Scan Science and Technology
Contact Leading Edge Experts & Companies
Adenines
The Experts below are selected from a list of 285 Experts worldwide ranked by ideXlab platform
Bern Kohler – One of the best experts on this subject based on the ideXlab platform.
-
Ultrafast Excited-State Dynamics of Adenine and Monomethylated Adenines in Solution: Implications for the Nonradiative Decay Mechanism
Journal of the American Chemical Society, 2003Co-Authors: Boiko Cohen, Patrick M. Hare, Bern KohlerAbstract:The DNA base adenine and four monomethylated Adenines were studied in solution at room temperature by femtosecond pump−probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S1 state) populated by a UV pump pulse. In H2O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 ± 0.03 ps and 8.8 ± 1.2 ps. In contrast, signals from monomethylated Adenines decay monoexponentially. The S1 lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (τ = 4.23 ± 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H2…
-
Ultrafast Excited-State Dynamics of Adenine and Monomethylated Adenines in Solution: Implications for the Nonradiative Decay Mechanism
Journal of the American Chemical Society, 2003Co-Authors: Boiko Cohen, Patrick M. Hare, Bern KohlerAbstract:The DNA base adenine and four monomethylated Adenines were studied in solution at room temperature by femtosecond pump−probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S1 state) populated by a UV pump pulse. In H2O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 ± 0.03 ps and 8.8 ± 1.2 ps. In contrast, signals from monomethylated Adenines decay monoexponentially. The S1 lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (τ = 4.23 ± 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H2…
Bas Van Steensel – One of the best experts on this subject based on the ideXlab platform.
-
damid mapping of in vivo protein genome interactions using tethered dna adenine methyltransferase
Methods in Enzymology, 2006Co-Authors: Frauke Greil, Celine Moorman, Bas Van SteenselAbstract:A large variety of proteins bind to specific parts of the genome to regulate gene expression, DNA replication, and chromatin structure. DamID is a powerful method used to map the genomic interaction sites of these proteins in vivo. It is based on fusing a protein of interest to Escherichia coli DNA adenadeninehyltransferase (dam). Expression of this fusion protprotein in vivo leads to preferential methylation of Adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine‐methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization. We and others have successfully applied DamID to the genome‐wide identification of interaction sites of several transcription factors and other chromatin‐associated proteins. This chapter discusses DamID technology in detail, and a step‐by‐step experimental protocol is provided for use in Drosophila cell lines.
-
damid mapping of in vivo protein genome interactions using tethered dna adenine methyltransferase
Methods in Enzymology, 2006Co-Authors: Frauke Greil, Celine Moorman, Bas Van SteenselAbstract:A large variety of proteins bind to specific parts of the genome to regulate gene expression, DNA replication, and chromatin structure. DamID is a powerful method used to map the genomic interaction sites of these proteins in vivo. It is based on fusing a protein of interest to Escherichia coli DNA adenadeninehyltransferase (dam). Expression of this fusion protprotein in vivo leads to preferential methylation of Adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine‐methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization. We and others have successfully applied DamID to the genome‐wide identification of interaction sites of several transcription factors and other chromatin‐associated proteins. This chapter discusses DamID technology in detail, and a step‐by‐step experimental protocol is provided for use in Drosophila cell lines.
Ken F. Jarrell – One of the best experts on this subject based on the ideXlab platform.
-
bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
Frontiers in Microbiology, 2017Co-Authors: Yan Ding, Alison Berezuk, Cezar M. Khursigara, Ken F. JarrellAbstract:In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three adenine deletion version in the spontaneous mutant.
-
bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
Frontiers in Microbiology, 2017Co-Authors: Yan Ding, Alison Berezuk, Cezar M. Khursigara, Ken F. JarrellAbstract:In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three adenine deletion version in the spontaneous mutant.
Juan Niclosgutierrez – One of the best experts on this subject based on the ideXlab platform.
