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Depurination - Wikipedia, the free encyclopedia Depurination is DNA alteration in which the hydrolysis of a purine base (Adenine or Guanine) from the deoxyribose-phosphate backbone occurs. After a depurination, the sugar phosphate backbone remains and the sugar ring has a hydroxyl (-OH) group in the place of the Adenine or Guanine. One of the main causes of depurination is the presence of endogenous metabolites in cell undergoing chemical reactions. en.wikipedia.org /wiki/Depurination   (137 words)

Kinetic studies on depurination and detritylation of CPG-bound intermediates during oligonucleotide synthesis -- Septak ... The observed depurination half-time for N -benzoyl protected 5'-DMT-dA-CPG support in the presence of 3% DCA (1.3 h) is consistent with the literature data for 2% DCA (6). Ratio C is the half-time of trimer depurination divided by that of the dimer DMT-Tp-dA-CPG. As expected, using the modified depurination assay format with the ternary CPG mixture, the observed dA depurination half-times are in good agreement with the corresponding values obtained using binary CPG mixture shown in Table 1. nar.oxfordjournals.org /cgi/content/full/24/15/3053   (3933 words)

Methods for testing oligonucleotide arrays - Patent 5843655 Depurinated oligonucleotides are prone to backbone cleavage when exposed to alkaline conditions. This reveals depurination by a reduction in surface tag in the regions subjected to the test conditions relative to that elsewhere on the surface. The method of this invention for determining the extent of depurination takes advantage of the fact that depurinated oligonucleotides are subject to cleavage and, thereby, to detection. www.freepatentsonline.com /5843655.html   (7611 words)

BDSP - Base documentaire - Visualisation de la notice DNA-adduct formation, depurination and imidazole ringopening were followed in vitro using styrene oxide, ethyleneimine and dimethyl sulfate. Depurination was found to be about 50 times faster in nucleosides than in double-stranded DNA. This apparent discrepancy in depurination between alkylated and intact bases suggests the possibility of developing a sensitive method for monitoring of DNA alkylations formed by electrophillic chemicals, which might be based on labelling of apurinic sites and utilized for in vivo studies as well. www.bdsp.tm.fr /Base/Scripts/ShowA.bs?bqRef=44861   (149 words)

Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is ... To determine the position of depurination in the rRNA, a sequencing ladder of DNA corresponding to the yeast 25S rRNA was separated on the same gel. The extent of depurination was quantified by calculating the ratio of the depurination fragment (Dep.) to the 25S rRNA fragment (rRNA) and plotted (C). that ribosome depurination in trans is not sufficient for cytotoxicity. nar.oxfordjournals.org /cgi/content/full/32/14/4244   (7956 words)

JBC -- Li and McClure 273 (36): 23558 Partial depurination of the DNA was performed as described (22) with some modifications. Assay for the Effects of Prenicking and Depurination on Open Complex Formation-- Open complex formation on the prenicked or depurinated DNA was assayed using the gel retardation method as described (26, Position-dependent Effects of Depurination on Open Complex Formation-- Representative portions of the sequencing autoradiograms resulting from the depurination studies are shown in Fig. www.jbc.org /cgi/content-nw/full/273/36/23558   (5692 words)

Pokeweed antiviral protein isoforms PAP-I, PAP-II, and PAP-III depurinate RNA of human immunodeficiency virus (HIV)-1. Depurination of viral RNA was monitored by directly measuring the amount of the adenine base released from the viral RNA species using quantitative high-performance liquid chromatography. In contrast to the three PAP isoforms, ricin A chain (RTA) failed to cause detectable depurination of viral RNA even at 5 microM, although it was as effective as PAP in inhibiting protein synthesis in cell-free translation assays. These findings indicate that the highly conserved active site residues responsible for the depurination of rRNA by PAP or RTA are not sufficient for the recognition and depurination of viral RNA. www.aegis.com /aidsline/1999/oct/A99A0768.html   (460 words)

Isolation and Characterization of an RIP (Ribosome-Inactivating Protein)-Like Protein from Tobacco with Dual Enzymatic ... as manifested by the depurination of yeast rRNA. B, Gel filtration fractions were checked for depurination activity using yeast ribosomes as a substrate as described in "Materials and Methods." C, Fractions 31 and 32 were pooled together and fractionated on porous HS (cation exchange column). The depurination assay was conducted according to Tumer et al. www.plantphysiol.org /cgi/content/full/134/1/171   (6159 words)

