DynOmics: dynamics of structural proteome and beyond.

abstract：:Oxanine (O) is a deamination product derived from guanine with the nitrogen at the N1 position substituted by oxygen. Cytosine, thymine, adenine, guanine as well as oxanine itself can be incorporated by Klenow Fragment to pair with oxanine in a DNA template with similar efficiency, indicating that oxanine in DNA may c...

journal_title：Nucleic acids research

authors： Hitchcock TM,Gao H,Cao W

更新日期：2004-08-02 00:00:00

abstract：:Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, co...

journal_title：Nucleic acids research

authors： dos Reis M,Wernisch L,Savva R

更新日期：2003-12-01 00:00:00

abstract：:A new E. coli strain has been constructed that contains the dinD1::LacZ+ fusion and is deficient in methylation-dependent restriction systems (McrA-, McrBC-, Mrr-). This strain has been used to clone restriction endonuclease genes directly into E. coli. When E. coli cells are not fully protected by the cognate methyla...

journal_title：Nucleic acids research

authors： Fomenkov A,Xiao JP,Dila D,Raleigh E,Xu SY

更新日期：1994-06-25 00:00:00

abstract：:The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...

journal_title：Nucleic acids research

authors： Adams RL,McKay EL,Douglas JT,Burdon RH

更新日期：1977-09-01 00:00:00

abstract：:Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl gro...

journal_title：Nucleic acids research

authors： Zuo S,Boorstein RJ,Teebor GW

更新日期：1995-08-25 00:00:00

abstract：:Gap closure is a challenging phase in microbial random shotgun genome sequencing projects, particularly since genome assemblies are often complicated by the presence of repeat elements, insertion sequences and other similar factors that contribute to sequence misassemblies. While it is well recognized that the conserv...

journal_title：Nucleic acids research

authors： Herron-Olson L,Freeman J,Zhang Q,Retzel EF,Kapur V

更新日期：2003-09-01 00:00:00

abstract：:The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...

journal_title：Nucleic acids research

authors： Urban M,Cuzick A,Rutherford K,Irvine A,Pedro H,Pant R,Sadanadan V,Khamari L,Billal S,Mohanty S,Hammond-Kosack KE

更新日期：2017-01-04 00:00:00

abstract：:The heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a multi-tasking protein that acts in the cytoplasm and nucleus. We have explored the possibility that this protein is associated with telomeres and participates in their maintenance. Rat brain hnRNP A2 was shown to have two nucleic acid binding sites. In the pr...

journal_title：Nucleic acids research

authors： Moran-Jones K,Wayman L,Kennedy DD,Reddel RR,Sara S,Snee MJ,Smith R

更新日期：2005-01-19 00:00:00

abstract：:Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...

journal_title：Nucleic acids research

authors： Gilson E,Perrin D,Hofnung M

更新日期：1990-07-11 00:00:00

abstract：:Human U6 small nuclear RNA (U6 snRNA), an abundant snRNA required for splicing of pre-mRNAs, contains several post-transcriptional modifications including a single m6A (N-6-methyladenosine) at position 43. This A-43 residue is critical for the function of U6 snRNA in splicing of pre-mRNAs. Yeast and plant U6 snRNAs al...

journal_title：Nucleic acids research

authors： Shimba S,Bokar JA,Rottman F,Reddy R

更新日期：1995-07-11 00:00:00

abstract：:Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...

journal_title：Nucleic acids research

authors： Rong Y,Ji SY,Zhu YZ,Wu YW,Shen L,Fan HY

更新日期：2019-12-02 00:00:00

abstract：:Cells internalized synthetic oligonucleotides (oligos) in culture. The hybridization of these molecules to target RNA in the living cell was subsequently detected and characterized after fixation of the cells, with or without previous detergent extraction. Hybridized oligo was distinguished from free oligo in the cell...

journal_title：Nucleic acids research

authors： Politz JC,Taneja KL,Singer RH

更新日期：1995-12-25 00:00:00

abstract：:We present the preparation of an ion exchange paper which can be used as a solid carrier in the transfer of RNA from gels. In addition to detection by blot hybridization to specific probes, transferred RNA can be characterized by cell-free translation in situ. Preparation of the paper is simple, inexpensive and reprod...

journal_title：Nucleic acids research

authors： Saris CJ,Franssen HJ,Heuyerjans JH,van Eenbergen J,Bloemers HP

更新日期：1982-08-25 00:00:00

abstract：:A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter...

journal_title：Nucleic acids research

authors： Vaid R,Wen J,Mannervik M

更新日期：2020-05-21 00:00:00

abstract：:The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...

