Abstract：
:A multivariate statistical method called correspondence analysis was used to examine the codon usage of one-hundred-and-one nuclear genes of maize (Zea mays L.). Forty percent of the variation in codon usage was due to bias toward G or C-ending versus A or U-ending codons. Differences in levels of G-ending codons showed the weakest correlation with the major codon usage bias. The bias toward C or U versus A or G in the silent third nucleotide position of synonymous codons accounted for approximately 10% of the variation in codon usage. The G+C content of the silent third nucleotide position of coding regions was not strongly correlated with G+C content of introns. Codon usage was strongly biased toward codons ending in G or C for a number of highly expressed genes including most light-regulated chloroplast proteins, ABA-induced proteins, histones, and anthocyanin biosynthetic enzymes. Codon usage of genes encoding storage proteins and regulatory proteins, such as transposases, kinases, phosphatases and transcription factors, was more random than that of genes encoding cytosolic enzymes with similar bias toward G or C-ending codons. Codon usage in maize may reflect both regional bias on nucleotide composition and selection on the silent third nucleotide position.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Fennoy SL,Bailey-Serres Jdoi
10.1093/nar/21.23.5294subject
Has Abstractpub_date
1993-11-25 00:00:00pages
5294-300issue
23eissn
0305-1048issn
1362-4962journal_volume
21pub_type
杂志文章abstract：:TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1043
更新日期：2007-01-01 00:00:00
abstract：:Resolvase enzymes that cleave DNA four-way (Holliday) junctions are required for poxvirus replication, but clinically useful inhibitors have not been developed. Here, we report an assay for resolvase cleavage activity based on fluorescence polarization (FP) for high-throughput screening and mechanistic studies. Initia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks325
更新日期：2012-09-01 00:00:00
abstract：:Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.9933
更新日期：1988-11-11 00:00:00
abstract：:Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn358
更新日期：2008-08-01 00:00:00
abstract：:The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the lin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.9.3703
更新日期：1987-05-11 00:00:00
abstract：:Symmetry considerations of the kind of structures which can be generated when dimers of histones f2al-f3 and f2a2-f2b interact lead to the following conclusions: chromatin subunits based on closed-shell structures give rise to discrete, non-interacting nucleoprotein subunits with the histones arranged at random along ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.3.405
更新日期：1975-03-01 00:00:00
abstract：:Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp866
更新日期：2010-01-01 00:00:00
abstract：:We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky712
更新日期：2018-09-28 00:00:00
abstract：:NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1159
更新日期：2017-01-25 00:00:00
abstract：:The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAS...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw348
更新日期：2016-07-08 00:00:00
abstract：:The paper presents measurements of the difference in the melting temperature of a colE1 DNA region when it is located inside the DNA helix and at its end. A direct comparison of calculations based on the rigorous theory of helix-coil transition with experimental data for .2 M Na+ (the conditions for fully reversible m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5469
更新日期：1981-10-24 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 previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.17.6343
更新日期：1985-09-11 00:00:00
abstract：:Transcriptional regulation of the delta-aminolevulinic acid synthetase gene of Rhizobium meliloti was investigated under conditions of normal vegetative growth and during symbiosis with the legume host alfalfa. S1 nuclease mapping and DNA sequence analysis indicated that transcription originates from two sites separat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.16.5965
更新日期：1985-08-26 00:00:00
abstract：:Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated prote...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz555
更新日期：2019-08-22 00:00:00
abstract：:USF is a helix-loop-helix transcription factor that, like Myc, recognizes the DNA binding motif CACGTG. Two different forms of USF, characterized by apparent molecular weights of 43,000 and 44,000, were originally identified in HeLa cells by biochemical analysis. Clones for the 43-kDa USF were first characterized, but...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.3.427
更新日期：1994-02-11 00:00:00
abstract：:The C (pifC) protein of miniF represses transcription of its own gene by binding to the pif operator (pifO); it is also needed for replication initiated from the miniF primary origin (ori-1). We have determined the nucleotide sequence of the C gene. The gene has been inserted into an expression vector under Ptrp contr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.24.9699
更新日期：1986-12-22 00:00:00
abstract：:The HpaR-mediated regulation of the hpa-meta operon (Pg promoter) of the 4-hydroxyphenylacetic acid catabolic pathway of Escherichia coli has been studied. The HpaR regulator was purified to homogeneity showing that it is able to bind selectively to 4-hydroxyphenylacetic, 3-hydroxyphenylacetic and 3,4-dihydroxyphenyla...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg851
更新日期：2003-11-15 00:00:00
abstract：:Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq590
更新日期：2010-11-01 00:00:00
abstract：:A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.suppl.r403
更新日期：1988-01-01 00:00:00
abstract：:Adenosine to inosine editing of mRNA from the human 5-HT2C receptor gene (HTR2C) occurs at five exonic positions (A-E) in a stable stem-loop that includes the normal 5' splice site of intron 5 and is flanked by two alternative splice sites. Using in vitro editing, we identified a novel editing site (F) located in the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh536
更新日期：2004-04-15 00:00:00
abstract：:The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.3.459
更新日期：1990-02-11 00:00:00
abstract：:We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.18.6341
更新日期：1983-09-24 00:00:00
abstract：:Human apolipoprotein (apo) B mRNA is edited in a tissue specific reaction, to convert glutamine codon 2153 (CAA) to a stop translation codon. The RNA editing product templates and hybridises as uridine, but the chemical nature of this reaction and the physical identity of the product are unknown. After editing in vitr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.6.1197
更新日期：1991-03-25 00:00:00
abstract：:The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki317
更新日期：2005-03-23 00:00:00
abstract：:Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn918
更新日期：2009-02-01 00:00:00
abstract：:The entire nucleotide sequence of the Ad. 2 EcoRI D fragment has been determined using the Maxam and Gilbert method. This sequence of 2678 bp contains informations relative to late mRNAs ending at position 78 and for which an AATAAA sequence corresponding to their 3' ends is found at residue number 833. Position of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.10.2173
更新日期：1980-05-24 00:00:00
abstract：:Human prostatic acid phosphatase (PAcP) is a prostate epithelium-specific differentiation antigen. Cellular PAcP functions as a neutral protein tyrosine phosphatase and is involved in regulating androgen-promoted prostate cancer cell proliferation. Despite the fact that the promoter of the PAcP gene has been cloned, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh677
更新日期：2004-07-07 00:00:00
abstract：:We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.9.2423
更新日期：1991-05-11 00:00:00
abstract：:The small proline-rich protein genes ( SPRRs ) code for precursors of the cornified cell envelope, and are specifically expressed during keratinocyte terminal differentiation. The single intron of SPRR2A enhanced the activity of the SPRR2A promoter in transient transfection assays. This enhancement was position depend...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5288
更新日期：1998-12-01 00:00:00