Pokeweed Antiviral Protein Regulates the Stability of Its Own mRNA by a Mechanism That Requires Depurination but Can Be ... We quantify the extent of rRNA depurination in PAP depurinates yeast ribosomes in trans, we induced PAP expression C, the extent of depurination shown in B was quantified by calculating the ratio of the depurination fragment to the 25 S rRNA fragment; this ratio was expressed as a percent of the depurination observed in vitro. www.jbc.org /cgi/content/full/277/44/41428   (6092 words)

Specific Contacts between Residues in the DNA-Binding Domain of the TyrR Protein and Bases in the Operator of the tyrP ... Depurination (A+G) and depyrimidation (C+T) reactions were carried out as described by Brunelle and Schleif (9). A+G and T+C, depurination and depyrimidation reactions, respectively; B, bound lane derived from the TyrR-DNA complex; UB, unbound lane derived from the free DNA. Depurination (A+G) analysis using the wild-type TyrR protein and the mutant TyrR protein TA495. jb.asm.org /cgi/content/full/181/8/2338   (4896 words)

Biocompare - Product Literature Center One major factor contributing to the inability of standard PCR to amplify long segments of DNA is template degradation during exposure to high temperatures in buffers that are unable to maintain pH. This is due to depurination, the hydrolysis of the N-glycosidic bond between the base and the sugar of a DNA molecule. Although depurination is a rare event, occurring approximately once every 25 kb of single-stranded DNA per minute, its effect on long-range PCR is more profound because long templates simply have more sites that are susceptible to depurination. www.biocompare.com /techart.asp?id=667   (1185 words)

John Jay Science Dept Faculty Translational inhibition by ribosome depurination has been hypothesized to be responsible for RIP’s cytotoxicity. Recently, mutagenesis studies of PAP have separated the ribosome depurination activity from anti-viral activity. The molecular mechanism by which these toxins cause apoptosis and mRNA depurination is unknown. web.jjay.cuny.edu /~science/Friedland.html   (244 words)

ABRF Electronic Discussion Group viewed: Re: DNA syn - depurina Depurination will invariably result in backbone cleavage on deprotection, explain the n+1 shoulder on your CE with depurination. depurination) do not seem to be your problem, and because by milder www.abrf.org /archives/hmail/0014/0087.html   (315 words)

Glen Research Glen Report Because 2-amino-dA is very susceptible to depurination during the acidic deblocking step of DNA synthesis, mild deprotecting groups like PAC to protect both amino groups should not be used. The combination of N2-isobutyryl and N6-formamidine protecting groups in our earlier monomer (1) stabilized the monomer to depurination but made it very slow to deprotect, requiring 7 days in ammonium hydroxide at 55° or 17 hours at 55° in AMA for complete removal. After a significant development effort, we are happy to announce a new 2-amino-dA monomer (2) which appears to solve all of the earlier problems: deprotection is fast and effective in ammonium hydroxide; it is stabilized to depurination during synthesis; and the cost is only about 20% of the earlier monomer. www.glenres.com /GlenReports/GR11-13.html   (951 words)

Athens '97 Cell Factories Poster Heat- induced DNA damages should be repaired in hyperthermophiles, but it is not clear to what extent their repair systems have to be be efficient. This indicates that the protection effect of salt on the thermodegradation of double-stranded DNA is not mediated by the stabilization of the double-helix, but by a direct protection of the N- glycosidic bond at high temperature. Fig1: Depurination and subsequent cleavage of the phosphodiester bond www-archbac.u-psud.fr /Meetings/athensgr97/AthenGr97Poster.html   (602 words)

Estrogen-Induced Depurination of DNA: A Novel Target for Breast Cancer Prevention - Storming Media Abstract: The hypothesis that depurinating estrogen-DNA adducts initiate breast cancer by generating mutations is at the center of the research in this BCCOE. Inhibition of this adduct formation is anticipated to reduce estrogen-induced mutagenesis, neoplastic transformation and development of tumors. The profile of estrogen metabolites, conjugates, and depurinating DNA adducts and the expression of estrogen-metabolizing enzymes will be analyzed. www.stormingmedia.us /87/8786/A878624.html   (312 words)

A DNA enzyme with N-glycosylase activity -- Sheppard et al. 97 (14): 7802 -- Proceedings of the National Academy of ... The uncatalyzed rate of depurination of the target deoxyguanosine was determined by incubating 1 µM 5'- for depurination as well, which is favored under acidic conditions. acid-catalyzed depurination (28), involving protonation of N7 of the target guanosine. www.pnas.org /cgi/content/full/97/14/7802   (4467 words)

