A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4).

Abstract:

:Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607-4616]. Our goal is to elucidate on a structural level how AAF-dG can be harbored in the Dpo4 active site opposite an incoming dCTP, using molecular modeling and molecular dynamics simulations, since AAF-dG prefers the syn glycosidic torsion. Both anti and syn conformations of the templating AAF-dG in a Dpo4 ternary complex were investigated. All four dNTPs were studied. We found that an anti glycosidic torsion with C1'-exo deoxyribose conformation allows AAF-dG to be Watson-Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting. The AAF is situated in the Dpo4 major groove open pocket with fluorenyl rings 3'- and acetyl 5'-directed along the modified strand, irrespective of dNTP. With AAF-dG syn, the fluorenyl rings are in the small minor groove pocket and the active site region is highly distorted. The anti-AAF-dG conformation with C1'-exo sugar pucker can explain the preferential incorporation of dC by Dpo4. Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Wang L,Broyde S

doi

10.1093/nar/gkj479

keywords:

subject

Has Abstract

pub_date

2006-02-01 00:00:00

pages

785-95

issue

3

eissn

0305-1048

issn

1362-4962

pii

34/3/785

journal_volume

34

pub_type

杂志文章
  • The effects of mercury-substitution on the hybridisation characteristics of nucleic acids.

    abstract::The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.8.2357

    authors: Brown TD,Balmain A

    更新日期:1979-12-20 00:00:00

  • Conserved principles of mammalian transcriptional regulation revealed by RNA half-life.

    abstract::RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp542

    authors: Friedel CC,Dölken L,Ruzsics Z,Koszinowski UH,Zimmer R

    更新日期:2009-09-01 00:00:00

  • Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.

    abstract::Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx970

    authors: Okuda M,Nakazawa Y,Guo C,Ogi T,Nishimura Y

    更新日期:2017-12-15 00:00:00

  • The structural integrity exerted by N-terminal pyroglutamate is crucial for the cytotoxicity of frog ribonuclease from Rana pipiens.

    abstract::Onconase, a cytotoxic ribonuclease from Rana pipiens, possesses pyroglutamate (Pyr) at the N-terminus and has a substrate preference for uridine-guanine (UG). To identify residues responsible for onconase's cytotoxicity, we cloned the rpr gene from genomic DNA and expressed it in Escherichia coli BL21(DE3). The recomb...

    journal_title:Nucleic acids research

    pub_type: 评论,杂志文章

    doi:10.1093/nar/gkg746

    authors: Liao YD,Wang SC,Leu YJ,Wang CF,Chang ST,Hong YT,Pan YR,Chen C

    更新日期:2003-09-15 00:00:00

  • Bacillus subtilis RecN binds and protects 3'-single-stranded DNA extensions in the presence of ATP.

    abstract::Bacillus subtilis RecN appears to be an early detector of breaks in double-stranded DNA. In vivo, RecN forms discrete nucleoid-associated structures and in vitro exhibits Mg2+-dependent single-stranded (ss) DNA binding and ssDNA-dependent ATPase activities. In the presence of ATP or ADP, RecN assembles to form large n...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki533

    authors: Sanchez H,Alonso JC

    更新日期:2005-04-22 00:00:00

  • Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP.

    abstract::We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.13.6205

    authors: Inokuchi Y,Jacobson AB,Hirose T,Inayama S,Hirashima A

    更新日期:1988-07-11 00:00:00

  • A study of the interaction between ethidium bromide and rye chromatin: comparison with calf thymus chromatin.

    abstract::We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/3.9.2193

    authors: LaRue H,Pallotta D

    更新日期:1976-09-01 00:00:00

  • Fluorescent RNA cytochemistry: tracking gene transcripts in living cells.

    abstract::The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/29.5.1013

    authors: Pederson T

    更新日期:2001-03-01 00:00:00

  • P4P: a peptidome-based strain-level genome comparison web tool.

    abstract::Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx389

    authors: Blanco-Míguez A,Fdez-Riverola F,Lourenço A,Sánchez B

    更新日期:2017-07-03 00:00:00

  • Control of mRNA decapping by autoinhibition.

