Abstract：
:To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271-287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690-3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into 'interaction matrices' revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schneider B,Cerný J,Svozil D,Cech P,Gelly JC,de Brevern AGdoi
10.1093/nar/gkt1273subject
Has Abstractpub_date
2014-03-01 00:00:00pages
3381-94issue
5eissn
0305-1048issn
1362-4962pii
gkt1273journal_volume
42pub_type
杂志文章abstract：:A peptide initiation factor purified from rat liver and promoting the binding of initiator tRNA and model initiators to 40S and 80S ribosome at an acid pH liberates methionine and N-acetylmethionine from Trna Met f at neutral reaction. Phenylalanyl-tRNA, N-acetylphenylalanyl-tRNA and methionyl-tRNA Met m are not hydro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.11.2119
更新日期：1975-11-01 00:00:00
abstract：:A minor tRNA-Glu1 constituent of a preparation of E. coli B tRNA-Glu (Oak Ridge) has a guanosine residue at position 66 rather than an adenosine as in the tRNA-Glu2 described by Ohashi et al. (3). Automated sequential degradation was used to sequence this region. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.4.469
更新日期：1975-04-01 00:00:00
abstract：:The primary structure of the E. coli rpoC gene (5321 base pairs) coding the beta'-subunit of RNA polymerase as well as its adjacent segment have been determined. The structure analysis of the peptides obtained by cleavage of the protein with cyanogen bromide and trypsin has confirmed the amino acid sequence of the bet...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.13.4035
更新日期：1982-07-10 00:00:00
abstract：:One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-tran...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh465
更新日期：2004-07-01 00:00:00
abstract：:The P. falciparum pPFrep20 repetitive element from the Palo Alto Uganda strain has been isolated and sequenced. The Palo Alto pPFrep20 repeat (pPFPArep20) has a clustered subtelomeric location and on chromosome 1 has been deleted from one end. Analysis of chromosome 1 from 5 other strains has revealed that pPFrep20 se...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.10.4331
更新日期：1988-05-25 00:00:00
abstract：:We have examined the behaviour of the beta-interferon promoter in mouse F9 embryonal carcinoma cells. In undifferentiated cells, the beta-interferon promoter is not responsive to dsRNA or to Sendai virus. In cells stimulated to differentiate into parietal endoderm by treatment with retinoic acid, the beta-interferon p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.21.4489
更新日期：1994-10-25 00:00:00
abstract：:WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki421
更新日期：2005-07-01 00:00:00
abstract：:The database of imprinted genes and parent-of-origin effects in animals (http://www.otago.ac.nz/IGC ) is a collation of genes and phenotypes for which parent-of-origin effects have been reported. The database currently includes over 220 entries, which describe over 40 imprinted genes in human, mouse and other animals....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.275
更新日期：2001-01-01 00:00:00
abstract：:Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nasc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv666
更新日期：2015-09-18 00:00:00
abstract：:Initiation of sporulation in Bacillus subtilis is controlled by several regulators which affect activation by phosphorylation of the key response regulator Spo0A or transcription of Spo0A-P-dependent genes. In vivo overexpression of one of these regulators, sinR , results in suppression of transcription from the Spo0A...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.16.3806
更新日期：1998-08-15 00:00:00
abstract：:We have isolated 2'-Fluoro-substituted RNA aptamers that bind to streptavidin (SA) with an affinity around 7 +/- 1.8 nM, comparable with that of recently described peptide aptamers. Binding to SA was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. Mutagen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.10.e45
更新日期：2002-05-15 00:00:00
abstract：:During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw172
更新日期：2016-05-19 00:00:00
abstract：:The nucleotide sequence of the Klebsiella pneumoniae ntrA gene has been determined. NtrA encodes a 53,926 Dalton acidic polypeptide; a calculated molecular weight which is significantly lower than that determined by SDS polyacrylamide gel analysis. NtrA is followed by another open-reading frame (orf) of at least 75 am...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.21.7607
更新日期：1985-11-11 00:00:00
abstract：:Cis-elements (-933 to -641) upstream of the human M creatine kinase gene cap site contain an enhancer that confers developmental and tissue-specific expression to the chloramphenicol acetyltransferase gene in C2C12 myogenic cells transfected in culture. Division of the enhancer at -770 into a 5' fragment that includes...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.9.2313
更新日期：1992-05-11 00:00:00
abstract：:The c-myc proto-oncogene encodes a highly unstable mRNA. Stabilized, truncated myc transcripts have been found in several human and murine tumors of hematopoietic origin. Recently, two tumors expressing 3' truncated c-myc mRNAs that were five times more stable than normal myc transcripts, were described. We have tried...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.9.2387
更新日期：1991-05-11 00:00:00
abstract：:Initiation of Adenovirus (Ad) DNA replication occurs by a protein-priming mechanism in which the viral precursor terminal protein (pTP) and DNA polymerase (pol) as well as two nuclear DNA-binding proteins from uninfected HeLa cells are required. Biochemical studies on the pTP and DNA polymerase proteins separately hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.6.2431
更新日期：1988-03-25 00:00:00
abstract：:The base pairing properties of oligonucleotide duplexes containing 8-aza-7-deaza-2'-deoxyisoguanosine, its 7-bromo or its 7-iodo derivative are described. The nucleosides were synthesized on a convergent route, protected and converted into phosphoramidites. Oligonucleotides were prepared on a solid-phase and were hybr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg926
更新日期：2003-12-15 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
pub_type： 杂志文章
doi：10.1093/nar/gkz1180
更新日期：2020-02-20 00:00:00
abstract：:The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random l...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.11.4639
更新日期：1986-06-11 00:00:00
abstract：:Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.21.5937
更新日期：1991-11-11 00:00:00
abstract：:MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1258
更新日期：2016-01-04 00:00:00
abstract：:Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often preve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq953
更新日期：2011-03-01 00:00:00
abstract：:Cdc13 is an essential protein from Saccharomyces cerevisiae that caps telomeres by protecting the C-rich telomeric DNA strand from degradation and facilitates telomeric DNA replication by telomerase. In vitro, Cdc13 binds TG-rich single-stranded telomeric DNA with high affinity and specificity. A previously identified...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf554
更新日期：2002-10-01 00:00:00
abstract：:Using circular dichroism spectroscopy, UV absorption spectroscopy and polyacrylamide gel electrophoresis, we studied conformational properties of guanine-rich DNA strands of the fragile X chromosome repeats d(GGC)n, d(GCG)n and d(CGG)n, with n = 2, 4, 8 and 16. These strands are generally considered in the literature ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh179
更新日期：2004-01-12 00:00:00
abstract：:G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that R...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa442
更新日期：2020-07-09 00:00:00
abstract：:5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx473
更新日期：2017-06-20 00:00:00
abstract：:The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx312
更新日期：2017-07-03 00:00:00
abstract：:The complete nucleotide sequences of the various precursor 5S RNA species occurring in Bacillus licheniformis have been elucidated. The B. licheniformis precursors contain a 5'-precursor-specific segment of 95 nucleotides which is four times as long as the corresponding segment of the p5S RNAs from the closely related...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.19.4535
更新日期：1980-10-10 00:00:00
abstract：:A hybrid plasmid was constructed containing beta-lactamase gene of plasmid pBR322 and cloned coding sequences of bovine growth hormone (BGH). The constructed plasmid contains all DNA sequences required to encode BGH, and when used as a hybridization probe it detects one growth hormone gene in the bovine genome. The cl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.1.19
更新日期：1981-01-10 00:00:00
abstract：:The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.5.1053
更新日期：1981-03-11 00:00:00
