3did Update: domain-domain and peptide-mediated interactions of known 3D structure.

abstract：:Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures o...

journal_title：Nucleic acids research

authors： DuPrez K,He F,Chen Z,Hilario E,Fan L

更新日期：2020-06-19 00:00:00

abstract：:Sequencing of the 3'-untranslated region of the CCT8 gene of the fungal pathogen Candida albicans revealed that the CCT8 coding region overlaps 13 bp with the coding region of the convergently orientated TRP1 gene. The same overlap was found in three strains with different genetic backgrounds. 3'-RACE was used to dete...

journal_title：Nucleic acids research

authors： Gerads M,Ernst JF

更新日期：1998-11-15 00:00:00

abstract：:The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene...

journal_title：Nucleic acids research

authors： O'Brien EA,Zhang Y,Wang E,Marie V,Badejoko W,Lang BF,Burger G

更新日期：2009-01-01 00:00:00

abstract：:A modification of previously described methods of electron microscopic gene mapping and of gene enrichment based on the avidin-biotin interaction is presented. The modification consists of coupling cytochrome-c instead of pentane diamine to the oxidized 2', 3' terminus of an RNA by Schiff base formation and BH-4 reduc...

journal_title：Nucleic acids research

authors： Sodja A,Davidson N

更新日期：1978-02-01 00:00:00

abstract：:The complete sequences of three kinetoplast DNA minicircles (B4, D3 and D12) from Leishmania tarentolae are reported. All L. tarentolae minicircles encode single gRNAs localized within the variable region approximately 150 bp from the conserved region. The 5' termini and tentative 3' termini of the new gRNAs were dete...

journal_title：Nucleic acids research

authors： Sturm NR,Simpson L

更新日期：1991-11-25 00:00:00

abstract：:The Escherichia coli cyclic AMP receptor protein (CRP) is a global regulator that controls transcription initiation from more than 100 promoters by binding to a specific DNA sequence within cognate promoters. Many genes in the CRP regulon have been predicted simply based on the presence of DNA-binding sites within gen...

journal_title：Nucleic acids research

authors： Zheng D,Constantinidou C,Hobman JL,Minchin SD

更新日期：2004-11-01 00:00:00

abstract：:Thiol-activated neocarzinostatin chromophore abstracts tritium from the 5', but not from the 1' or 2' positions of deoxyribose in DNA and incorporates it into a stable, non-exchangeable form. The abstracted tritium remains covalently associated with the chromophore or its degradation product after treatment with acid ...

journal_title：Nucleic acids research

authors： Kappen LS,Goldberg IH

更新日期：1985-03-11 00:00:00

abstract：:The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensi...

journal_title：Nucleic acids research

authors： Henrich T,Ramialison M,Quiring R,Wittbrodt B,Furutani-Seiki M,Wittbrodt J,Kondoh H,Medaka Expression Pattern Database.

更新日期：2003-01-01 00:00:00

abstract：:Human foamy or spuma virus (HFV) codes for a distinct set of pol gen products. To determine the minimal requirements for the HFV enzymatic activities, defined residues of the reverse transcriptase (RT) and ribo-nuclease H (RNase H) domain of the HFV pol gene were mutated by site-specific PCR mutagenesis. The mutant ge...

journal_title：Nucleic acids research

authors： Kögel D,Aboud M,Flügel RM

更新日期：1995-07-25 00:00:00

abstract：:The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI ...

journal_title：Nucleic acids research

authors： Miyake T,Migita K,Sakaki Y

更新日期：1983-10-11 00:00:00

abstract：:Starting from a synthetic E. coli promoter with the consensus sequences at -35 and -10 regions, a sequence CAT frequently occurred in the RNA start points of natural promoters was introduced in the downstream of the consensus sequences, and the sequences around the RNA start points as well as the relative positions of...

journal_title：Nucleic acids research

authors： Aoyama T,Takanami M

更新日期：1985-06-11 00:00:00

abstract：:A computer program, BRUCE, was developed for the identification of transfer-messenger RNA (tmRNA) genes. The program employs heuristic algorithms to search for a tRNA(Ala)-like secondary structure surrounding a short sequence encoding the tag peptide. In the 57 completely sequenced bacterial genomes where tmRNA genes ...

journal_title：Nucleic acids research

authors： Laslett D,Canback B,Andersson S

更新日期：2002-08-01 00:00:00

abstract：:Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium ...

journal_title：Nucleic acids research

authors： Sulima SO,Gülay SP,Anjos M,Patchett S,Meskauskas A,Johnson AW,Dinman JD

更新日期：2014-02-01 00:00:00

abstract：:The web software SIC provides a tool to search for short inverted segments (length 3-5000 bp) in a DNA sequence. The sequence is assumed to follow a Markov model. A statistic which is sensitive to inversion is presented. Searching inverted segments is done by a scanning approach after the user specifies the size of th...