    abstract::5' mediated cytoplasmic RNA decay is a conserved cellular process in eukaryotes. While the functions of the structured core domains in this pathway are well-studied, the role of abundant intrinsically disordered regions (IDRs) is lacking. Here we reconstitute the Dcp1:Dcp2 complex containing a portion of the disordere...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky233

    authors: Paquette DR,Tibble RW,Daifuku TS,Gross JD

    更新日期:2018-07-06 00:00:00

  • Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.

    abstract::Two CTAG-recognizing restriction and modification (R/M) systems, designated MthZI and MthFI, were identified in the thermophilic archaeon Methanobacterium thermoformicicum strains Z-245 and FTF, respectively. Further analysis revealed that the methyltransferase (MTase) genes are plasmid-located in both strains. The pl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.19.5047

    authors: Nölling J,de Vos WM

    更新日期:1992-10-11 00:00:00

  • Unrecognized sequence homologies may confound genome-wide association studies.

    abstract::Genome-wide association studies (GWAS) have become a preferred method to identify new genetic susceptibility loci. This technique aims to understanding the molecular etiology of common diseases, but in many cases, it has led to the identification of loci with no obvious biological relevance. Herein, we show that previ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks169

    authors: Galichon P,Mesnard L,Hertig A,Stengel B,Rondeau E

    更新日期:2012-06-01 00:00:00

  • Structure of the yeast Pml1 splicing factor and its integration into the RES complex.

    abstract::The RES complex was previously identified in yeast as a splicing factor affecting nuclear pre-mRNA retention. This complex was shown to contain three subunits, namely Snu17, Bud13 and Pml1, but its mode of action remains ill-defined. To obtain insights into its function, we have performed a structural investigation of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn894

    authors: Brooks MA,Dziembowski A,Quevillon-Cheruel S,Henriot V,Faux C,van Tilbeurgh H,Séraphin B

    更新日期:2009-01-01 00:00:00

  • Chemical synthesis of a gene for somatomedin C.

    abstract::A synthetic gene for somatomedin C, a human growth factor, has been assembled by a single ligation of 23 oligodeoxyribonucleotides, which were chemically synthesized by an improved solid phase phosphotriester method. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.8.2959

    authors: Sproat BS,Gait MJ

    更新日期:1985-04-25 00:00:00

  • Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs.

    abstract::The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal effi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq616

    authors: Berger SM,Pesold B,Reber S,Schönig K,Berger AJ,Weidenfeld I,Miao J,Berger MR,Gruss OJ,Bartsch D

    更新日期:2010-09-01 00:00:00

  • A novel NGS library preparation method to characterize native termini of fragmented DNA.

    abstract::Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library prepa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa128

    authors: Harkins KM,Schaefer NK,Troll CJ,Rao V,Kapp J,Naughton C,Shapiro B,Green RE

    更新日期:2020-05-07 00:00:00

  • A novel route to product specificity in the Suv4-20 family of histone H4K20 methyltransferases.

    abstract::The delivery of site-specific post-translational modifications to histones generates an epigenetic regulatory network that directs fundamental DNA-mediated processes and governs key stages in development. Methylation of histone H4 lysine-20 has been implicated in DNA repair, transcriptional silencing, genomic stabilit...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt776

    authors: Southall SM,Cronin NB,Wilson JR

    更新日期:2014-01-01 00:00:00

  • All three RNA recognition motifs and the hinge region of HuC play distinct roles in the regulation of alternative splicing.

    abstract::The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins contains a divergent N-terminus,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt166

    authors: Hinman MN,Zhou HL,Sharma A,Lou H

    更新日期:2013-05-01 00:00:00

  • Large-scale opening of A + T rich regions within supercoiled DNA molecules is suppressed by salt.

    abstract::Large-scale cooperative helix opening has been previously observed in A + T rich sequences contained in supercoiled DNA molecules at elevated temperatures. Since it is well known that helix melting of linear DNA is suppressed by addition of salt, we have investigated the effects of added salts on opening transitions i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.11.2042

    authors: Bowater RP,Aboul-ela F,Lilley DM

    更新日期:1994-06-11 00:00:00

  • Sequence-specific functions of the early palindrome domain within the SV40 core origin of replication.

    abstract::The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure, but may be involved in the initiation of SV40 DNA replication in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:

    authors: Kim YS,Kang HS

    更新日期:1989-11-25 00:00:00

  • Characterization of L1 retrotransposition with high-throughput dual-luciferase assays.

