当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.

Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.

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 Res

journal_title

Nucleic acids research

authors

Germann MW,Kalisch BW,Lundberg P,Vogel HJ,van de Sande JH

doi

10.1093/nar/18.6.1489

subject

Has Abstract

pub_date

1990-03-25 00:00:00

pages

1489-98

issue

6

eissn

0305-1048

issn

1362-4962

journal_volume

18

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Sequence of E. coli tRNA-Glu1 by automated sequential degradation.

    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

    authors： Uziel M,Weinberger AJ

    更新日期：1975-04-01 00:00:00

  • Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases.

    abstract：:The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/17.23.9823

    authors： Klimasauskas S,Timinskas A,Menkevicius S,Butkienè D,Butkus V,Janulaitis A

    更新日期：1989-12-11 00:00:00

  • Binding of two DNA molecules by type II topoisomerases for decatenation.

    abstract：:Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks843

    authors： Kumar R,Riley JE,Parry D,Bates AD,Nagaraja V

    更新日期：2012-11-01 00:00:00

  • The role of acetylation in rDNA transcription.

    abstract：:Treatment of NIH 3T3 cells with trichostatin A (TSA), an inhibitor of histone deacetylase (HDAC), resulted in a dose-dependent increase in transcription from a rDNA reporter and from endogenous rRNA genes. Chromatin immunoprecipitation using anti-acetyl-histone H4 antibodies demonstrated a direct effect of TSA on the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.20.4114

    authors： Hirschler-Laszkiewicz I,Cavanaugh A,Hu Q,Catania J,Avantaggiati ML,Rothblum LI

    更新日期：2001-10-15 00:00:00

  • Synthesis and hybridization analysis of a small library of peptide-oligonucleotide conjugates.

    abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.13.3136

    authors： Harrison JG,Balasubramanian S

    更新日期：1998-07-01 00:00:00

  • KH domains with impaired nucleic acid binding as a tool for functional analysis.

    abstract：:In eukaryotes, RNA-binding proteins that contain multiple K homology (KH) domains play a key role in coordinating the different steps of RNA synthesis, metabolism and localization. Understanding how the different KH modules participate in the recognition of the RNA targets is necessary to dissect the way these protein...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks368

    authors： Hollingworth D,Candel AM,Nicastro G,Martin SR,Briata P,Gherzi R,Ramos A

    更新日期：2012-08-01 00:00:00

  • Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases.

    abstract：:The histone methyl transferase Suv39H1 is involved in silencing by pericentric heterochromatin. It specifically methylates K9 of histone H3, thereby creating a high affinity binding site for HP1 proteins. We and others have shown recently that it is also involved in transcriptional repression by the retinoblastoma pro...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/30.2.475

    authors： Vaute O,Nicolas E,Vandel L,Trouche D

    更新日期：2002-01-15 00:00:00

  • Slow non-specific accumulation of 2'-deoxy and 2'-O-methyl oligonucleotide probes at mitochondria in live cells.

    abstract：:Molecular beacons (MBs) have the potential to provide a powerful tool for rapid RNA detection in living cells, as well as monitoring the dynamics of RNA expression in response to external stimuli. To exploit this potential, it is necessary to distinguish true signal from background signal due to non-specific interacti...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq050

    authors： Rhee WJ,Bao G

    更新日期：2010-05-01 00:00:00

  • Subcellular distribution of human RDM1 protein isoforms and their nucleolar accumulation in response to heat shock and proteotoxic stress.

    abstract：:The RDM1 gene encodes a RNA recognition motif (RRM)-containing protein involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. We previously reported a cDNA encoding the full-length human RDM1 protein. Here, we describe the identification of 11 human cDNAs encoding RDM1 protein isoforms. Th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm753

    authors： Messaoudi L,Yang YG,Kinomura A,Stavreva DA,Yan G,Bortolin-Cavaillé ML,Arakawa H,Buerstedde JM,Hainaut P,Cavaillé J,Takata M,Van Dyck E

    更新日期：2007-01-01 00:00:00

  • Genome-scale design of PCR primers and long oligomers for DNA microarrays.

    abstract：:During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg752

    authors： Haas SA,Hild M,Wright AP,Hain T,Talibi D,Vingron M

    更新日期：2003-10-01 00:00:00

  • A novel E4BP4 element drives circadian expression of mPeriod2.

    abstract：:Period2 (Per2) is an essential component of the mammalian clock mechanism and robust circadian expression of Per2 is essential for the maintenance of circadian rhythms. Although recent studies have shown that the circadian E2 enhancer (a non-canonical E-box) accounts for most of the circadian transcriptional drive of ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl868

    authors： Ohno T,Onishi Y,Ishida N

    更新日期：2007-01-01 00:00:00

  • Selective release of HMG nonhistone proteins during DNase digestion of Tetrahymena chromatin at different stages of the cell cycle.

    abstract：:The possible role of LG-1, a Tetrahymena specific HMG protein found in the macronuclear chromatin (Hamana, K. and Iwai, K. (1979) J. Biochem. 86, 789-794), was examined in relation to the chromatin structure. The chromatin isolated from cells synchronized at different stages of the cell cycle contained about one molec...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/8.22.5275

    authors： Hamana K,Zama M

    更新日期：1980-11-25 00:00:00

  • Tumour suppressor ING1b maintains genomic stability upon replication stress.

    abstract：:The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is important for preventing genomic instability and cancer development. Previously, it was shown that cells deficient in tum...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1337

    authors： Wong RP,Lin H,Khosravi S,Piche B,Jafarnejad SM,Chen DW,Li G

    更新日期：2011-05-01 00:00:00

  • Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes.

