Abstract：
:We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzyme and also showed only weak binding to EcoRI in the absence of the cofactor Mg2+. In contrast, hairpins with larger loops are hydrolyzed by the enzyme at the scission site next to the loop although the substrate with a A4 loop is significantly more resistant than the oligonucleotide containing a T4 loop. The hairpin structures with 3 loop residues were found to be thermally most stable while larger hairpin loops resulted in structures with lower melting temperatures. The T-loop hairpins are thermally more stable than the hairpins containing the same number of A residues in the loop. As judged from proton NMR spectroscopy and the thermodynamic data, the base pair closest to the hairpin loop did form in all cases studied. The hairpin loops did, however, affect the conformation of the stem structure of the hairpins. From 31P and 1H NMR spectroscopy we conclude that the perturbation of the stem structure is stronger for smaller hairpin loops and that the extent of the perturbation is limited to 2-3 base pairs for hairpins with T3 or A4 loops. Our results demonstrate that hairpin loops modulate the conformation of the stem residues close to the loop and that this in turn reduces the substrate activity for DNA sequence specific proteins.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Germann MW,Kalisch BW,Lundberg P,Vogel HJ,van de Sande JHdoi
10.1093/nar/18.6.1489subject
Has Abstractpub_date
1990-03-25 00:00:00pages
1489-98issue
6eissn
0305-1048issn
1362-4962journal_volume
18pub_type
杂志文章abstract：:Mitochondrial DNA from human tissue culture cells contains heterogeneous sequences located within a previously identified, evolutionarily conserved region termed CSB-2. CSB-2 is located near the origin of heavy-strand mitochondrial DNA synthesis and the major transcriptional promoters for each strand of human mitochon...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.22.8093
更新日期：1985-11-25 00:00:00
abstract：:In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki672
更新日期：2005-06-24 00:00:00
abstract：:The rpoH genes encoding homologs of Escherichia coli sigma 32 (heat shock sigma factor) were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), Serratia marcescens (gamma), Proteus mirabilis (gamma), Agrobacterium tumefaciens (alpha) and Zymomonas mob...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：
更新日期：1995-11-11 00:00:00
abstract：:Procaryotic DNA polymerases contain an associated 3'----5' exonuclease activity which provides a proofreading function and contributes substantially to replication fidelity. DNA polymerases of the eucaryotic herpes-type viruses contain similar associated exonuclease activities. We have investigated the fidelity of pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.1185
更新日期：1987-02-11 00:00:00
abstract：:The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.2.318
更新日期：1997-01-15 00:00:00
abstract：:Cell cycle checkpoints induced by DNA damage play an integral role in preservation of genomic stability by allowing cells to limit the propagation of deleterious mutations. The retinoblastoma tumor suppressor (RB) is crucial for the maintenance of the DNA damage checkpoint function because it elicits cell cycle arrest...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg919
更新日期：2004-01-02 00:00:00
abstract：:iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARS...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp291
更新日期：2009-07-01 00:00:00
abstract：:The binary Cre-lox conditional knockout system requires an essential part of the target gene to be flanked by loxP sites, enabling excision in vivo upon Cre expression. LoxP sites are introduced by homologous recombination, together with a selectable marker. However, this marker can disturb gene expression and should ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng021
更新日期：2003-03-01 00:00:00
abstract：:RNA helicases of the DEAD-box protein family form the largest group of helicases. The human DEAD-box protein 1 (DDX1) plays an important role in tRNA and mRNA processing, is involved in tumor progression and is also hijacked by several virus families such as HIV-1 for replication and nuclear export. Although important...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv106
更新日期：2015-03-11 00:00:00
abstract：:We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn1008
更新日期：2009-03-01 00:00:00
abstract：:2'-O-(2-methoxyethyl) (2'-MOE) RNA possesses favorable pharmocokinetic properties that make it a promising option for the design of oligonucleotide drugs. Telomerase is a ribonucleoprotein that is up-regulated in many types of cancer, but its potential as a target for chemotherapy awaits the development of potent and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.8.1683
更新日期：2001-04-15 00:00:00
abstract：:Oriented DNA films prepared by the wet-spinning technique have been complexed with several ligands: the anthracycline antibiotic violamycin BI, the dipeptide L-carnosine, and the oligopeptide antibiotic netropsin. The formation of the DNA-ligand complexes is accompanied by dramatic changes of the conformational flexib...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.23.9165
更新日期：1984-12-11 00:00:00
abstract：:Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the oc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.18.3778
更新日期：1995-09-25 00:00:00
abstract：:Insertion of the insertion sequence Is2(I) directly before the galE gene of the galactose operon results in a Gal minus phenotype (1, 2). The Gal-constitutive allele galc200 (and its deletion derivative galc200 delta 31) arise from such a Gal minus mutant by the insertion of LS2(II) DNA within the LS2(I) sequence (3)....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.16.5015
更新日期：1982-08-25 00:00:00
abstract：:Sox proteins belong to the HMG box superfamily of DNA-binding proteins and are found throughout the animal kingdom. They are involved in the regulation of such diverse developmental processes as germ layer formation, organ development and cell type specifi-cation. Hence, deletion or mutation of Sox proteins often resu...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/27.6.1409
更新日期：1999-03-15 00:00:00
abstract：:Bacillus stearothermophilus large ribosomal subunits were reconstituted in the presence of 5S rRNAs from different origins and tested for their biological activities. The results obtained have shown that eubacterial and archaebacterial 5S rRNAs can easily substitute for B. stearothermophilus 5S rRNA in the reconstitut...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.8.3511
更新日期：1988-04-25 00:00:00
abstract：:It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.20.e101
更新日期：2001-10-15 00:00:00
abstract：:Analysis of the human VK (ref. 2) gene locus led to the detection of a new sequence family (L sequences). Its copy number is in the range of 10(2). The L sequences, which are about 500 bp long, are found as part of the 3' flanking regions of a clustered set of human VKI genes but they occur also separate from the gene...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.13.5265
更新日期：1984-07-11 00:00:00
abstract：:A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.12.2302
更新日期：1996-06-15 00:00:00
abstract：:The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki209
更新日期：2005-01-26 00:00:00
abstract：:We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer l...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.5.1137
更新日期：1990-03-11 00:00:00
abstract：:The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.563
更新日期：1992-02-11 00:00:00
abstract：:5' Terminal cap structures of hnRNA have been characterized and the extent of capping determined as a function of embryonic development. Sea urchin embryo hnRNA contains only the type-1 cap, m7GpppNmpNp, with the type-2 cap, which has a 2'-0-methylated subpenultimate nucleotide, being associated only with stable small...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.6.2307
更新日期：1979-01-01 00:00:00
abstract：:Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper protein (HBZ) is expressed in all cases of ATL and is directly associated with virus pathogenicity. The two isoforms of the HBZ protein are synthesized from antisense messenger RNAs (mRN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky802
更新日期：2018-11-16 00:00:00
abstract：:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.6.2215
更新日期：1989-03-25 00:00:00
abstract：:To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.8931
更新日期：1989-11-25 00:00:00
abstract：:The gene encoding myelin basic protein (MBP) contains multiple activator sequences spanning upstream of its transcriptional initiation site which differentially promote transcription in glial cells. The proximal activator sequence, designated MB1, activates transcription in a glial cell type specific manner. This sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.545
更新日期：1992-02-11 00:00:00
abstract：:RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular u...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.12.2311
更新日期：1997-06-15 00:00:00
abstract：:Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.18.4537
更新日期：1981-09-25 00:00:00
abstract：:2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in y...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr896
更新日期：2012-03-01 00:00:00