-
unravelling the versatile metal binding modes of adenine looking at the molecular recognition patterns of deaza and aza Adenines in mixed ligand metal complexes
Coordination Chemistry Reviews, 2013Co-Authors: Alicia Dominguezmartin, Maria Pilar Brandiblanco, Antonio Matillahernandez, Hanan El Bakkali, Valeria Marina Nurchi, Josefa Maria Gonzalezperez, Alfonso Castineiras, Juan NiclosgutierrezAbstract:Abstract To better understand the extreme versatility of adenine as a ligand, the metal binding patterns of some closely related N-ligands have been carefully analysed. All the selected ligands comply with the requirement of having at least one N-heterocyclic atom in each cycle of the purine skeleton. The N-ligands are: (a) deaza-Adenines [7-azaindole (H7azain), 4-azabenzimidazole (H4abim), 5-azabenzimidazole (H5abim), 7-deaza-adenine (H7deaA), purine (Hpur)] (b) adenine isomers [2-aminopurine (H2AP), 4-aminopyrazolo[3,4- d ]pyrimidine (H4app), 7-amino[1,2,4]triazolo[1,5- a ]pyrimidine (7atp)] and (c) aza-Adenines [2,6-diaminopurine (Hdap), 8-aza-adenine (H8aA)]. The different molecular recognition patterns are reviewed on the basis of the available structural information in the Cambridge Structural Database, version 5.33 (updated Nov. 2012). No restraints have been placed concerning the neutral or charged species of these N-ligands or the metal ions involved in the coordination. Attention is paid to the proton tautomerism and its metal binding patterns, highlighting many examples where the molecular recognition pattern is carried out by the cooperation of a metal N bond and an intra-molecular inter-ligand H-bonding interaction.
-
structural insights on the molecular recognition patterns between n 6 substituted Adenines and n aryl methyl iminodiacetate copper ii chelates
Journal of Inorganic Biochemistry, 2013Co-Authors: Alicia Dominguezmartin, Antonio Matillahernandez, Alfonso Castineiras, Angel Garciaraso, Catalina Cabot, Duane Choquesillolazarte, Inmaculada Pereztoro, Juan NiclosgutierrezAbstract:Abstract For a better understanding of the metal binding pattern of N6-substituted Adenines, six novel ternary Cu(II) complexes have been structurally characterized by single crystal X-ray diffraction: [Cu(NBzIDA)(HCy5ade)(H2O)] · H2O (1), [Cu(NBzIDA)(HCy6ade)(H2O)] · H2O (2), [Cu(FurIDA)(HCy6ade)(H2O)] · H2O (3), [Cu(MEBIDA)(HBAP)(H2O)] · H2O (4), [Cu(FurIDA)(HBAP)]n (5) and {[Cu(NBzIDA)(HdimAP)] · H2O}n (6). In these compounds NBzIDA, FurIDA and MEBIDA are N-substituted iminodiacetates with a non-coordinating aryl-methyl pendant arm (benzyl in NBzIDA, p-tolyl in MEBIDA and furfuryl in FurIDA) whereas HBAP, HCy5ade, HCy6ade and HdimAP are N6-substituted adenine derivatives with a N-benzyl, N-cyclopentyl, N-cyclohexyl or two N-methyl groups, respectively. Regardless of the molecular (1–4) or polymeric (5–6) nature of the studied compounds, the Cu(II) centre exhibits a type 4 + 1 coordination where the tridentate IDA-like chelators adopt a mer-conformation. In 1–5 the N6-R-Adenines use their most stable tautomer H(N9)adenine-like, and molecular recognition consists of the cooperation of the Cu N3(purine) bond and the intra-molecular interligand N9 H · · · O(coordinated carboxy) interaction. In contrast, N6,N6-dimethyl-adenine shows the rare tautomer H(N3)dimAP in 6, so that the molecular recognition with the Cu(NBzIDA) chelate consist of the Cu N9 bond and the N3 H · · · O intra-molecular interligand interaction. Contrastingly to the cytokinin activity found in the free ligands HBAP (natural cytokinin), HCy5ade and HCy6ade, the corresponding Cu(II) ternary complexes did not show any activity.
Partho Ghosh – One of the best experts on this subject based on the ideXlab platform.