    abstract：:In most bacteria, two tRNAs decode the four arginine CGN codons. One tRNA harboring a wobble inosine (tRNA(Arg)ICG) reads the CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNA(Arg)CCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicutes lack the gene en...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt356

    authors： Yokobori S,Kitamura A,Grosjean H,Bessho Y

    更新日期：2013-07-01 00:00:00

  • mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5.

    abstract：:Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv469

    authors： Mock U,Machowicz R,Hauber I,Horn S,Abramowski P,Berdien B,Hauber J,Fehse B

    更新日期：2015-06-23 00:00:00

  • The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.

    abstract：:We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz905

    authors： Dans PD,Balaceanu A,Pasi M,Patelli AS,Petkevičiūtė D,Walther J,Hospital A,Bayarri G,Lavery R,Maddocks JH,Orozco M

    更新日期：2019-12-02 00:00:00

  • UV stalled replication forks restart by re-priming in human fibroblasts.

    abstract：:Restarting stalled replication forks is vital to avoid fatal replication errors. Previously, it was demonstrated that hydroxyurea-stalled replication forks rescue replication either by an active restart mechanism or by new origin firing. To our surprise, using the DNA fibre assay, we only detect a slightly reduced for...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr420

    authors： Elvers I,Johansson F,Groth P,Erixon K,Helleday T

    更新日期：2011-09-01 00:00:00

  • Helicobacter pylori DprA alleviates restriction barrier for incoming DNA.

    abstract：:Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformatio...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt024

    authors： Dwivedi GR,Sharma E,Rao DN

    更新日期：2013-03-01 00:00:00

  • Sequence data handling by computer.

    abstract：:The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editin...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/4.11.4037

    authors： Staden R

    更新日期：1977-11-01 00:00:00

  • Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.

    abstract：:Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq602

    authors： Hestand MS,Klingenhoff A,Scherf M,Ariyurek Y,Ramos Y,van Workum W,Suzuki M,Werner T,van Ommen GJ,den Dunnen JT,Harbers M,'t Hoen PA

    更新日期：2010-09-01 00:00:00

  • WormBase: a modern Model Organism Information Resource.

    abstract：:WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz920

    authors： Harris TW,Arnaboldi V,Cain S,Chan J,Chen WJ,Cho J,Davis P,Gao S,Grove CA,Kishore R,Lee RYN,Muller HM,Nakamura C,Nuin P,Paulini M,Raciti D,Rodgers FH,Russell M,Schindelman G,Auken KV,Wang Q,Williams G,Wright AJ

    更新日期：2020-01-08 00:00:00

  • Analysis of the RNA structural elements involved in the binding of the transcription factor III A from Xenopus laevis.

    abstract：:Xenopus laevis 5S rRNA isolated from 7S particles or transcribed in vitro is found to adopt two alternative conformations. These two conformers contain different structural elements within the major TF III A binding domain, which, when isolated as RNA fragments, still interact with the transcription factor. Chemical m...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.15.6313

    authors： Pieler T,Guddat U,Oei SL,Erdmann VA

    更新日期：1986-08-11 00:00:00

  • Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals.

    abstract：:We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar struc...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa629

    authors： Cabaj MK,Dominiak PM

    更新日期：2020-09-04 00:00:00

  • E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands.

    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

    authors： Paul T,Voter AF,Cueny RR,Gavrilov M,Ha T,Keck JL,Myong S

    更新日期：2020-07-09 00:00:00

  • The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation.

    abstract：:The major mRNA degradation pathway involves deadenylation of the target molecule followed by decapping and, finally, 5'-->3' exonuclease digestion of the mRNA body. While yeast factors involved in the decapping and exonuclease degradation steps have been identified, the nature of the factor(s) involved in the deadenyl...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.12.2448

    authors： Daugeron MC,Mauxion F,Séraphin B

    更新日期：2001-06-15 00:00:00

  • Database for mobile group II introns.

    abstract：:Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We hav...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg049

    authors： Dai L,Toor N,Olson R,Keeping A,Zimmerly S

    更新日期：2003-01-01 00:00:00

  • Multiple heterogeneities in the transcribed spacers of ribosomal DNA from Xenopus laevis.

    abstract：:Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.3.629

    authors： Stewart MA,Hall LM,Maden BE

    更新日期：1983-02-11 00:00:00

  • Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus.

    abstract：:The human Werner syndrome protein, WRN, is a member of the RecQ helicase family and contains 3'-->5' helicase and 3'-->5' exonuclease activities. Recently, we showed that the exonuclease activity of WRN is greatly stimulated by the human Ku heterodimer protein. We have now mapped this interaction physically and functi...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkf482

    authors： Karmakar P,Snowden CM,Ramsden DA,Bohr VA

    更新日期：2002-08-15 00:00:00

  • Some KpnI family members are associated with the Alu family in the human genome.

    abstract：:The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.19.6837

    authors： Miyake T,Migita K,Sakaki Y

    更新日期：1983-10-11 00:00:00

  • RING1A and BMI1 bookmark active genes via ubiquitination of chromatin-associated proteins.

    abstract：:During mitosis the chromatin undergoes dramatic architectural changes with the halting of the transcriptional processes and evacuation of nearly all transcription associated machinery from genes and promoters. Molecular bookmarking of genes during mitosis is a mechanism of faithfully transmitting cell-specific transcr...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv1223

    authors： Arora M,Packard CZ,Banerjee T,Parvin JD

    更新日期：2016-03-18 00:00:00