Abstract:
:For the first time mosaic nucleic acids composed of 50% RNA and 50% DNA can be obtained as transcripts with T7 RNA polymerase. Two NTPs could be replaced simultaneously in a transcription reaction. This means more than 40 deoxynucleotides were inserted in one transcript. Previously, a maximum of two deoxynucleotides could be incorporated and 2'-O-methyl-NTPs were not substrates at all. We obtained reasonable transcript yields with a maximal level of 99% 2'-O-methyl-NTPs, and the products contained up to 58% 2'-O-methylnucleotides at more than 20 positions. Sequence-specific nucleotide incorporation was monitored by sequence ladders (partial alkali or iodine cleavage). No base misincorporations were detected with 100% dGTP, dCTP and dTTP, and with partial incorporation of dATP alpha S, 2'-O-methyl-GTP alpha S and 2'-O-methyl-CTP alpha S, whereas they were found with dATP, 2'-O-methyl-ATP alpha S and 2'-O-methyl-UTP alpha S. Quantitative data allow predetermined modification levels of partially modified transcripts. Highly modified transcripts can be used for structural and functional studies, in modification interference approaches and for in vitro evolution procedures. Modification interference studies revealed a small number of important phosphate and ribose moieties in RNase P substrates. The conversion of T7 RNA polymerase to a DNA polymerase extends the observation that there is no absolute distinction between RNA and DNA polymerases. Accordingly, an adapted concept of a primordial RNA world is presented.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Conrad F,Hanne A,Gaur RK,Krupp Gdoi
10.1093/nar/23.11.1845subject
Has Abstractpub_date
1995-06-11 00:00:00pages
1845-53issue
11eissn
0305-1048issn
1362-4962pii
5w0052journal_volume
23pub_type
杂志文章abstract::Many types of DNA structures are generated in response to DNA damage, repair and recombination that require processing via specialized nucleases. DNA hairpins represent one such class of structures formed during V(D)J recombination, palindrome extrusion, DNA transposition and some types of double-strand breaks. Here w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1059
更新日期:2012-03-01 00:00:00
abstract::PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw935
更新日期:2017-01-04 00:00:00
abstract::Several lines of evidence indicate that differences in DNA repair capacity are an important source of variability in cancer risk. However, traditional assays for measurement of DNA repair activity in human samples are laborious and time-consuming. DNA glycosylases are the first step in base excision repair of a variet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni166
更新日期:2005-10-21 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
pub_type: 杂志文章
doi:10.1093/nar/17.24.10439
更新日期:1989-12-25 00:00:00
abstract::A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkz124
更新日期:2019-04-23 00:00:00
abstract::TOP mRNAs are vertebrate transcripts which contain a 5'terminal oligopyrimidine tract (5'TOP), encode for ribosomal proteins and elongation factors 1alpha and 2, and are candidates for growth-dependent translational control mediated through their 5'TOP. In the present study we show that elongation factor 2 (EF2) mRNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.5.995
更新日期:1997-03-01 00:00:00
abstract::The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw157
更新日期:2016-06-02 00:00:00
abstract::RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ signi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1273
更新日期:2015-02-27 00:00:00
abstract::The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.7.3097
更新日期:1987-04-10 00:00:00
abstract::Human somatic cells have essentially no telomerase activity. Telomerase is linked to tumor genesis and is a valuable marker for malignant growth. Extreme paucity of the enzyme neccessitated development of a PCR-based assay, 'telomeric repeat amplification protocol' (TRAP). Unfortunately, this method is not without dif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.4.919
更新日期:1997-02-15 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
pub_type: 杂志文章
doi:10.1093/nar/gkl255
更新日期:2006-07-01 00:00:00
abstract::Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx638
更新日期:2017-09-19 00:00:00
abstract::We report here the construction of engineered endonuclease database (EENdb) (http://eendb.zfgenetics.org/), a searchable database and knowledge base for customizable engineered endonucleases (EENs), including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). EENs are artificial...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1144
更新日期:2013-01-01 00:00:00
abstract::A common aim in ChIP-seq experiments is to identify changes in protein binding patterns between conditions, i.e. differential binding. A number of peak- and window-based strategies have been developed to detect differential binding when the regions of interest are not known in advance. However, careful consideration o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku351
更新日期:2014-06-01 00:00:00
abstract::The gene for the small subunit of human calcium-activated neutral protease was isolated and sequenced. It is 11 kb long and comprises 11 exons. No TATA or CAT box was found upstream of the possible transcription initiation sites, but there are three so-called G-C box sequences and one G-C box-like sequence, which are ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.22.8805
更新日期:1986-11-25 00:00:00
abstract::We have determined the genomic structure of the fosB gene and shown that it consists of 4 exons and 3 introns at positions also found in the c-fos gene. By deletion analysis we have characterized a region upstream of the TATA box which is the promoter region of the gene. Several consensus sequences have been identifie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.343
更新日期:1992-01-25 00:00:00
abstract::Aspects of the metabolism of RNA have been studied in enzymatically isolated protoplasts from cotyledon and first leaf mesophyll tissue of two cultivars of cucumber. The first leaf mesophyll protoplasts incorporated (3H)-uridine into ribosomal RNA at a constant rate for up to 25 hr in a simple salts medium and for up ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.7.1111
更新日期:1975-07-01 00:00:00
abstract::Methylation of CpG motifs in DNA is involved in the control of gene expression and in several other epigenic effects. It suppresses also the immuno-stimulation properties of bacterial or viral DNAs that contain CPGS: However, effects of methylation on the DNA structure and dynamics are not clear. Here we carried out a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2314
更新日期:2001-06-01 00:00:00
abstract::DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.21.4303
更新日期:1995-11-11 00:00:00
abstract::Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new appro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1175
更新日期:2020-12-08 00:00:00
abstract::A novel expression system was established that allows expression and propagation of the human hepatitis B virus (HBV) genome in cultured animal cells. An overlength HBV genome encoding the viral pregenomic RNA was put under transcriptional control of the human metallothionein IIA promoter thereby replacing the endogen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.24.10117
更新日期:1987-12-23 00:00:00
abstract::Translational repression (TR) plays an important role in post-transcriptional regulation of gene expression and embryonic development in metazoans. TR also regulates the expression of a subset of the cytoplasmic mRNA population during development of fertilized female gametes of the unicellular malaria parasite, Plasmo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1142
更新日期:2008-03-01 00:00:00
abstract::Nuclear receptors for the thyroid hormone and vitamin A and D cooperate with the retinoid X receptor (RXR) in activating the transcription. Although the hormone response elements for these receptors have been proposed in which spacing of the direct repeated motifs determine the specificity (so called 3-4-5 rule), vita...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.2902
更新日期:1994-08-11 00:00:00
abstract::Preparations of chicken, rat and human nuclear 5S RNA contain two sets of molecules. The set with the lowest electrophoretic mobility (5Sa) contains RNAs identical or closely related to ribosomal 5S RNA from the corresponding animal species. In HeLa cells and rat brain, we only detected an RNA identical to the ribosom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.4.769
更新日期:1981-02-25 00:00:00
abstract::Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr750
更新日期:2012-01-01 00:00:00
abstract::PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg022
更新日期:2003-01-01 00:00:00
abstract::Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.5.1107
更新日期:2001-03-01 00:00:00
abstract::We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki1003
更新日期:2005-12-23 00:00:00
abstract::The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr323
更新日期:2011-07-01 00:00:00
abstract::The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky618
更新日期:2018-09-06 00:00:00