Abstract:
:Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼10(5) target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Adams NM,Olmsted IR,Haselton FR,Bornhop DJ,Wright DWdoi
10.1093/nar/gkt165subject
Has Abstractpub_date
2013-05-01 00:00:00pages
e103issue
9eissn
0305-1048issn
1362-4962pii
gkt165journal_volume
41pub_type
杂志文章abstract::The S-adenosylmethionine (AdoMet) analog sinefungin is a natural product antibiotic that inhibits nucleic acid methyltransferases and arrests the growth of unicellular eukarya and eukaryal viruses. The basis for the particular sensitivity of fungi and protozoa to sinefungin is not known. Here we report the isolation a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm817
更新日期:2007-01-01 00:00:00
abstract::Many small RNAs contribute essential activities to eukaryotic cells. In mammalian genomes dispersed repetitive sequences which exhibit homology to small RNAs often exist as pseudogenes which can complicate identification, localization, and analysis of the authentic gene. We mapped a productive human 7SK small nuclear ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.5.722
更新日期:1994-03-11 00:00:00
abstract::Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1's function has remaine...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt082
更新日期:2013-04-01 00:00:00
abstract::The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mappi...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/gkj146
更新日期:2006-01-01 00:00:00
abstract::DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm334
更新日期:2007-07-01 00:00:00
abstract::The rDNA cluster in Saccharomyces cerevisiae is located 450 kb from the left end and 610 kb from the right end of chromosome XII and consists of approximately 150 tandemly repeated copies of a 9.1 kb rDNA unit. To explore the biological significance of this specific chromosomal context, chromosome XII was split at bot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl293
更新日期:2006-05-31 00:00:00
abstract::Fluorescence anisotropy and fluorescence correlation spectroscopy measurements of rhodamine-labeled DNA oligonucleotide duplexes have been used to determine equilibrium binding constants for DNA binding of the prokaryotic transcription activator protein NtrC. Measurements were made with wild-type NtrC from Escherichia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.6.1373
更新日期:1998-03-15 00:00:00
abstract::Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa550
更新日期:2020-09-18 00:00:00
abstract::Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt423
更新日期:2013-08-01 00:00:00
abstract::Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1229
更新日期:2018-02-28 00:00:00
abstract::Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx376
更新日期:2017-07-03 00:00:00
abstract::In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1133
更新日期:2015-12-02 00:00:00
abstract::Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky787
更新日期:2018-10-12 00:00:00
abstract::Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solutio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.336
更新日期:2001-01-01 00:00:00
abstract::The novel deoxyribonucleotide alpha-[d(CpCpTpTpCpC)] and its complement beta-[d(GpGpApApGpG)] were synthesized by the phosphotriester method. 1H-NMR-NOE examination of the alpha-hexamer revealed that the cytosine and thymine bases appear to adopt anti conformations in this strand. In addition the deoxyribose of the th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.12.5019
更新日期:1986-06-25 00:00:00
abstract::The Epstein-Barr virus gene BRLF1 encodes the transcription factor R, which is a sequence-specific DNA-binding protein important for the switch from latency to a productive cycle. We have defined a repertoire of specific R-binding sites using a GST-R fusion protein and a pool of 23 bp random DNA sequences. The R-bound...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1172
更新日期:1994-04-11 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::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::SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg535
更新日期:2003-07-01 00:00:00
abstract::P53-binding protein 1 (53BP1) mediates DNA repair pathway choice and promotes checkpoint activation. Chromatin marks induced by DNA double-strand breaks and recognized by 53BP1 enable focal accumulation of this multifunctional repair factor at damaged chromatin. Here, we unveil an additional level of regulation of 53B...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz138
更新日期:2019-04-08 00:00:00
abstract::The complete nucleotide sequence of the mitochondrial DNA of the amphioxus Branchiostoma lanceolatum has been determined. This mitochondrial genome is small (15 076 bp) because of the short size of the two rRNA genes and the tRNA genes. In addition, this genome contains a very short non-coding region (57 bp) with no s...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1998-07-01 00:00:00
abstract::Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolites.org/) provides a hig...
journal_title:Nucleic acids research
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doi:10.1093/nar/gky321
更新日期:2018-07-02 00:00:00
abstract::Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the stan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl773
更新日期:2006-01-01 00:00:00
abstract::SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn762
更新日期:2009-01-01 00:00:00
abstract::FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms. RIK...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.116
更新日期:2002-01-01 00:00:00
abstract::Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv566
更新日期:2015-07-13 00:00:00
abstract::Initiation of reverse transcription is a complex and regulated process in all retroviruses. Several base pairing interactions have been proposed to occur between the HIV-1 RNA genome and the specific tRNA(lys3) primer. The tRNA primer can form up to 21 bp with the primer binding site (PBS), and an additional 8 bp inte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg714
更新日期:2003-09-01 00:00:00
abstract::We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR meltin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng116
更新日期:2003-09-15 00:00:00
abstract::The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for downloa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh023
更新日期:2004-01-01 00:00:00
abstract::U6 RNA is a member of a class of small abundant stable nuclear RNAs that are essential for splicing. In all species examined so far, the U6 RNA is a RNA polymerase III transcript. The U6 gene of the fission yeast Schizosaccharomyces pombe is unusual in that it is interrupted by an intron whose structure is similar to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.19.7821
更新日期:1989-10-11 00:00:00