journal_title：Nucleic acids research

authors： Robelin D,Richard H,Prum B

更新日期：2003-07-01 00:00:00

abstract：:Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...

journal_title：Nucleic acids research

authors： Cliffe LJ,Kieft R,Southern T,Birkeland SR,Marshall M,Sweeney K,Sabatini R

更新日期：2009-04-01 00:00:00

abstract：:For the rapid and sensitive detection of p53 'hot spot' mutations, we combined polymerase chain reaction based single-strand conformational polymorphism (PCR-SSCP) analysis with sequence specific-clamping by peptide nucleic acids (PNAs) in a one-step reaction tube protocol. For this purpose, we designed two PNA molecu...

journal_title：Nucleic acids research

authors： Behn M,Schuermann M

更新日期：1998-03-01 00:00:00

abstract：:MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different...

journal_title：Nucleic acids research

authors： Aparicio-Puerta E,Jáspez D,Lebrón R,Koppers-Lalic D,Marchal JA,Hackenberg M

更新日期：2019-01-08 00:00:00

abstract：:The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in gen...

journal_title：Nucleic acids research

authors： Huret JL,Dessen P,Bernheim A

更新日期：2003-01-01 00:00:00

abstract：:Insertion of microRNA target sequences into the flavivirus genome results in selective tissue-specific attenuation and host-range restriction of live attenuated vaccine viruses. However, previous strategies for miRNA-targeting did not incorporate a mechanism to prevent target elimination under miRNA-mediated selective...

journal_title：Nucleic acids research

authors： Tsetsarkin KA,Liu G,Shen K,Pletnev AG

更新日期：2016-04-20 00:00:00

abstract：:The 3374 nucleotide sequence of RNA2 from the British PEBV strain SP5 has been determined. The RNA includes three open reading frames flanked by 5' and 3' noncoding regions of 509 and 480 nucleotides. The open reading frames specify coat protein, a 29.6K product homologous to the 29.1K product of TRV(TCM) RNA2 and a 2...

journal_title：Nucleic acids research

authors： Goulden MG,Lomonossoff GP,Davies JW,Wood KR

更新日期：1990-08-11 00:00:00

abstract：:We have shown previously that DNA demethylation by chick embryo 5-methylcytosine (5-MeC)-DNA glycosylase needs both protein and RNA. Amino acid sequences of nine peptides derived from a highly purified 5-MeC-DNA glycosylase complex were identified by Nanoelectrospray ionisation mass spectrometry to be identical to the...

journal_title：Nucleic acids research

authors： Jost JP,Schwarz S,Hess D,Angliker H,Fuller-Pace FV,Stahl H,Thiry S,Siegmann M

更新日期：1999-08-15 00:00:00

abstract：:Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data ...

journal_title：Nucleic acids research

authors： Gelfand MS,Koonin EV,Mironov AA

更新日期：2000-02-01 00:00:00

abstract：:Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...

journal_title：Nucleic acids research

authors： Zheng X,Yang J,Zhou C,Zhang C,Zhang Q,Wei X

更新日期：2019-02-20 00:00:00

abstract：:We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR meltin...

journal_title：Nucleic acids research

authors： Masny A,Płucienniczak A

更新日期：2003-09-15 00:00:00

abstract：:The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...

journal_title：Nucleic acids research

authors： Hain J,Reiter WD,Hüdepohl U,Zillig W

更新日期：1992-10-25 00:00:00

abstract：:Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...

journal_title：Nucleic acids research

authors： Margraf T,Schenk G,Torda AE

更新日期：2009-07-01 00:00:00

abstract：:Release of phosphorothioate antisense oligonucleotides (PS-ASOs) from late endosomes (LEs) is a rate-limiting step and a poorly defined process for productive intracellular ASO drug delivery. Here, we examined the role of Golgi-endosome transport, specifically M6PR shuttling mediated by GCC2, in PS-ASO trafficking and...

journal_title：Nucleic acids research

authors： Liang XH,Sun H,Hsu CW,Nichols JG,Vickers TA,De Hoyos CL,Crooke ST

更新日期：2020-02-20 00:00:00

abstract：:Chromatin boundaries regulate gene expression by modulating enhancer-promoter interactions and insulating transcriptional influences from organized chromatin. However, mechanistic distinctions between these two aspects of boundary function are not well understood. Here we show that SF1, a chromatin boundary located in...

journal_title：Nucleic acids research

authors： Majumder P,Roy S,Belozerov VE,Bosu D,Puppali M,Cai HN

更新日期：2009-07-01 00:00:00

abstract：:The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting...

journal_title：Nucleic acids research

authors： Martinez HM

更新日期：1988-03-11 00:00:00

abstract：:Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by essential genes are con...

journal_title：Nucleic acids research

authors： Zhang R,Ou HY,Zhang CT

更新日期：2004-01-01 00:00:00