    abstract::Recent studies employing genome-wide approaches have provided an unprecedented view of the scope of L1 activities on structural variations in the human genome, and further reinforced the role of L1s as one of the major driving forces behind human genome evolution. The rapid identification of novel L1 elements by these...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1076

    authors: Xie Y,Rosser JM,Thompson TL,Boeke JD,An W

    更新日期:2011-02-01 00:00:00

  • Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases.

    abstract::DNA2 nuclease/helicase is a structure-specific nuclease, 5'-to-3' helicase, and DNA-dependent ATPase. It is involved in multiple DNA metabolic pathways, including Okazaki fragment maturation, replication of 'difficult-to-replicate' DNA regions, end resection, stalled replication fork processing, and mitochondrial geno...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/gkz1101

    authors: Zheng L,Meng Y,Campbell JL,Shen B

    更新日期:2020-01-10 00:00:00

  • Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases.

    abstract::Nucleobase analogs 5-methylisocytosine ((Me)isoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing d(Me)isoC and disoG using modified ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki628

    authors: Ahle JD,Barr S,Chin AM,Battersby TR

    更新日期:2005-06-02 00:00:00

  • Genome-wide mapping of histone H4 serine-1 phosphorylation during sporulation in Saccharomyces cerevisiae.

    abstract::We previously showed that histone H4 serine-1 phosphorylation (H4S1ph) is evolutionarily conserved during gametogenesis, and contributes to post-meiotic nuclear compaction and to full completion of sporulation in the yeast Saccharomyces cerevisiae. Previous studies showed that H4S1ph and another modification of the sa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq218

    authors: Govin J,Schug J,Krishnamoorthy T,Dorsey J,Khochbin S,Berger SL

    更新日期:2010-08-01 00:00:00

  • Opposing roles of mitochondrial and nuclear PARP1 in the regulation of mitochondrial and nuclear DNA integrity: implications for the regulation of mitochondrial function.

    abstract::The positive role of PARP1 in regulation of various nuclear DNA transactions is well established. Although a mitochondrial localization of PARP1 has been suggested, its role in the maintenance of the mitochondrial DNA is currently unknown. Here we investigated the role of PARP1 in the repair of the mitochondrial DNA i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1089

    authors: Szczesny B,Brunyanszki A,Olah G,Mitra S,Szabo C

    更新日期:2014-12-01 00:00:00

  • Studies on the ability of partially iodinated 16S RNA to participate in 30S ribosome assembly.

    abstract::Deproteinated 16S RNA was iodinated at pH 5.0 in an aqueous solution containing TlCl3 plus KI for 1-5 hours at 42 degrees C. Under these conditions 33 moles of iodine are incorporated per mole of RNA. As judged by sucrose gradient sedimentation, the iodinated RNA does not exhibit any large alteration in conformation a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/3.11.3001

    authors: Schendel PL,Craven GR

    更新日期:1976-11-01 00:00:00

  • Update of the Diatom EST Database: a new tool for digital transcriptomics.

    abstract::The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn905

    authors: Maheswari U,Mock T,Armbrust EV,Bowler C

    更新日期:2009-01-01 00:00:00

  • Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.

    abstract::Controller (C) proteins regulate the timing of the expression of restriction and modification (R-M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn448

    authors: McGeehan JE,Streeter SD,Thresh SJ,Ball N,Ravelli RB,Kneale GG

    更新日期:2008-08-01 00:00:00

  • Unique translation initiation of mRNAs-containing TISU element.

    abstract::Translation Initiator of Short 5' UTR (TISU) is a unique regulatory element of both transcription and translation initiation. It is present in a sizable number of genes with basic cellular functions and a very short untranslated region (5' UTR). Here, we investigated translation initiation from short 5' UTR mRNAs with...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr484

    authors: Elfakess R,Sinvani H,Haimov O,Svitkin Y,Sonenberg N,Dikstein R

    更新日期:2011-09-01 00:00:00

  • In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.

    abstract::Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky152

    authors: Smyth RP,Smith MR,Jousset AC,Despons L,Laumond G,Decoville T,Cattenoz P,Moog C,Jossinet F,Mougel M,Paillart JC,von Kleist M,Marquet R

    更新日期:2018-05-18 00:00:00