MolecularInfo.com For genomic DNA hybridization, hydrolyze the DNA partially by acid depurination prior to alkali denaturation. For acid depurination, soak the gel for 10-15 minutes in Acid Depurination Solution at room temperature. For plasmid DNA (or bacteriophage DNA) hybridization, acid depurination is not necessary. www.molecularinfo.com /MTM/J/J1/J1-1.html   (1100 words)

Nilgun Tumer   (Site not responding. Last check: 2007-10-20) We recently showed that PAP inhibits frameshifting and retrotransposition of Ty1 in yeast and identified yeast chromosomal mutants that are resistant to PAP. Hudak, K., Bauman, J. and Tumer, N. Pokeweed antiviral protein binds to the cap structure of eukaryotic mRNA and depurinates the mRNA downstream of the cap structure. Baranwal, V. K., Tumer, N. and Kapoor, H. Depurination of ribosomal RNA and inhibition of viral RNA translation by an antiviral protein of Celosia cristata. lifesci.rutgers.edu /~molbiosci/Professors/tumer.html   (641 words)

Oxidative damage and direct adducts in calf thymus DNA induced by the pentachlorophenol metabolites, ... Screen intensified autoradiography was for 4 h for (A) and (B) and 2 h for (C) and (D) at –80°C. To induce depurination of DNA adducts, the Cl BQ-modified DNA depurination and that they are unlikely to undergo depurination/depyrimidination McCoull,K.D., Rindgen,D., Blair,I.A. and Penning,T.M. (1999) Synthesis and characterization of polycyclic aromatic hydrocarbon o-quinone depurinating N7-guanine adducts. carcin.oxfordjournals.org /cgi/content/full/22/4/627   (4957 words)

Depurination for DNA blotting - BioForum For fragments below 10 kb, depurination is unnecessary. For fragments over 10 kb, depurination is helpful. By the way, cosmid southern blotting is much easier than genomic southern blotting, omit the depurination step or not, in my opinion, doens't affect the final result. www.protocol-online.org /forums/index.php?showtopic=20945&view=getnewpost   (320 words)

Self-catalyzed site-specific depurination of guanine residues within gene sequences -- Amosova et al. 103 (12): 4392 -- ... Self-catalyzed site-specific depurination of guanine residues within gene sequences -- Amosova et al. Self-catalyzed site-specific depurination of guanine residues within gene sequences That residue is uniquely depurinated with a rate some www.pnas.org /cgi/content/abstract/103/12/4392   (256 words)

Depurination for DNA blotting - BioForum When doing a southern blot, one of the steps is depurination (usually in HCL 0.25N) to make the transfer of the large DNA fragments easier. You should treat the gel with 0.25 M HCl no more than 10 min according to a manufactor's instruction of ROCHE. The bromophenol blue will be changed from blue to yellow during depurination, it is an indication of success of depurination and is always less than 10 min. protocol-online.org /forums/index.php?showtopic=20945&view=getnewpost   (320 words)

Alkylating Agents - The Merck Veterinary Manual Alkylating agents form highly reactive intermediate compounds that are able to transfer alkyl groups to DNA. Alkylation can result in miscoding of DNA strands, incomplete repair of alkylated segments (which leads to strand breakage or depurination), excessive cross-linking of DNA, and inhibition of strand separation at mitosis. Monofunctional alkylating agents transfer a single alkyl group and usually result in miscoding of DNA, strand breakage, or depurination. www.merckvetmanual.com /mvm/htm/bc/191702.htm   (541 words)

ETTA Depurination - 24,000 Events per Day - 10.2% of Daily Damage "One of the most prevalent lesions in DNA is the apurinic/apyrimidinic (AP) site, which is derived from the cleavage of the N-glycosyl bond by DNA glycosylase or by spontaneous depurination. AP sites are repaired by AP endonucleases during the process of base excision repair; however, an imbalance in this DNA repair system may cause mutations as well as cell death. 216.147.56.223 /testing.html   (570 words)

Pokeweed Antiviral Protein Accesses Ribosomes by Binding to L3 -- Hudak et al. 274 (6): 3859 -- Journal of Biological ...   (Site not responding. Last check: 2007-10-20) Unlike wild-type yeast, ribosomes from mak8-1 cells are not depurinated L3 is required for PAP to bind to ribosomes and depurinate the Pokeweed Antiviral Protein Regulates the Stability of Its Own mRNA by a Mechanism That Requires Depurination but Can Be Separated from Depurination of the alpha -Sarcin/Ricin Loop of rRNA intl.jbc.org /cgi/content/abstract/274/6/3859   (599 words)

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