High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.

abstract：:We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...

journal_title：Nucleic acids research

authors： Kröger M,Wahl R,Rice P

更新日期：1993-07-01 00:00:00

abstract：:The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...

journal_title：Nucleic acids research

authors： Holm L,Sander C

更新日期：1996-01-01 00:00:00

abstract：:Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...

journal_title：Nucleic acids research

authors： Zhang S,Tian D,Tran NH,Choi KP,Zhang L

更新日期：2014-11-10 00:00:00

abstract：:Chromatin footprinting in Drosophila tissue culture cells has detected the binding of a non-histone protein at +8 of the distal Adh RNA start site, on a 10-bp direct repeat motif abutting a nucleosome positioned over the inactive Adh distal promoter. Alternatively the active promoter is bound by a transcription initia...

journal_title：Nucleic acids research

authors： Benyajati C,Ewel A,McKeon J,Chovav M,Juan E

更新日期：1992-09-11 00:00:00

abstract：:Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-c...

journal_title：Nucleic acids research

authors： Gong W,Zhou D,Ren Y,Wang Y,Zuo Z,Shen Y,Xiao F,Zhu Q,Hong A,Zhou X,Gao X,Li T

更新日期：2008-01-01 00:00:00

abstract：:The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...

journal_title：Nucleic acids research

authors： Jónsson SR,Haché G,Stenglein MD,Fahrenkrug SC,Andrésdóttir V,Harris RS

更新日期：2006-01-01 00:00:00

abstract：:Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is involved in base excision DNA repair (BER) and in regulation of gene expression, acting as a redox co-activator of several transcription factors. Recent findings highlight a novel role for APE1 in RNA metabolism, which is modulated by nuc...

journal_title：Nucleic acids research

authors： Fantini D,Vascotto C,Marasco D,D'Ambrosio C,Romanello M,Vitagliano L,Pedone C,Poletto M,Cesaratto L,Quadrifoglio F,Scaloni A,Radicella JP,Tell G

更新日期：2010-12-01 00:00:00

abstract：:Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Streptococcus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs (frequent words). The character and extent of frequent words are strikingly different among these genomes. The frequent words...

journal_title：Nucleic acids research

authors： Mrázek J,Gaynon LH,Karlin S

更新日期：2002-10-01 00:00:00

abstract：:We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to tr...

journal_title：Nucleic acids research

authors： Schweikert G,Behr J,Zien A,Zeller G,Ong CS,Sonnenburg S,Rätsch G

更新日期：2009-07-01 00:00:00

abstract：:Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...

journal_title：Nucleic acids research

authors： Kang DD,Sibille E,Kaminski N,Tseng GC

更新日期：2012-01-01 00:00:00

abstract：:Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mecha...

journal_title：Nucleic acids research

authors： Li X,Peng Y,Qu X

更新日期：2006-08-02 00:00:00

abstract：:Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...

journal_title：Nucleic acids research

authors： Kuzmich S,Marky LA,Jones RA

更新日期：1983-05-25 00:00:00

abstract：:Detailed models are presented for the triple-stranded polynucleotide helices of poly (U)-poly (A)-poly (U) (two forms), poly (U)-poly d (A) -poly (U), poly d(C)-poly d(I)-poly d(C), poly d(T)-polyd(A)-poly d(T) and poly (I)-poly (A)-poly (I). The models were genrated using a computerized, linked-atom procedure which p...

journal_title：Nucleic acids research

authors： Arnott S,Bond PJ,Selsing E,Smith PJ

更新日期：1976-10-01 00:00:00

abstract：:We previously determined that a linear co-polymer of histidine and lysine (HK) in combination with liposomes enhanced the transfection efficiency of cationic liposomes. In the current study, we designed a series of HK polymers with increased branching and/or histidine/lysine ratio to determine if either variable affec...

journal_title：Nucleic acids research

authors： Chen QR,Zhang L,Stass SA,Mixson AJ

更新日期：2001-03-15 00:00:00

abstract：:A cDNA clone named 1A11 was isolated in a screen for genes that are activated by both mesoderm inducing factors FGF and activin in animal explants of Xenopus laevis embryos. In undisturbed embryos, 1A11 is expressed during the gastrula stage in the entire marginal zone where mesoderm originates, and later in the somit...

journal_title：Nucleic acids research

authors： Greene JM,Otani H,Good PJ,Dawid IB

更新日期：1993-05-25 00:00:00

abstract：:Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational...

journal_title：Nucleic acids research

authors： Eitan Y,Kashi Y

更新日期：2002-06-15 00:00:00

abstract：:Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic lo...

