AP are increased more than 20-fold, allowing each Thymine DNA glycosylase to remove more than one uracil or Thymine from C·U and SMeG·T mismatches in DNA. In contrast, magnesium does not increase the dissociation of Thymine DNA glycosylase from G·AP sites sufficiently to allow it to remove more than one Thymine from G·T mismatches. The bound Thymine DNA glycosylase prevents human apurinic endonuclease 1 (HAP1) cutting the apurinic site, so unless the glycosylase was displaced, the repair of apurinic sites would be very slow. However, HAP1 significantly increases the rate of dissociation of Thymine DNA glycosylase from apurinic sites, presumably through direct interaction with the bound glycosylase. This effect is concentration-dependent and at the probable normal concentration of HAP1 in cells the dissociation would be fast. This interaction couples the first step in base excision repair, the glycosylase, to the second step, the apurinic endonuclease. The other proteins involved in base excision repair, polymerase β, XRCC1, and DNA ligase III, do not affect the dissociation of Thymine DNA glycosylase from the apurinic site.
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the purification of a mismatch specific Thymine dna glycosylase from hela cells
Journal of Biological Chemistry, 1993Co-Authors: Petra Neddermann, Josef JiricnyAbstract:Abstract G/T mispairs that arise in the DNA of higher eukaryotes as a result of spontaneous hydrolytic deamination of 5-methylcytosine to Thymine must be corrected to G/C pairs. We describe here the purification to apparent homogeneity of the enzyme that initiates this repair process by excising the mispaired Thymine from the hetero-duplex to generate an apyrimidinic site. The enzymatic activity could be attributed to a 55-kDa polypeptide, which was purified from extracts of HeLa cells by a combination of conventional and DNA-affinity chromatography. The enzyme is a mismatch-specific Thymine-DNA N-glycosylase, capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired Thymine. In addition to the G/T, the enzyme can remove Thymine also from C/T and T/T mispairs in the order G/T > C/T > T/T. It has no detectable endonucleolytic activity on apyrimidinic sites and does not catalyze the removal of Thymine from A/T pairs or from single-stranded DNA.
Louise Prakash - One of the best experts on this subject based on the ideXlab platform.
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accuracy of Thymine Thymine dimer bypass by saccharomyces cerevisiae dna polymerase η
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Todd M Washington, Robert E Johnson, Satya Prakash, Louise PrakashAbstract:The Saccharomyces cerevisiae RAD30 gene functions in error-free replication of UV-damaged DNA. RAD30 encodes a DNA polymerase, Pol η, which inserts two adenines opposite the two Thymines of a cis-syn Thymine–Thymine (T–T) dimer. Here we use steady-state kinetics to determine the accuracy of DNA synthesis opposite the T–T dimer. Surprisingly, the accuracy of DNA synthesis opposite the damaged DNA is nearly indistinguishable from that opposite nondamaged DNA, with frequencies of misincorporation of about 10−2 to 10−3. These studies support the hypothesis that unlike most DNA polymerases, Pol η is able to tolerate distortions in DNA resulting from damage, which then enables the polymerase to utilize the intrinsic base pairing ability of the T–T dimer.
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efficient bypass of a Thymine Thymine dimer by yeast dna polymerase polη
Science, 1999Co-Authors: Robert E Johnson, Louise PrakashAbstract:The RAD30 gene of the yeast Saccharomyces cerevisiae is required for the error-free postreplicational repair of DNA that has been damaged by ultraviolet irradiation. Here, RAD30 is shown to encode a DNA polymerase that can replicate efficiently past a Thymine-Thymine cis-syn cyclobutane dimer, a lesion that normally blocks DNA polymerases. When incubated in vitro with all four nucleotides, Rad30 incorporates two adenines opposite the Thymine-Thymine dimer. Rad30 is the seventh eukaryotic DNA polymerase to be described and hence is named DNA polymerase η.
Peter F Swann - One of the best experts on this subject based on the ideXlab platform.
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human Thymine dna glycosylase binds to apurinic sites in dna but is displaced by human apurinic endonuclease 1
Journal of Biological Chemistry, 1999Co-Authors: Timothy R. Waters, Josef Jiricny, Paola Gallinari, Peter F SwannAbstract:Abstract In vitro, following the removal of Thymine from a G·T mismatch, Thymine DNA glycosylase binds tightly to the apurinic site it has formed. It can also bind to an apurinic site opposite S 6-methylthioguanine (SMeG) or opposite any of the remaining natural DNA bases. It will therefore bind to apurinic sites formed by spontaneous depurination, chemical attack, or other glycosylases. In the absence of magnesium, the rate of dissociation of the glycosylase from such complexes is so slow (k off 1.8 − 3.6 × 10−5 s−1; i.e. half-life between 5 and 10 h) that each molecule of glycosylase removes essentially only one molecule of Thymine. In the presence of magnesium, the dissociation rates of the complexes with C·AP andSMeG·AP are increased more than 20-fold, allowing each Thymine DNA glycosylase to remove more than one uracil or Thymine from C·U and SMeG·T mismatches in DNA. In contrast, magnesium does not increase the dissociation of Thymine DNA glycosylase from G·AP sites sufficiently to allow it to remove more than one Thymine from G·T mismatches. The bound Thymine DNA glycosylase prevents human apurinic endonuclease 1 (HAP1) cutting the apurinic site, so unless the glycosylase was displaced, the repair of apurinic sites would be very slow. However, HAP1 significantly increases the rate of dissociation of Thymine DNA glycosylase from apurinic sites, presumably through direct interaction with the bound glycosylase. This effect is concentration-dependent and at the probable normal concentration of HAP1 in cells the dissociation would be fast. This interaction couples the first step in base excision repair, the glycosylase, to the second step, the apurinic endonuclease. The other proteins involved in base excision repair, polymerase β, XRCC1, and DNA ligase III, do not affect the dissociation of Thymine DNA glycosylase from the apurinic site.
