Abstract：
:Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly-born genes. Reasons are: (i) NSF(a) frequently appears on the antisense strand of GC-rich bacterial genes; (ii) base compositions at three positions in the codon are nearly symmetrical between the gene having around 55% GC content and the corresponding NSF(a); (iii) amino acid compositions of actual proteins are also similar to those of hypothetical proteins from the GC-rich NSF(a); and (iv) proteins from NSF(a) of 60% or more GC content are flexible enough to adapt to various molecules encountered as novel substrates, due to the high glycine content. To support our proposition, using a computer we generated hypothetical antisense sequences with the same base compositions as of NSF(a) at each base position in the codon, and examined properties of resulting proteins encoded by the imaginary genes. It was confirmed that NSF(a) of GC-rich gene carrying about 60% GC content is competent enough for a newly-born gene.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ikehara K,Amada F,Yoshida S,Mikata Y,Tanaka Adoi
10.1093/nar/24.21.4249subject
Has Abstractpub_date
1996-11-01 00:00:00pages
4249-55issue
21eissn
0305-1048issn
1362-4962pii
6w0117journal_volume
24pub_type
杂志文章abstract：:A putative role for mammalian polynucleotide kinases that possess both 5'-phosphotransferase and 3'-phosphatase activity is the restoration of DNA strand breaks with 5'-hydroxyl termini or 3'-phosphate termini, or both, to a form that supports the subsequent action of DNA repair polymerases and DNA ligases, i.e. 5'-ph...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.19.4395
更新日期：1998-10-01 00:00:00
abstract：:Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By multimerizing the MDB domain of Mbd1, we engineered a poly-MBD protein that displays methyl-CpG-specific binding in vitro with a dissoci...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl527
更新日期：2006-08-07 00:00:00
abstract：:Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks681
更新日期：2012-10-01 00:00:00
abstract：:Human cells are, in general, poor recipients of foreign DNA, which has severely hampered the cloning of genes by direct phenotypic correction of deficient human cell lines after DNA mediated gene transfer. In this communication a methodology is presented which largely circumvents this problems. The method relies on th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.18.4861
更新日期：1991-09-25 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：:Simian virus 40 (SV40) nucleoprotein complexes were extracted from nuclei of infected monkey cells and fractionated on neutral sucrose density gradients. Complexes which contained replicating SV40 DNA (95S) separated well from those containing closed circular supercoiled viral DNA (75S). DNA polymerase activity was as...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.5.1715
更新日期：1978-05-01 00:00:00
abstract：:The human 5S rRNA genes are found in clusters of tandem repeated units. We have cloned and partially characterized six restriction fragments from two clusters of 2.3 kb and 1.6 kb repeats, respectively. Four fragments from the cluster of 2.3 kb repeats contain a 5S rRNA gene and one fragment contains a gene variant wi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.15.4147
更新日期：1991-08-11 00:00:00
abstract：:UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustere...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1022
更新日期：2019-01-08 00:00:00
abstract：:We analysed the genetic stability of two subtelomeric genes of the human malaria parasite Plasmodium falciparum. A PCR based assay, using a telomere and a target-gene specific primer was used to detect potential chromosome rearrangements. We show that chromosome breakage and the formation of new telomeres occur freque...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.7.1491
更新日期：1992-04-11 00:00:00
abstract：:1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.20.5689
更新日期：1991-10-25 00:00:00
abstract：:The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.8.2801
更新日期：1978-08-01 00:00:00
abstract：:The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx198
更新日期：2017-06-02 00:00:00
abstract：:The Kluyveromyces lactis gene encoding the general transcription factor IIB (TFIIB) was isolated from a genomic library by complementation of the cold-sensitive phenotype conferred by a mutation in the SUA7 gene, which encodes TFIIB in Saccharomyces cerevisiae. DNA sequence analysis of the KI-SUA7 gene revealed a 357 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.15.3413
更新日期：1993-07-25 00:00:00
abstract：:Genetic therapy holds great promise for the treatment of inherited or acquired genetic diseases; however, its breakthrough is hampered by the lack of suitable gene delivery systems. Dumbbell-shaped DNA minimal vectors represent an attractive, safe alternative to the commonly used viral vectors which are fraught with r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv583
更新日期：2015-10-15 00:00:00
abstract：:The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.7.1542
更新日期：2000-04-01 00:00:00
abstract：:Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw059
更新日期：2016-05-05 00:00:00
abstract：:Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1280
更新日期：2016-01-08 00:00:00
abstract：:A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.17.3583
更新日期：1999-09-01 00:00:00
abstract：:In vivo and in vitro RNA splicing experiments have demonstrated that the intron splicing machineries are not interchangeable in all organisms. These differences have prevented the efficient in vivo expression of monocot genes containing introns in dicot plants and the in vitro excision of some plant introns in HeLa ce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.14.7159
更新日期：1988-07-25 00:00:00
abstract：:The Deciphering the Mechanisms of Developmental Disorders (DMDD) consortium is a research programme set up to identify genes in the mouse, which if mutated (or knocked-out) result in embryonic lethality when homozygous, and initiate the study of why disruption of their function has such profound effects on embryo deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1138
更新日期：2016-01-04 00:00:00
abstract：:DNA was purified from double minutes isolated from MTX-resistant EL4/8 mouse lymphoma cells, digested to completion with Bam H1 restriction endonuclease and cloned in lambda-1059. The properties of the library suggest that the DNA from which it was made was not detectably contaminated with non-dm chromosome material, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.21.6597
更新日期：1982-11-11 00:00:00
abstract：:The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks420
更新日期：2012-07-01 00:00:00
abstract：:The resonance Raman spectrum of native DNA has been obtained using excitation at 257 nm. In a first part, the spectral lines are assigned to the different nucleotide bases which provide the resonance effect. In a second part, the interactions of DNA with basic peptides (Arginine Methylester, Lysine Methylester, Arginy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.5.1707
更新日期：1982-03-11 00:00:00
abstract：:With the abundant mammalian lncRNAs identified recently, a comprehensive annotation resource for these novel lncRNAs is an urgent need. Since its first release in November 2016, AnnoLnc has been the only online server for comprehensively annotating novel human lncRNAs on-the-fly. Here, with significant updates to mult...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa368
更新日期：2020-07-02 00:00:00
abstract：:In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.845
更新日期：1984-01-11 00:00:00
abstract：:Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational metho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki841
更新日期：2005-09-14 00:00:00
abstract：:Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists datab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1157
更新日期：2014-01-01 00:00:00
abstract：:We have isolated a pigment cell-specific cDNA clone from a B16 mouse melanoma cDNA library by differential hybridization. The mRNA of isolated cDNA is highly expressed in B16 melanoma cells and in black mouse (C57BL/6) skin, but is not detectable in mouse neuroblastoma cells nor in K1735 mouse amelanotic melanoma cell...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2413
更新日期：1986-03-25 00:00:00
abstract：:A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1055
更新日期：2016-01-08 00:00:00
abstract：:Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.3.604
更新日期：2001-02-01 00:00:00
