Abstract：
:The ability of the tumor suppressor protein, p53, to recognize certain types of DNA lesions may represent one of the mechanisms by which this protein modulates cellular response to DNA damage. p53 DNA binding properties are regulated by several factors, such as post-translational modifications including phosphorylation and acetylation, regulation by its own C-terminal domain and interactions with other cellular proteins. Substrates resembling Holliday junctions and extra base bulges were used to study the effect of three nuclear proteins, HMG-1, HMG I(Y) and hMSH2-hMSH6, on the lesion binding properties of p53. Gel retardation assays revealed that the three proteins had varying effects on p53 binding to these substrates. HMG-1 did not influence p53 binding to Holliday junctions or 3-cytosine bulges. HMG I(Y) rapidly dissociated p53 complexes with Holliday junctions but not 3-cytosine bulges. Finally, the mismatch repair protein complex, hMSH2-hMSH6, enhanced p53 binding to both substrates by 3-4-fold. Together, these results demonstrate that p53 DNA binding activity is highly influenced by the presence of other proteins, some having a dominant effect while others have a negative effect.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Subramanian D,Griffith JDdoi
10.1093/nar/30.11.2427keywords:
subject
Has Abstractpub_date
2002-06-01 00:00:00pages
2427-34issue
11eissn
0305-1048issn
1362-4962journal_volume
30pub_type
杂志文章abstract：:WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg092
更新日期：2003-01-01 00:00:00
abstract：:Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq661
更新日期：2010-12-01 00:00:00
abstract：:Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg754
更新日期：2003-10-01 00:00:00
abstract：:The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 am...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.2.307
更新日期：1991-01-25 00:00:00
abstract：:The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displaceme...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf515
更新日期：2002-09-15 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
pub_type： 杂志文章
doi：10.1093/nar/gkl323
更新日期：2006-07-01 00:00:00
abstract：:A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku155
更新日期：2014-04-01 00:00:00
abstract：:We have developed a novel method of genetic library construction on magnetic microbeads based on solid-phase single-molecule PCR in a fine and robust water-phase compartment formed in water-in-oil (w/o) emulsions. In this method, critically diluted DNA fragments were distributed over the emulsion as templates, where b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni143
更新日期：2005-10-06 00:00:00
abstract：:In order to examine the nature of the complex formation between the ribosomal protein S1 and nucleic acids three methods were used: Inhibition of the reaction of n-ethyl[2.3 14C]-maleimide with S1 by the addition of oligonucleotides; adsorption of the complexes to nitrocellulose filters; and equilibrium dialysis. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.10.3627
更新日期：1977-10-01 00:00:00
abstract：:The extrusion kinetics of two cruciforms derived from unrelated DNA sequences differ markedly. Kinetic barriers exist for both reactions, necessitating elevated temperatures before extrusion proceeds at measureable speeds, but the dependence upon temperature and ionic strength is quite different for the two sequences....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.5.1443
更新日期：1985-03-11 00:00:00
abstract：:The nucleotide sequences of the 5S rRNAs of the oomycete water molds Saprolegnia ferax and Pythium hydnosporum and of the chytrid water molds Blastocladiella simplex and Phlyctochytrium irregulare were determined by chemical and enzymatic partial degradation of 3' and 5' end-labelled molecules, followed by gel sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.18.5717
更新日期：1982-09-25 00:00:00
abstract：:The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq464
更新日期：2010-07-01 00:00:00
abstract：:Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm615
更新日期：2007-01-01 00:00:00
abstract：:Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database). It integrates...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl912
更新日期：2007-01-01 00:00:00
abstract：:Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz149
更新日期：2019-05-07 00:00:00
abstract：:The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (T[]U), which is the deaminat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh342
更新日期：2004-03-12 00:00:00
abstract：:Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.24.10213
更新日期：1989-12-25 00:00:00
abstract：:Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genom...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr017
更新日期：2011-05-01 00:00:00
abstract：:Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1053
更新日期：2015-01-01 00:00:00
abstract：:This laboratory has established in previous studies that Pmel 17, a gene expressed specifically in melanocytes, maps near the silver coat color locus (si/si) on mouse chromosome 10. In the current study, we have focused on determining whether or not the si allele carries a mutation in Pmel 17. Pmel 17 cDNA clones, iso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.1.154
更新日期：1995-01-11 00:00:00
abstract：:The structure in solution of an RNA fragment (218 nucleotides long) containing part of E. coli 16S rRNA domain 2 has been studied using the intrinsic photoaffinity probe 4-thiouridine (s4U). In vitro transcription with T7 polymerase, in the presence of s4U triphosphate yielded complete RNA molecules. An affinity elect...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.13.3653
更新日期：1991-07-11 00:00:00
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
更新日期：2010-09-01 00:00:00
abstract：:The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog map...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa936
更新日期：2021-01-08 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
pub_type： 杂志文章
doi：10.1093/nar/13.18.6483
更新日期：1985-09-25 00:00:00
abstract：:Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp051
更新日期：2009-04-01 00:00:00
abstract：:A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4409
更新日期：1999-11-15 00:00:00
abstract：:The origin of replication of the c-myc gene in HeLa cells was previously identified at low resolution within 3.5 kb 5' to the P1 promoter, based on replication fork polarity and the location of DNA nascent strands. To define the initiation events in the c-myc origin at higher resolution the template bias of nascent DN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.10.1887
更新日期：1996-05-15 00:00:00
abstract：:Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.18.8835
更新日期：1988-09-26 00:00:00
abstract：:Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1365
更新日期：2017-05-05 00:00:00
abstract：:Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM tradi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz489
更新日期：2019-09-05 00:00:00
