Temperature mediated variation of DNA secondary structure in (A.T) clusters; evidence by use of the oligopeptide netropsin as a structural probe.

Abstract:

:The titration viscometric investigation of the multi-mode interaction of netropsin (Nt) with (A.T) clusters of NaDNA12 and NH4DNA10 has been extended to different temperatures. The position of two boundaries on the r-scale (r= [Nt]bound/[DNA-P]) with increasing temperature steadily (rI/II) or more abruptly (rO/I) shifts to lower values. For the most (A.T) rich Nt-binding sites of modes (O), (I) and (II) this observation suggests the existence of an equilibrium between different DNA secondary structures with a different translation per base pair. The mode specific changes delta L1Nt of DNA contour length as induced by one Nt molecule proved to be almost independent of temperature. Concomitant stiffening effects increase with decreasing temperature, contrary to initial expectation. Conformational variability of (A.T) clusters may represent an essential feature in specific or selective DNA-protein interaction.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Reinert KE,Geller D,Stutter E

doi

10.1093/nar/9.10.2335

subject

Has Abstract

pub_date

1981-05-25 00:00:00

pages

2335-49

issue

10

eissn

0305-1048

issn

1362-4962

journal_volume

9

pub_type

杂志文章
  • PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.

    abstract::Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1035

    authors: Chow CN,Zheng HQ,Wu NY,Chien CH,Huang HD,Lee TY,Chiang-Hsieh YF,Hou PF,Yang TY,Chang WC

    更新日期:2016-01-04 00:00:00

  • RNA surveillance by uridylation-dependent RNA decay in Schizosaccharomyces pombe.

    abstract::Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz043

    authors: Chung CZ,Jaramillo JE,Ellis MJ,Bour DYN,Seidl LE,Jo DHS,Turk MA,Mann MR,Bi Y,Haniford DB,Duennwald ML,Heinemann IU

    更新日期:2019-04-08 00:00:00

  • Helix opening in deoxyribonucleic acid from a proton nuclear magnetic resonance study of imino and amino protons in d(CG)3.

    abstract::All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.21.8269

    authors: Fazakerley GV,van der Marel GA,van Boom JH,Guschlbauer W

    更新日期:1984-11-12 00:00:00

  • Protein structure prediction using sparse dipolar coupling data.

    abstract::Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a struct...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh204

    authors: Qu Y,Guo JT,Olman V,Xu Y

    更新日期:2004-01-26 00:00:00

  • Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.

    abstract::Homing endonucleases (HEs) cut long DNA target sites with high specificity to initiate and target the lateral transfer of mobile introns or inteins. This high site specificity of HEs makes them attractive reagents for gene targeting to promote DNA modification or repair. We have generated several hundred catalytically...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp004

    authors: Li H,Pellenz S,Ulge U,Stoddard BL,Monnat RJ Jr

    更新日期:2009-04-01 00:00:00

  • DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.

    abstract::The DECIPHER database (https://decipher.sanger.ac.uk/) is an accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >2...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt937

    authors: Bragin E,Chatzimichali EA,Wright CF,Hurles ME,Firth HV,Bevan AP,Swaminathan GJ

    更新日期:2014-01-01 00:00:00

  • Unique organization of the human BCR gene promoter.

    abstract::The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.23.7119

    authors: Zhu QS,Heisterkamp N,Groffen J

    更新日期:1990-12-11 00:00:00

  • Crystal structure of the 5hmC specific endonuclease PvuRts1I.

    abstract::PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 Å resolution. Although the protein has bee...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku186

    authors: Kazrani AA,Kowalska M,Czapinska H,Bochtler M

    更新日期:2014-05-01 00:00:00

  • Nucleotide sequence of the EcoRI D fragment of adenovirus 2 genome.

    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

    authors: Hérissé J,Courtois G,Galibert F

    更新日期:1980-05-24 00:00:00

  • DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels.

    abstract::The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw352

    authors: Frykholm K,Berntsson RP,Claesson M,de Battice L,Odegrip R,Stenmark P,Westerlund F

    更新日期:2016-09-06 00:00:00

  • Structural classification of zinc fingers: survey and summary.

    abstract::Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and transla...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg161

    authors: Krishna SS,Majumdar I,Grishin NV

    更新日期:2003-01-15 00:00:00

  • BMI1 is a target gene of E2F-1 and is strongly expressed in primary neuroblastomas.

    abstract::The oncogene BMI1 encodes a polycomb group transcription factor that is required for embryonic development and self-renewal of stem cells. Despite these important functions little is known about the regulation of BMI1 expression. A cDNA microarray based search for target genes of E2F-1 in neuroblastoma cells expressin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl119

    authors: Nowak K,Kerl K,Fehr D,Kramps C,Gessner C,Killmer K,Samans B,Berwanger B,Christiansen H,Lutz W

    更新日期:2006-03-31 00:00:00

  • DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar.

    abstract::Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku269

    authors: Wilson KA,Kellie JL,Wetmore SD

    更新日期:2014-06-01 00:00:00

  • Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h.

    abstract::Site-directed, Ligase-Independent Mutagenesis (SLIM) is a novel PCR-mediated mutagenesis approach that can accommodate all three sequence modification types (insertion, deletion and substitution). The method utilizes an inverse PCR amplification of the template by two tailed long primers and two short primers in a sin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnh172

    authors: Chiu J,March PE,Lee R,Tillett D

    更新日期:2004-12-07 00:00:00

  • Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protein.

