Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.

abstract：:The centromere complex is a multicomponent structure essential for faithful chromosome transmission. Here we show that the S. cerevisiae centromere protein Cpf1 bends centromere DNA element I (CDEI) with the bend angle ranging from 66 degrees to 71 degrees. CDEI DNA sequences that carry point mutations which lead to r...

journal_title：Nucleic acids research

authors： Niedenthal RK,Sen-Gupta M,Wilmen A,Hegemann JH

更新日期：1993-10-11 00:00:00

abstract：:In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant propo...

journal_title：Nucleic acids research

authors： Tsirigos A,Rigoutsos I

更新日期：2005-02-16 00:00:00

abstract：:The anticancer drug cisplatin reacts with DNA leading to the formation of interstrand and intrastrand cross-links that are the critical cytotoxic lesions. In contrast to cells bearing mutations in other components of the nucleotide excision repair apparatus (XPB, XPD, XPG and CSB), cells defective for the ERCC1-XPF st...

journal_title：Nucleic acids research

authors： De Silva IU,McHugh PJ,Clingen PH,Hartley JA

更新日期：2002-09-01 00:00:00

abstract：:The presence of the C.C mispair in a defined duplex oligodeoxynucleotide enhanced its capacity to serve as a substrate for highly purified human DNA methyltransferase. Analysis of tritiated reaction products showed that the C.C mispair acted as a "methylation acceptor" in that it was itself rapidly methylated. The m5C...

journal_title：Nucleic acids research

authors： Smith SS,Hardy TA,Baker DJ

更新日期：1987-09-11 00:00:00

abstract：:Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis...

journal_title：Nucleic acids research

authors： Sanges R,Hadzhiev Y,Gueroult-Bellone M,Roure A,Ferg M,Meola N,Amore G,Basu S,Brown ER,De Simone M,Petrera F,Licastro D,Strähle U,Banfi S,Lemaire P,Birney E,Müller F,Stupka E

更新日期：2013-04-01 00:00:00

abstract：:Human telomerase reverse transcriptase (hTERT), the catalytic subunit of human telomerase, contains conserved motifs common to retroviral reverse transcriptases and telomerases. Within the C motif of hTERT is the Leu866-Val867-Asp868-Asp869 tetrapeptide that includes a catalytically essential aspartate dyad. Site-dire...

journal_title：Nucleic acids research

authors： Drosopoulos WC,Prasad VR

更新日期：2007-01-01 00:00:00

abstract：:While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alig...

journal_title：Nucleic acids research

authors： Lu Y,Sze SH

更新日期：2009-02-01 00:00:00

abstract：:Telomeres play a central role in human cancer, cardiovascular aging and possibly longevity. However, present methods to measure telomere length are fraught with shortcomings that limit their use. Here, we describe a novel method to measure the relative telomere DNA content by dot blot analysis. In each dot, the DNA co...

journal_title：Nucleic acids research

authors： Kimura M,Aviv A

更新日期：2011-07-01 00:00:00

abstract：:The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on ...

journal_title：Nucleic acids research

authors： Kogure H,Handa Y,Nagata M,Kanai N,Güntert P,Kubota K,Nameki N

更新日期：2014-03-01 00:00:00

abstract：:When B cells differentiate into plasma cells, there is a large increase in the cellular content of mRNA coding for immunoglobulin. This increase cannot be fully accounted for by the increase in rate of transcription of the genes. We have investigated the possibility that the half-life of mu heavy chain mRNA increases ...

journal_title：Nucleic acids research

authors： Cox A,Emtage JS

更新日期：1989-12-25 00:00:00

abstract：:Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to i...

journal_title：Nucleic acids research

authors： Siahpirani AF,Roy S

更新日期：2017-02-28 00:00:00

abstract：:The human transcription factor EF-1A binds to the purine-rich E1A core enhancer sequence in the adenovirus E1A and E4 and polyomavirus enhancer regions. The consensus binding site for EF-1A resembles that of members of the ets domain protein family. EF-1A activation of transcription requires a dimeric binding site. An...

journal_title：Nucleic acids research

authors： Bolwig GM,Bruder JT,Hearing P

更新日期：1992-12-25 00:00:00

abstract：:The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...

journal_title：Nucleic acids research

authors： Bee L,Marini S,Pontarin G,Ferraro P,Costa R,Albrecht U,Celotti L

更新日期：2015-02-27 00:00:00

abstract：:The transactivator Staf, which contains seven contiguous zinc fingers of the C(2)-H(2)type, exerts its effects on gene expression by binding to specific targets in vertebrate small nuclear RNA (snRNA) and snRNA-type gene promoters. Here, we have investigated the interaction of the Staf zinc finger domain with the opti...

journal_title：Nucleic acids research

authors： Schaub M,Krol A,Carbon P

更新日期：2000-05-15 00:00:00

abstract：:The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfa...

