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*  "Repair of heteroduplex DNA molecules with multibase loops in Escherich" by Margaretha Carraway and Martin G. Marinus
The repair of both the mismatch and the loops was directed by the state of dam methylation of the DNA chains and was dependent ... We conclude that multibase loops in DNA can be removed only as a consequence of corepair by dam-directed mismatch repair. ... Repair of heteroduplex molecules containing 410- and 514-base loops was observed when a 1-base deletion-insertion mismatch was ... A high efficiency of repair (95%) was found even when the mismatch and the loops were 1,448 nucleotides apart. ...
  https://escholarship.umassmed.edu/oapubs/665/
*  TIGR00571
GO:0006306: DNA methylation biological_process. GO:0009007: site-specific DNA-methyltransferase (adenine-specific) activity ... species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch ... All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the ... This family includes several phage methylases and a number of different restriction enzyme chromosomal site-specific ...
  http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR00571
*  DNA methylation - Wikipedia
... adenine methylation) GATC sites in an oligonucleotide labeled with a fluorophore and quencher. The adenine methyltransferase ... site-specific methyl-directed DNA endonucleases, which hydrolyze only methylated DNA. ChIP-on-chip assays, which is based on ... If there is a mis-match, it is recorded and the percentage of DNA for which the mis-match is present is noted. This gives the ... CpG sites that target each gene. DNA methylation marks, are genomic regions with specific methylation pattern in a specific ...
  https://en.wikipedia.org/wiki/DNA_methylation
*  Restriction enzyme - Wikipedia
DNA-binding) site in addition to both restriction (DNA cleavage) and modification (DNA methyltransferase) activity. Typical ... All types of enzymes recognize specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific ... This enzyme shows selectivity by cleaving only at one site that either does not have a mismatch or is kinetically preferred out ... Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise ...
  https://en.wikipedia.org/wiki/Restriction_enzyme
*  DNA repair - Wikipedia
Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind ... May 2013). "Different patterns of DNA methylation of the two distinct O6-methylguanine-DNA methyltransferase (O6-MGMT) promoter ... is strongly associated with specific mutations in the DNA mismatch repair pathway. BRCA1 and BRCA2, two famous genes whose ... The third type of DNA damage reversed by cells is certain methylation of the bases cytosine and adenine. When only one of the ...
  https://en.wikipedia.org/wiki/DNA_repair
*  ASMscience | DNA Methylation
DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is ... although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain ... and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are ... and decrease the stability of short direct repeats andare necessary for site-directed mutagenesis and to probe eukaryotic ...
  http://www.asmscience.org/content/journal/ecosalplus/10.1128/ecosalplus.4.4.5
*  Base Flipping
... catalysed chemical reaction or for a specific protein binding interaction ... DNA) to expose an out‐of‐stack base, which can then be a substrate for an enzyme‐ ... adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nature Structural Biology 8: 121-125. ... 1998) Crystal structure of a G:T/U mismatchspecific DNA glycosylase: mismatch recognition by complementary‐strand interactions ...
  http://www.els.net/WileyCDA/ElsArticle/refId-a0002714.html
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Site-specific recombinases are proteins that bind to distinct DNA target sequences. The Cre/lox system was first described in ... Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues ... cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific M ... Transmission of HLA-linked polymorphisms in Gag to HLA-mismatched recipients has been associated with reduced set point viral ...
  https://www.jove.com/visualize/abstract/22292089/site-specific-integration-foreign-dna-into-minimal-bacterial-human
*  Norbert O. Reich | Department of Chemistry - UC Santa Barbara
Proximal recognition sites facilitate intrasite hopping by DNA adenine methyltransferase: mechanistic exploration of epigenetic ... Coupling sequence-specific recognition to DNA modification, Estabrook RA, Nguyen TT, Fera N, Reich NO., J Biol Chem. 2009 Aug ... while mammalian DNA is modified only at cytosine C5. The bacterial enzymes are involved in restriction/modification, mismatch ... S-Adenosyl methionine-dependent DNA methyltransferases modify DNA sequence-specifically. Bacterial DNA is modified at both ...
