Abstract:
:The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis of linear DNA, we could distinguish between re-arrangements or trapping of the DNA on the surface. Conditions of re-arrangements to an almost equilibrated state can be achieved at appropriate PL surface concentrations. We could show that the ability of re-arrangements depends on the salt concentration of the adsorption/imaging buffer. Comparing the statistical analysis of the linear DNA with SFM images of scDNA suggested that irregular scDNA conformations are formed under conditions of trapping, whereas plectonemic structures are favoured under conditions of surface re-arrangements. Salt-dependent changes in the scDNA conformation over the range of 10-100 mM NaCl, as characterised by the parameters writhe and the superhelix radius r, are observable only under conditions that enable surface re-arrangements. The measured values of writhe suggest that the scDNA loses approximately one-half of the supercoils during the binding to the surface. At the same time r increases systematically with decreasing writhe, thus the scDNA topology remains determined by the constraints on supercoiling during the binding to PL-coated mica.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bussiek M,Mücke N,Langowski Jdoi
10.1093/nar/gng137keywords:
subject
Has Abstractpub_date
2003-11-15 00:00:00pages
e137issue
22eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introd...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky467
更新日期:2018-07-02 00:00:00
abstract::The macronuclear genome of Euplotes crassus contains two different genes, EFA1 and EFA2, encoding EF-1alpha proteins. They are derived from micronuclear precursors in the course of a sexual process termed conjugation. We have found that two apparent micronuclear precursors exist for EFA1. They differ in their potentia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.16.3195
更新日期:1996-08-15 00:00:00
abstract::Organisms exposed to reactive oxygen species, generated endogenously during respiration or by environmental conditions, undergo oxidative stress. Stress response can either repair the damage or activate one of the programmed cell death (PCD) mechanisms, for example apoptosis, and finally end in cell death. One strikin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1100
更新日期:2008-05-01 00:00:00
abstract::We present YOGY a web-based resource for orthologous proteins from nine eukaryotic organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe and Saccharomyces cerevisiae. Using a gene name from any o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl311
更新日期:2006-07-01 00:00:00
abstract::Recurrent chromosome aberrations are an important resource when associating human pathologies to specific genes. However, for technical reasons a large number of chromosome breakpoints are defined only at the level of cytobands and many of the genes involved remain unidentified. We developed a web-based information sy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki061
更新日期:2005-01-01 00:00:00
abstract::The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa666
更新日期:2020-09-18 00:00:00
abstract::The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.12.2873
更新日期:1998-06-15 00:00:00
abstract::A new method for specific reamplification of DDRT-PCR products is presented. After transient ligation of the primary DDRT-PCR fragments into a T-vector, the cDNAs of interest were reamplified by hemi-nested PCR and thermally asymmetric cycles. In contrast to the originally described protocol, this method of reamplific...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.4.1130
更新日期:1998-02-15 00:00:00
abstract::The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.260
更新日期:2002-01-01 00:00:00
abstract::Telomeres play a central role in human cancer, cardiovascular aging and possibly longevity. However, present methods to measure telomere length are fraught with shortcomings that limit their use. Here, we describe a novel method to measure the relative telomere DNA content by dot blot analysis. In each dot, the DNA co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr235
更新日期:2011-07-01 00:00:00
abstract::The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni162
更新日期:2005-10-13 00:00:00
abstract::To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx125
更新日期:2017-05-05 00:00:00
abstract::The extrusion kinetics of two cruciforms derived from unrelated DNA sequences differ markedly. Kinetic barriers exist for both reactions, necessitating elevated temperatures before extrusion proceeds at measureable speeds, but the dependence upon temperature and ionic strength is quite different for the two sequences....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.5.1443
更新日期:1985-03-11 00:00:00
abstract::The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1012
更新日期:2014-01-01 00:00:00
abstract::Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PR...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1091
更新日期:2018-01-04 00:00:00
abstract::This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx815
更新日期:2017-11-16 00:00:00
abstract::The 3374 nucleotide sequence of RNA2 from the British PEBV strain SP5 has been determined. The RNA includes three open reading frames flanked by 5' and 3' noncoding regions of 509 and 480 nucleotides. The open reading frames specify coat protein, a 29.6K product homologous to the 29.1K product of TRV(TCM) RNA2 and a 2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.15.4507
更新日期:1990-08-11 00:00:00
abstract::Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.703
更新日期:1999-01-15 00:00:00
abstract::The deoxyoligonucleotide 5' AATCGGGCATGGATT (15-mer) was synthesized containing 12 phosphoramidate linkages derived from 2 primary and 2 secondary amines. The oligonucleotides were purified by reverse phase HPLC and characterized by PAGE. The thermal stability of the duplexes derived from these compounds, when hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.11.4831
更新日期:1988-06-10 00:00:00
abstract::RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz427
更新日期:2019-06-20 00:00:00
abstract::We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Cur...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl254
更新日期:2006-07-01 00:00:00
abstract::The role of thymine dimerization for previously reported U.V. induced conformational changes has been proved using acetophenone as sensitizer for the specific thymine dimerization upon irradiation at 313 nm. CD results demonstrate that formation of pyrimidine dimers cause typical conformational changes of the DNA B he...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.2.179
更新日期:1975-02-01 00:00:00
abstract::Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by mul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1378
更新日期:2014-04-01 00:00:00
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
更新日期:1995-07-11 00:00:00
abstract::The long interspersed repeated DNA family of rats (LINE or L1Rn family) contains about 40,000 6.7-kilobase (kb) long members (1). LINE members may be currently mobile since their presence or absence causes allelic variation at three single copy loci (2, 3): insulin 1, Moloney leukemia virus integration 2 (Mlvi-2) (4),...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.9.3717
更新日期:1986-05-12 00:00:00
abstract::Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1234
更新日期:2021-01-25 00:00:00
abstract::Cloned DNA from the EcoRI J fragment of EBV has been used as template for in vitro transcription experiments using cell-free extracts prepared from HeLa or KB cells. Two EBV specific RNAs each about 175 bases in length were synthesised and nuclease 51 mapping experiments determined that these in vitro products corresp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.11.3407
更新日期:1982-06-11 00:00:00
abstract::We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.5783
更新日期:1988-07-11 00:00:00
abstract::The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide suga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.555
更新日期:1999-01-15 00:00:00
abstract::Slime mold, plant and insect dihydropyrimidine amidohydrolases (DHPases, EC 3.5.2.2), which catalyze the second step of pyrimidine and several anti-cancer drug degradations, were cloned and shown to functionally replace a defective DHPase enzyme in the yeast Saccharomyces kluyveri. The yeast and slime mold DHPases wer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg258
更新日期:2003-03-15 00:00:00