journal_title：Nucleic acids research

authors： Han A,Kang HJ,Cho Y,Lee S,Kim YJ,Gong S

更新日期：2006-07-01 00:00:00

abstract：:G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...

journal_title：Nucleic acids research

authors： Lu Q,Schierer T,Kang SG,Henderson E

更新日期：1998-04-01 00:00:00

abstract：:Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...

journal_title：Nucleic acids research

authors： Rageul J,Park JJ,Jo U,Weinheimer AS,Vu TTM,Kim H

更新日期：2019-05-07 00:00:00

abstract：:The Escherichia coli RuvC protein is an endonuclease that resolves Holliday junctions. In vitro, the protein shows efficient structure-specific binding of Holliday junctions, yet the rate of junction resolution is remarkably low. We have mapped the sites of cleavage on a synthetic junction through which a crossover ca...

journal_title：Nucleic acids research

authors： Shah R,Bennett RJ,West SC

更新日期：1994-07-11 00:00:00

abstract：:The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and oth...

journal_title：Nucleic acids research

authors： Blake JA,Bult CJ,Eppig JT,Kadin JA,Richardson JE,Mouse Genome Database Group.

更新日期：2014-01-01 00:00:00

abstract：:The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...

journal_title：Nucleic acids research

authors： Muchhal US,Schwartzbach SD

更新日期：1994-12-25 00:00:00

abstract：:Targeted modulation of gene expression represents a valuable approach to understand the mechanisms governing gene regulation. In a therapeutic context, it can be exploited to selectively modify the aberrant expression of a disease-causing gene or to provide the target cells with a new function. Here, we have establish...

journal_title：Nucleic acids research

authors： Mlambo T,Nitsch S,Hildenbeutel M,Romito M,Müller M,Bossen C,Diederichs S,Cornu TI,Cathomen T,Mussolino C

更新日期：2018-05-18 00:00:00

abstract：:Intramolecular RNA cross-links were induced within the large ribosomal subunit of E. coli by mild ultraviolet irradiation. Regions of the 23S RNA previously implicated in interactions with ribosomal-bound tRNA were then specifically excised by addressed cleavage using ribonuclease H, in conjunction with synthetic comp...

journal_title：Nucleic acids research

authors： Mitchell P,Osswald M,Schueler D,Brimacombe R

更新日期：1990-08-11 00:00:00

abstract：:Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previ...

journal_title：Nucleic acids research

authors： Ullrich S,Guigó R

更新日期：2020-02-20 00:00:00

abstract：:A method for quantifying the proportion of supercoiled circular (SC) forms in DNA solutions is described. The method (SCFluo) takes advantage of the reversible denaturation property of SC forms and the high specificity of the PicoGreen fluorochrome for double-stranded (ds)DNA. Fluorescence values of forms capable of r...

journal_title：Nucleic acids research

authors： Levy MS,Lotfian P,O'Kennedy R,Lo-Yim MY,Shamlou PA

更新日期：2000-06-15 00:00:00

abstract：:A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...

journal_title：Nucleic acids research

authors： Wang W,Shen P,Thiyagarajan S,Lin S,Palm C,Horvath R,Klopstock T,Cutler D,Pique L,Schrijver I,Davis RW,Mindrinos M,Speed TP,Scharfe C

更新日期：2011-01-01 00:00:00

abstract：:New linker phosphoramidite reagents containing a cleavable 3'-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphor...

journal_title：Nucleic acids research

authors： Pon RT,Yu S

更新日期：2004-01-29 00:00:00

abstract：:The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures...

journal_title：Nucleic acids research

authors： Arefian E,Kiani J,Soleimani M,Shariati SA,Aghaee-Bakhtiari SH,Atashi A,Gheisari Y,Ahmadbeigi N,Banaei-Moghaddam AM,Naderi M,Namvarasl N,Good L,Faridani OR

更新日期：2011-07-01 00:00:00

abstract：:Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is ...

journal_title：Nucleic acids research

authors： Kato-Inui T,Takahashi G,Hsu S,Miyaoka Y

更新日期：2018-05-18 00:00:00

abstract：:In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centri...

journal_title：Nucleic acids research

authors： Uyar B,Yusuf D,Wurmus R,Rajewsky N,Ohler U,Akalin A

更新日期：2017-06-02 00:00:00

abstract：:The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% inte...

journal_title：Nucleic acids research

authors： Shomer B,Yagil G

更新日期：1999-11-15 00:00:00