  http://www.chem.ucsb.edu/node/512
*  DNA base flipping - Wikipedia
... permanganate is used to detect thymine residues that have been flipped out by cytosine-C5 and adenine-N6 methyltransferases. ... DNA glycosylases interact with DNA, flipping bases to determine a mismatch. An example of base excision repair occurs when a ... Web. 16 Mar. 2014. . Grosjean, [edited by] Henri (2009). DNA and RNA modification enzymes : structure, mechanism, function and ... This enzyme recognizes a specific sequence of the DNA (5'-GCGC-3') and methylates the first cytosine base of the sequence at ...
  https://en.wikipedia.org/wiki/DNA_base_flipping
*  http://ufdc.ufl.edu/UFE0043084/00001
Kaina, B., Margison, G.P., and Christmann, M. (2010). Targeting O methylguanine DNA methyltransferase with specific inhibito rs ... Recruitment of mismatch repair proteins to the site of DNA damage in human cells. J Cell Sci 121, 3146 3154. Kadyrov, F.A., ... 1998). Bax and adenine nucleotide translocator cooperate in the mitochondrial control of apoptosis. Science 281, 2027 2031. ... Stojic, L., Brun, R., and Jiricny, J. (2004). Mismatch re pair and DNA damage signalling. DNA Repair (Amst) 3, 1091 1101. Stupp ...
  http://ufdc.ufl.edu/UFE0043084/00001
*  Restriction enzyme - Photos and All Basic Informations
DNA cleavage) and modification (DNA methyltransferase) activity.[30][36] Type II[edit] Type II site-specific deoxyribonuclease ... This enzyme shows selectivity by cleaving only at one site that either does not have a mismatch or is kinetically preferred out ... Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise ... DNA) DNA Methylation DNA Methyltransferase Protein Motif Sequence Motif S-adenosyl-L-methionine Catalytic CRISPR DNA Binding ...
  http://wiki.metal-invest.pl/page_Restriction_enzyme.html
*  Patent US5856090 - DNA-methylase linking reaction - Google Patents
... the methylase conjugation element including a methylase binding site having at least one copy of a nucleotide sequence ... A plasmid suitable for use in this linkage reaction can comprise: (1) a gene fusion construct including a gene encoding a DNA ... The polypeptide determinant is expressed as a fusion protein together with the DNA methylase, which binds in vivo to a cytidine ... such as DNA methylases, provides a method of obtaining a covalent linkage between a nucleic acid segment and a polypeptide ...
  http://www.google.com/patents/US5856090?dq=6861155
*  TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets | BMC Genomics | Full Text
TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in ... to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in ... We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563-5, 2007; Nat Protoc 5:323-34, 2010 ... Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4630-0
*  Epigenetics - Wikipedia
Leonhardt H, Page AW, Weier HU, Bestor TH (November 1992). "A targeting sequence directs DNA methyltransferase to sites of DNA ... In Gammaproteobacteria, adenine methylation provides signals for DNA replication, chromosome segregation, mismatch repair, ... because they inherited the fear epigenetically by site-specific DNA methylation. These epigenetic changes lasted up to two ... Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine ...
  https://en.wikipedia.org/wiki/Epigenetic
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
One of the reasons is the loss-of-function null mutant of DNA methyltransferases is viable, thus providing a system to study ... cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific M ... Transmission of HLA-linked polymorphisms in Gag to HLA-mismatched recipients has been associated with reduced set point viral ... Approximately 5,000 lysine methylation sites were identified on different proteins, which are set by few dozens of protein ...
  https://www.jove.com/visualize/abstract/22295098/microrna-152-mediates-dnmt1-regulated-dna-methylation-estrogen
*  ASMscience | DNA Mismatch Repair
A dedicated site-specific endonuclease, MutH, is present, andMutL has no endonuclease activity; four exonucleases can ... A primary site of action appears to be on RecA, although subsequent steps of the recombination process can also be inhibited. ... In this review, the genetics of Very Short Patch (VSP) repair of T/G mismatches arising from deamination of 5- ... How this system discriminates between newlysynthesized and parental DNA strands is not clear. In E. coli and its relatives, ...