journal_title：Nucleic acids research

authors： El-Gebali S,Mistry J,Bateman A,Eddy SR,Luciani A,Potter SC,Qureshi M,Richardson LJ,Salazar GA,Smart A,Sonnhammer ELL,Hirsh L,Paladin L,Piovesan D,Tosatto SCE,Finn RD

更新日期：2019-01-08 00:00:00

abstract：:Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the ...

journal_title：Nucleic acids research

authors： Holub P,Lalakova J,Cerna H,Pasulka J,Sarazova M,Hrazdilova K,Arce MS,Hobor F,Stefl R,Vanacova S

更新日期：2012-07-01 00:00:00

abstract：:While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA-protein conjugates - offer the ability to combine the programmability of DNA with the competence of pro...

journal_title：Nucleic acids research

authors： Bernardinelli G,Högberg B

更新日期：2017-10-13 00:00:00

abstract：:Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...

journal_title：Nucleic acids research

authors： Zhang M,Schultz AK,Calef C,Kuiken C,Leitner T,Korber B,Morgenstern B,Stanke M

更新日期：2006-07-01 00:00:00

abstract：:The nucleotide sequences of eight partial and five full-length phaseolin cDNA clones show that phaseolin polypeptides are encoded by two distinct gene families which differ in their coding regions by the presence or absence of two different size direct repeats. The alpha-type phaseolin polypeptides are encoded by gene...

journal_title：Nucleic acids research

authors： Slightom JL,Drong RF,Klassy RC,Hoffman LM

更新日期：1985-09-25 00:00:00

abstract：:The U1 snRNP-specific 70K protein is one of the few snRNP proteins from higher eukaryotic cells that is phosphorylated in vivo (1,2). Immunoaffinity purified spliceosomal snRNPs (U1, U2, U5, and U4/U6) were tested for their ability to phosphorylate in vitro the U1-specific 70K protein. An snRNP-associated kinase activ...

journal_title：Nucleic acids research

authors： Woppmann A,Will CL,Kornstädt U,Zuo P,Manley JL,Lührmann R

更新日期：1993-06-25 00:00:00

abstract：:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously ...

journal_title：Nucleic acids research

authors： Lvovsky L,Ioshikhes I,Raja MC,Zevin-Sonkin D,Sobolev IA,Liberzon A,Shwartzburd J,Ulanovsky LE

更新日期：1998-12-01 00:00:00

abstract：:LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...

journal_title：Nucleic acids research

authors： Nair R,Rost B

更新日期：2004-07-01 00:00:00

abstract：:Recently, a few Na+-specific RNA-cleaving DNAzymes were reported, where nucleobases are likely to play critical roles in catalysis. The NaA43 and NaH1 DNAzymes share the same 16-nt Na+-binding motif, but differ in one or two nucleotides in a small catalytic loop. Nevertheless, they display an opposite pH-dependency, i...

journal_title：Nucleic acids research

authors： Ma L,Kartik S,Liu B,Liu J

更新日期：2019-09-05 00:00:00

abstract：:Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer repeated sequence including five inosines we show by uranyl photoprobing that a narrow minor groove varying in phase with the...

journal_title：Nucleic acids research

authors： Mollegaard NE,Bailly C,Waring MJ,Nielsen PE

更新日期：1997-09-01 00:00:00

abstract：:Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave...

journal_title：Nucleic acids research

authors： van Eijk MJ,Broekhof JL,van der Poel HJ,Hogers RC,Schneiders H,Kamerbeek J,Verstege E,van Aart JW,Geerlings H,Buntjer JB,van Oeveren AJ,Vos P

更新日期：2004-03-05 00:00:00

abstract：:Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...

journal_title：Nucleic acids research

authors： Burch JB,Martinson HG

更新日期：1980-11-11 00:00:00

abstract：:OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...

journal_title：Nucleic acids research

authors： Duan S,Han X,Akbari M,Croteau DL,Rasmussen LJ,Bohr VA

更新日期：2020-07-09 00:00:00

abstract：:The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the di...

journal_title：Nucleic acids research

authors： Hart DJ,Speight RE,Cooper MA,Sutherland JD,Blackburn JM

更新日期：1999-02-15 00:00:00

abstract：:Many proteins of the SNF2 family, which share a similar DNA-dependent ATPase/putative helicase domain, are involved in global transcriptional control and processing of DNA damage. We report here the partial cloning and characterization of 89B helicase, a gene encoding a new Drosophila melanogaster member of the SNF2 f...

journal_title：Nucleic acids research

authors： Goldman-Levi R,Miller C,Bogoch J,Zak NB

更新日期：1996-08-15 00:00:00

abstract：:We have synthesized a family of double-stranded cDNAs (ds cDNAs) using as a template the family of highly purified protamine mRNAs from rainbow trout testis. Individual pure protamine cDNA components were isolated by cloning this family of protamine ds cDNAs in a plasmid vector (pMB9). Clones containing protamine sequ...

journal_title：Nucleic acids research

authors： Gedamu L,Wosnick MA,Connor W,Watson DC,Dixon GH,Iatrou K

更新日期：1981-03-25 00:00:00