    abstract::We present the results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are es...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.13.2512

    authors: Stockley PG,Stonehouse NJ,Murray JB,Goodman ST,Talbot SJ,Adams CJ,Liljas L,Valegård K

    更新日期:1995-07-11 00:00:00

  • Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds.

    abstract::A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx942

    authors: Liu S,Peng P,Wang H,Shi L,Li T

    更新日期:2017-12-01 00:00:00

  • Conditional DNA repair mutants enable highly precise genome engineering.

    abstract::Oligonucleotide-mediated multiplex genome engineering is an important tool for bacterial genome editing. The efficient application of this technique requires the inactivation of the endogenous methyl-directed mismatch repair system that in turn leads to a drastically elevated genomic mutation rate and the consequent a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku105

    authors: Nyerges Á,Csorgő B,Nagy I,Latinovics D,Szamecz B,Pósfai G,Pál C

    更新日期:2014-04-01 00:00:00

  • A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells.

    abstract::Integration of foreign genes into plant genomes by the Agrobacterium T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.14.2744

    authors: Dietz A,Kay V,Schlake T,Landsmann J,Bode J

    更新日期:1994-07-25 00:00:00

  • HapZipper: sharing HapMap populations just got easier.

    abstract::The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techni...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks709

    authors: Chanda P,Elhaik E,Bader JS

    更新日期:2012-11-01 00:00:00

  • HeLa DNA polymerase alpha activity in vitro: specific stimulation by a non-enzymic protein factor.

    abstract::A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.1.221

    authors: Novak B,Baril EF

    更新日期:1978-01-01 00:00:00

  • 4'-Acylated thymidine 5'-triphosphates: a tool to increase selectivity towards HIV-1 reverse transcriptase.

    abstract::4'-Acylated thymidines represent a new class of DNA chain terminators, since they have been shown to act as post-incorporation chain-terminating nucleotides despite the presence of a free 3'-hydroxyl group. Here, we describe the action of the 4'-acetyl- (MeTTP) and 4'-propanoylthymidine 5'-triphosphate (EtTTP) on HIV-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.17.4063

    authors: Marx A,Amacker M,Stucki M,Hübscher U,Bickle TA,Giese B

    更新日期:1998-09-01 00:00:00

  • Aly and THO are required for assembly of the human TREX complex and association of TREX components with the spliced mRNA.

    abstract::The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1188

    authors: Chi B,Wang Q,Wu G,Tan M,Wang L,Shi M,Chang X,Cheng H

    更新日期:2013-01-01 00:00:00

  • Heteroduplexes of phiX174 and G4 DNAs: orientation to genetic map and comparison with predictions from nucleotide sequences.

    abstract::Heteroduplexes between the viral DNA of phiX174 and DNA from the replicative form (RF) of phage G4 were examined by electron microscopy. The single Eco RI site of G4-RF was utilized as a physical marker by preparing the heteroduplexes from the denatured, linear DNA obtained by restricting G4-RF with Eco RI endonucleas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.5.1979

    authors: Smiley BL,Warner RC

    更新日期:1979-01-01 00:00:00

  • PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.

    abstract::Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm854

    authors: Gong W,Zhou D,Ren Y,Wang Y,Zuo Z,Shen Y,Xiao F,Zhu Q,Hong A,Zhou X,Gao X,Li T

    更新日期:2008-01-01 00:00:00

  • Conformation transitions of eukaryotic polyribosomes during multi-round translation.

    abstract::Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20-30 translation rounds during 6-8 h in wheat germ extract at 25°C). Three distinct types of the conformation...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1270

    authors: Afonina ZA,Myasnikov AG,Shirokov VA,Klaholz BP,Spirin AS

    更新日期:2015-01-01 00:00:00

  • Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region.

    abstract::Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr259

    authors: Onyshchenko MI,Gaynutdinov TI,Englund EA,Appella DH,Neumann RD,Panyutin IG

    更新日期:2011-09-01 00:00:00

  • DNA-mediated coupling of ATPase, translocase and nuclease activities of a Type ISP restriction-modification enzyme.

    abstract::Enzymes involved in nucleic acid transactions often have a helicase-like ATPase coordinating and driving their functional activities, but our understanding of the mechanistic details of their coordination is limited. For example, DNA cleavage by the antiphage defense system Type ISP restriction-modification enzyme req...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa023

    authors: Chand MK,Carle V,Anuvind KG,Saikrishnan K

    更新日期:2020-03-18 00:00:00

  • Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life.

    abstract::A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky1009

    authors: Huang X,Albou LP,Mushayahama T,Muruganujan A,Tang H,Thomas PD

    更新日期:2019-01-08 00:00:00

  • Molecular cloning of MSSP-2, a c-myc gene single-strand binding protein: characterization of binding specificity and DNA replication activity.

    abstract::We have previously reported the human cDNA encoding MSSP-1, a sequence-specific double- and single-stranded DNA binding protein [Negishi, Nishita, Saëgusa, Kakizaki, Galli, Kihara, Tamai, Miyajima, Iguchi-Ariga and Ariga (1994) Oncogene, 9, 1133-1143]. MSSP-1 binds to a DNA replication origin/transcriptional enhancer ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.25.5576

    authors: Takai T,Nishita Y,Iguchi-Ariga SM,Ariga H

    更新日期:1994-12-25 00:00:00

  • Synthesis and biological evaluation of some phosphate triester derivatives of the anti-cancer drug araC.

    abstract::A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.18.7195

    authors: Jones BC,McGuigan C,Riley PA

    更新日期:1989-09-25 00:00:00