Abstract：
:The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) spectroscopy, an in situ label-free optical method. Probe density is controlled by varying immobilization conditions, including solution ionic strength, interfacial electrostatic potential and whether duplex or single stranded oligonucleotides are used. Independent of which probe immobilization strategy is used, we find that DNA films of equal probe density exhibit reproducible efficiencies and reproducible kinetics for probe/target hybridization. However, hybridization depends strongly on probe density in both the efficiency of duplex formation and the kinetics of target capture. We propose that probe density effects may account for the observed variation in target-capture rates, which have previously been attributed to thermodynamic effects.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Peterson AW,Heaton RJ,Georgiadis RMdoi
10.1093/nar/29.24.5163keywords:
subject
Has Abstractpub_date
2001-12-15 00:00:00pages
5163-8issue
24eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract：:The nucleotide sequence of the celD gene, encoding the previously crystallized endoglucanase D of Clostridium thermocellum, is reported. The enzyme shares a conserved, reiterated domain with the COOH-terminal end of endoglucanases A and B from the same organism. The overexpression in Escherichia coli of celD subcloned...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.21.8605
更新日期：1986-11-11 00:00:00
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
更新日期：2019-12-02 00:00:00
abstract：:Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.9933
更新日期：1988-11-11 00:00:00
abstract：:Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa131
更新日期：2020-05-07 00:00:00
abstract：:The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the lin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.9.3703
更新日期：1987-05-11 00:00:00
abstract：:In vivo footprinting experiments, augmented with gel shift and transfection analyses suggest that activation of the CYP1A1 gene by aryl hydrocarbons may be a multicomponent process. During the first 30 minutes of exposure to aryl hydrocarbon carcinogens and environmental contaminants, in vivo footprints appear at nine...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.9.1741
更新日期：1994-05-11 00:00:00
abstract：:The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families. Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg062
更新日期：2003-01-01 00:00:00
abstract：:The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1294
更新日期：2021-01-19 00:00:00
abstract：:The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa942
更新日期：2021-01-08 00:00:00
abstract：:COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles from given MSAs, constructs local profile-profile alignments and analytically estimates E-values for the detected similarities. Until now, CO...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm293
更新日期：2007-07-01 00:00:00
abstract：:Various environmental oxidative stresses are sensed by redox-sensitive regulators through cysteine thiol oxidation or modification. A few zinc-containing anti-sigma (ZAS) factors in actinomycetes have been reported to respond sensitively to thiol oxidation, among which RsrA from Streptomyces coelicolor is best charact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr477
更新日期：2011-09-01 00:00:00
abstract：UNLABELLED:Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm392
更新日期：2007-07-01 00:00:00
abstract：:A flow-injection (FI) device is combined, through the use of a low-volume (4 microl) flow cell, with an ultrasensitive surface plasmon resonance (SPR) spectrometer equipped with a bi-cell photodiode detector. The application of this novel FI-SPR device for sequence-specific ultratrace analysis of oligodeoxynucleotides...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf072
更新日期：2002-07-15 00:00:00
abstract：:The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn112
更新日期：2008-05-01 00:00:00
abstract：:The human prothrombin G20210A polymorphism located at the 3' cleavage site of the mRNA results in elevated plasma prothrombin levels and increased risk of venous thrombosis. This polymorphism has been shown to directly influence a variety of processes related to prothrombin mRNA metabolism. We have constructed plasmid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki245
更新日期：2005-02-17 00:00:00
abstract：:Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1266
更新日期：2018-02-28 00:00:00
abstract：:Microsatellites, such as (TG)n found at random throughout the genome, or as 3' extensions of Alu sequences are being increasingly used as genetic markers because of their pluriallelic character. The search for polymorphic microsatellites is time consuming, however, as it is necessary to sequence clones containing the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.6.1333
更新日期：1992-03-25 00:00:00
abstract：:I show that the recognition sequences of Type II restriction systems are correlated with the G + C content of the host bacterial DNA. Almost all restriction systems with G + C rich tetranucleotide recognition sequences are found in species with A + T rich genomes, whereas G + C rich hexanucleotide and octanucleotide r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.5.2283
更新日期：1988-03-25 00:00:00
abstract：:The bZip proteins GCN4 and C/EBP differ in their DNA binding specificities: GCN4 binds well to the pseudopalindromic AP1 site 5'-A4T3G2A1C0T1C2'A3'T4'-3' and to the palindromic ATF/CREB sequence 5'-A4T3G2A1-C0*G0'T1'C2'A3'T4'-3'; C/EBP preferentially recognizes the palindromic sequence 5'-A4T3T2G1C0*G0'C1'A2'-A3'T4'-3...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.20.4162
更新日期：1995-10-25 00:00:00
abstract：:Protein structures are an ensemble of atoms determined experimentally mostly by X-ray crystallography or Nuclear Magnetic Resonance. Studying 3D protein structures is a key point for better understanding protein function at a molecular level. We propose a set of accurate tools, for analysing protein structures, based ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt509
更新日期：2013-07-01 00:00:00
abstract：:The TcSNP database (http://snps.tcruzi.org) integrates information on genetic variation (polymorphisms and mutations) for different stocks, strains and isolates of Trypanosoma cruzi, the causative agent of Chagas disease. The database incorporates sequences (genes from the T. cruzi reference genome, mRNAs, ESTs and ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn874
更新日期：2009-01-01 00:00:00
abstract：:Signals setting the level of transcription of the tRNA-tufB operon have been studied by deletion mapping. TufB transcription was measured in vivo with plasmid-borne tRNA-tufB:galk operon fusions. Removal of the sequences from -133 to -58 with respect to the transcription start point, results in a 90% decrease of tufB ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.22.9515
更新日期：1987-11-25 00:00:00
abstract：:Helicase loading at a DNA replication origin often requires the dynamic interactions between the DNA helicase and an accessory protein. In E. coli, the DNA helicase is DnaB and DnaC is its loading partner. We used the method of hydrogen/deuterium exchange mass spectrometry to address the importance of DnaB-DnaC comple...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv961
更新日期：2016-01-08 00:00:00
abstract：:Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky032
更新日期：2018-04-20 00:00:00
abstract：:Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1167
更新日期：2019-02-20 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：:Analysis of large-scale gene expression studies usually begins with gene clustering. A ubiquitous problem is that different algorithms applied to the same data inevitably give different results, and the differences are often substantial, involving a quarter or more of the genes analyzed. This raises a series of import...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki536
更新日期：2005-05-10 00:00:00
abstract：:We have developed an effective, easy-to-use two-step system for the site-directed insertion of large genetic constructs into arbitrary positions in the Escherichia coli chromosome. The system uses lambda-Red mediated recombineering accompanied by the introduction of double-strand DNA breaks in the chromosome and a don...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1193
更新日期：2010-04-01 00:00:00
abstract：:The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.1
更新日期：1998-01-01 00:00:00
abstract：:The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki108
更新日期：2005-01-01 00:00:00