  http://www.asmscience.org/content/journal/ecosalplus/10.1128/ecosalplus.7.2.5
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... target DNA with primers flanking a CCGG site of interest (100-200 bp) is performed. If the CpG site contains 5- ... Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues ... cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific M ... Transmission of HLA-linked polymorphisms in Gag to HLA-mismatched recipients has been associated with reduced set point viral ...
  https://www.jove.com/visualize/abstract/21966393/no-effect-folic-acid-supplementation-on-global-dna-methylation-men
*  Publications | Reich Research Group - UC Santa Barbara
... non-specific DNA, Gel retardation studies with DNA substrates containing an abasic site substituted for the target adenine DNA ... Escherichia coli DNA adenine methyltransferase (Dam) plays essential roles in DNA replication, mismatch repair and gene ... sequence-specific DNA modification. Because many DNA methyltransferases and DNA repair enzymes induce similar DNA distortions, ... Methylation of GATC sites in Escherichia coli by DNA adenine methyltransferase (EcoDam) is essential for proper DNA replication ...
  http://www.chem.ucsb.edu/reichgroup/publications
*  Using shotgun sequence data to find active restriction enzyme genes
ORFs and tried to detect DNA-specific methyltransferase activity by looking for incorporation of 3H-SAM into λDNA or other DNA ... and sequence-specific DNA mismatch endonuclease. Nature. 1991;253:776-778. [PubMed] ... 40 sites for GRCGYC) and pBR322 DNA linearized with PstI (six sites for GRCGYC) in NEBuffer 4. No endonuclease activity was ... Functional characterization of HP0503: an adenine methyltransferase required for the virulence of Helicobacter pylori. Abstr. ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2615612/?lang=en-ca
*  Search: All Pfam signatures | InterPro | EMBL-EBI
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding (IPR014048) Pfam signature: PF01035 ... DNA/RNA non-specific endonuclease (IPR001604) Pfam signature: PF01223 Mur ligase, N-terminal catalytic domain (IPR000713) Pfam ... Ribosomal RNA adenine methyltransferase KsgA/Erm (IPR001737) Pfam signature: PF00398 Yeast PIR protein repeat (IPR000420) Pfam ...
  http://www.ebi.ac.uk/interpro/member-database/Pfam
*  Publications | NEB
Three-dimensional structure of the adenine-specific DNA methyltransferase M.Taq I in complex with the cofactor S- ... Purification of MboII methylase (GAAGmA) from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair ... M.Hhal binds tightly to substrates containing mismatches at the target base. Nucl.Acids Res.. Klimasauskas, S.and Roberts, R.J. ... A model for DNA binding and enzyme action derived from crystallographic studies of the TaqI N6-adenine-methyltransferase. Gene ...
  https://www.neb.com/research/publications?num=250&sorting=Year
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues ... Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5 ... cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific M ... Transmission of HLA-linked polymorphisms in Gag to HLA-mismatched recipients has been associated with reduced set point viral ...
  https://www.jove.com/visualize/abstract/25799415/association-between-thiopurine-s-methyltransferase-polymorphisms
*  Markers for pre-cancer and cancer cells and the method to interfere with cell proliferation therein - Andes Biotechnologies S.A.
McCulloch et al., "A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S- ... DNA fragmentation can be measured by TUNEL or by electrophoresis to reveal the ladder of DNA. Western blot analysis can also be ... 2001). "Organelle-specific initiation of cell death pathways," Nature Cell Biology 3(11):E255-E263. Fluiter et al. "In Vivo ... Generally, the longer the hybridizing nucleic acid, the more base mismatches with an RNA it may contain and still form a stable ...
  http://www.freepatentsonline.com/9903000.html
*  Chemical Reagents for Investigating the Major Groove of DNA - Current Protocols
Chemical modification provides an inexpensive and rapid method for characterizing the structure of DNA and its association with ... Sitespecific OsO4 modification of the B‐Z junctions formed at the (dA‐dC)32 region in supercoiled DNA. J. Biol. Chem. 261:7093 ... Binding of EcoP151 DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence. J. Mol. ... Effect of hemimethylation and methylation of adenine on the structure and stability of model DNA duplexes. Biochemistry 34: ...
  http://www.currentprotocols.com/WileyCDA/CPUnit/refId-nc0606.html