journal_title：Nucleic acids research

authors： Kautsar SA,Suarez Duran HG,Blin K,Osbourn A,Medema MH

更新日期：2017-07-03 00:00:00

abstract：:DNA damage tolerance (DDT) is responsible for genomic stability and cell viability by bypassing the replication block. In Saccharomyces cerevisiae DDT employs two parallel branch pathways to bypass the DNA lesion, namely translesion DNA synthesis (TLS) and error-free lesion bypass, which are mediated by sequential mod...

journal_title：Nucleic acids research

authors： Xu X,Lin A,Zhou C,Blackwell SR,Zhang Y,Wang Z,Feng Q,Guan R,Hanna MD,Chen Z,Xiao W

更新日期：2016-06-20 00:00:00

abstract：:Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...

journal_title：Nucleic acids research

authors： Rogers AK,Phillips CM

更新日期：2020-05-07 00:00:00

abstract：:Synchronous plasmodia of cycloheximide-sensitive and cycloheximide-resistant strains of Physarum polycephalum were labelled with 3[H]-deoxyadenosine in pulse and pulse-chase experiments in presence and absence of cycloheximide. The replication products were studied with alkaline sucrose gradient sedimentation analysis...

journal_title：Nucleic acids research

authors： Funderud S,Haugli F

更新日期：1977-02-01 00:00:00

abstract：:RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with argini...

journal_title：Nucleic acids research

authors： Rochat T,Bohn C,Morvan C,Le Lam TN,Razvi F,Pain A,Toffano-Nioche C,Ponien P,Jacq A,Jacquet E,Fey PD,Gautheret D,Bouloc P

更新日期：2018-09-28 00:00:00

abstract：:Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...

journal_title：Nucleic acids research

authors： Mamede R,Vila-Cerqueira P,Silva M,Carriço JA,Ramirez M

更新日期：2021-01-08 00:00:00

abstract：:Recent effective use of TAL Effectors (TALEs) has provided an important approach to the design and synthesis of sequence-specific DNA-binding proteins. However, it is still a challenging task to design and manufacture effective TALE modulators because of the limited knowledge of TALE-DNA interactions. Here we synthesi...

journal_title：Nucleic acids research

authors： Zhang H,Li J,Hou S,Wang G,Jiang M,Sun C,Hu X,Zhuang F,Dai Z,Dai J,Xi JJ

更新日期：2014-08-01 00:00:00

abstract：:Analysis of the human protein-tyrosine phosphatase (PTP) PTPRJ mRNA detected three in-frame AUGs at the 5'-end (starting at nt +14, +191 and +356) with no intervening stop codons. This tandem AUG arrangement is conserved between humans and the mouse and is unique among the genes of the classical PTPs. Until now it was...

journal_title：Nucleic acids research

authors： Karagyozov L,Godfrey R,Böhmer SA,Petermann A,Hölters S,Ostman A,Böhmer FD

更新日期：2008-08-01 00:00:00

abstract：:DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no single method can identify the location, direction and speed of replication forks with high resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthe...

journal_title：Nucleic acids research

authors： Georgieva D,Liu Q,Wang K,Egli D

更新日期：2020-09-04 00:00:00

abstract：:Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure reso...

journal_title：Nucleic acids research

authors： Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deléage G,Combet C

更新日期：2012-01-01 00:00:00

abstract：:We report the use of an engineered ribozyme to produce a circular human exon in vitro. Specifically, we have designed a derivative of a yeast self-splicing group II intron that is able to catalyze the formation of a circular exon encoding the first kringle domain (K1) of the human tissue plasminogen activator protein....

journal_title：Nucleic acids research

authors： Mikheeva S,Hakim-Zargar M,Carlson D,Jarrell K

更新日期：1997-12-15 00:00:00

abstract：:The DNA sequences at and around the junctions between viral and cellular DNA in the polyoma virus transformed mouse cell line, TS-A-3T3, have been determined. No common sequence specificity or structural features at the joins have been observed. The sequence indicates that the 94K truncated large T antigen found in TS...

journal_title：Nucleic acids research

authors： Ruley HE,Lania L,Chaudry F,Fried M

更新日期：1982-08-11 00:00:00

abstract：:To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for chromosomal tagging with one or more fluorescent protein genes (EGFP, EYFP, mRFP1, DsRed2). We used lambda-Red recombinati...

journal_title：Nucleic acids research

authors： Watt RM,Wang J,Leong M,Kung HF,Cheah KS,Liu D,Danchin A,Huang JD

更新日期：2007-01-01 00:00:00

abstract：:The TPA-inducible transcription factor AP-1, consisting of homo- or hetero-dimers of members of the Jun- and Fos-families, regulates transcription of a wide variety of genes containing the TPA response element (TRE). In P19 embryonal carcinoma (EC) cells, Jun D is the only component of AP-1 expressed, while in these c...

journal_title：Nucleic acids research

authors： den Hertog J,de Groot RP,de Laat SW,Kruijer W

更新日期：1992-01-11 00:00:00