-
T. aquaticus DGR.
, 2019Co-Authors: Sumit Handa, Kharissa L. Shaw, Partho GhoshAbstract:The T. aquaticus prophage DGR contains a gene encoding a variable protein (taqvp). The 3’ end of taqvp contains the variable region (VR) and initiation-of-mutagenic homing (IMH) sequence. The DGR also contains an accessory variability determinant (avd) gene, followed by an invariant template region (TR), which differs from VR mainly at Adenines. A sequence similar but not identical to the VR IMH occurs at the 3’ end of the TR and is called IMH*. Following these elements is a gene encoding a reverse trantranscriptase (rt). TR is transcribed to produce TR-RNA, which is reverse transcribed to produce TR-cDNA, with adenine-specific mutagenesis of the sequence accompanying reverse transcription. Adenine-mutagenized TR-cDNA homes to and replaces VR to yield a variant TaqVP.
-
template assisted synthesis of adenine mutagenized cdna by a retroelement protein complex
Nucleic Acids Research, 2018Co-Authors: Sumit Handa, Yong Jiang, Robert Foreman, Raymond F Schinazi, Jeff F Miller, Partho GhoshAbstract:Author(s): Handa, Sumit; Jiang, Yong; Tao, Sijia; Foreman, Robert; Schinazi, Raymond; Miller, Jeff; Ghosh, Partho | Abstract: ABSTRACT Diversity-generating retroelements (DGRs) create unparalleled levels of protein sequence variation through mutagenic retrohoming. Sequence information is transferred from an invariant template region ( TR ), through an RNA intermediate, to a protein-coding variable region. Selective infidelity at Adenines during transfer is a hallmark of DGRs from disparate bacteria, archaea, and microbial viruses. We recapitulated selective infidelity in vitro for the prototypical Bordetella bacteriophage DGR. A complex of the DGR reverse trantranscriptase bRT and pentameric accessory variability determinant (Avd) protein along with DGR RNA were necessary and sufficient for synthesis of template-primed, covalently linked RNA-cDNA molecules, as observed in vivo . We identified RNAcDNA molecules to be branched and most plausibly linked through 2′-5′ phosphodiester bonds. Adenine–mutagenesis was intrinsic to the bRT-Avd complex, which displayed unprecedented promiscuity while reverse transcribing Adenines of either DGR or non-DGR RNA templates. In contrast, bRT-Avd processivity was strictly dependent on the template, occurring only for the DGR RNA. This restriction was mainly due to a noncoding segment downstream of TR , which specifically bound Avd and created a privileged site for processive polymerization. Restriction to DGR RNA may protect the host genome from damage. These results define the early steps in a novel pathway for massive sequence diversification.
-
template assisted synthesis of adenine mutagenized cdna by a retroelement protein complex
bioRxiv, 2018Co-Authors: Sumit Handa, Yong Jiang, Robert Foreman, Raymond F Schinazi, Jeff F Miller, Partho GhoshAbstract:Diversity-generating retroelements (DGRs) create unparalleled levels of protein sequence variation through mutagenic retrohoming. Sequence information is transferred from an invariant template region (TR), through an RNA intermediate, to a protein-coding variable region. Selective infidelity at Adenines during transfer is a hallmark of DGRs from disparate bacteria, archaea, and microbial viruses. We recapitulated selective infidelity in vitro for the prototypical Bordetella bacteriophage DGR. A complex of the DGR reverse trantranscriptase bRT and pentameric accessory variability determinant (Avd) protein along with DGR RNA were necessary and sufficient for synthesis of template-primed, covalently linked RNA-cDNA molecules, as observed in vivo. We identified RNA-cDNA molecules to be branched and most plausibly linked through 29-59 phosphodiester bonds. Adenine–mutagenesis was intrinsic to the bRT-Avd complex, which displayed unprecedented promiscuity while reverse transcribing Adenines of either DGR or non-DGR RNA templates. In contrast, bRT-Avd processivity was strictly dependent on the template, occurring only for the DGR RNA. This restriction was mainly due to a noncoding segment downstream of TR, which specifically bound Avd and created a privileged site for processive polymerization. Restriction to DGR RNA may protect the host genome from damage. These results define the early steps in a novel pathway for massive sequence diversification.