Abstract:
:Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite substrate formed upon hybridization of target DNA with probe and upstream oligonucleotides. The assay is simple with two easy steps: a cleavage reaction, which generates fluorescent signal on microsphere surfaces, followed by flow cytometry analysis of the microspheres. Genomic DNA samples were genotyped for the SNP in the Apolipoprotein E gene at amino acid position 158. The assay successfully scored wild type, heterozygous and homozygous mutants. To our knowledge, this is the first report of a solid-support assay for detection of SNPs directly from genomic DNA without PCR amplification of the target.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rao KV,Stevens PW,Hall JG,Lyamichev V,Neri BP,Kelso DMdoi
10.1093/nar/gng066keywords:
subject
Has Abstractpub_date
2003-06-01 00:00:00pages
e66issue
11eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh289
更新日期:2004-02-23 00:00:00
abstract::Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1019
更新日期:2014-02-01 00:00:00
abstract::Plasmodium falciparum origin recognition complex 1 (ORC1) protein has been implicated in DNA replication and silencing var gene family. However, the mechanism and the domain structure of ORC1 related to the regulation of var gene family are unknown. Here we show that the unique N-terminus of PfORC1 (PfORC1N(1-238)) is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks202
更新日期:2012-07-01 00:00:00
abstract::A general procedure, based on a new activated alkyne linker, for the preparation of peptide-oligonucleotide conjugates (POCs) on solid support has been developed. With this linker, conjugation is effective at room temperature (RT) in millimolar concentration and submicromolar amounts. This is made possible since the u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr603
更新日期:2011-11-01 00:00:00
abstract::Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl158
更新日期:2006-07-01 00:00:00
abstract::Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh159
更新日期:2004-01-09 00:00:00
abstract::The unsymmetrical cyanine dye thiazole orange homodimer (TOTO) binds to single-stranded DNA (ssDNA, M13mp18 ssDNA) to form a fluorescent complex that is stable under the standard conditions of electrophoresis. The stability of this complex is indistinguishable from that of the corresponding complex of TOTO with double...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.7.1215
更新日期:1995-04-11 00:00:00
abstract::Plasmid DNA incubated in interphase Xenopus egg extracts is normally assembled into chromatin and then into synthetic nuclei which undergo one round of regulated replication. During a study of restriction endonuclease cut plasmid replication intermediates (RIs) by the Brewer-Fangman 2D gel electrophoresis technique, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.10.2187
更新日期:2000-05-15 00:00:00
abstract::Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz181
更新日期:2019-05-21 00:00:00
abstract::Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm760
更新日期:2007-01-01 00:00:00
abstract::Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that c...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/7.7.1913
更新日期:1979-12-11 00:00:00
abstract::Tight cell-cycle regulation of the histone H4-K20 methyltransferase PR-Set7 is essential for the maintenance of genome integrity. In mammals, this mainly involves the interaction of PR-Set7 with the replication factor PCNA, which triggers the degradation of the enzyme by the CRL4CDT2 E3 ubiquitin ligase. PR-Set7 is al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky034
更新日期:2018-04-06 00:00:00
abstract::One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.19.4556
更新日期:1993-09-25 00:00:00
abstract::Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-le...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.22.5347
更新日期:1980-11-25 00:00:00
abstract::The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.18.3605
更新日期:1997-09-15 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::5' Terminal cap structures of hnRNA have been characterized and the extent of capping determined as a function of embryonic development. Sea urchin embryo hnRNA contains only the type-1 cap, m7GpppNmpNp, with the type-2 cap, which has a 2'-0-methylated subpenultimate nucleotide, being associated only with stable small...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.6.2307
更新日期:1979-01-01 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::Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt416
更新日期:2013-07-01 00:00:00
abstract::The 3' splice site of the second intron (I2) of the human apolipoprotein-AII gene, (GT)16GGGCAG, is unique in that, although fully functional, a stretch of alternating guanine and thymine residues replaces the polypyrimidine tract usually associated with 3' splice junctions. The transient expression of successive 5' d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.9.3787
更新日期:1987-05-11 00:00:00
abstract::The chemical shifts of the well-resolved ring nitrogen protons of uracil and a series of substituted uracils, including pseudouridine (5-ribosyl-uracil) and uridine (1-ribosyl-uracil) were determined using nuclear magnetic resonance (NMR). The observed chemical shifts suggest the existence of an atypical syn conformat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.8.2747
更新日期:1977-08-01 00:00:00
abstract::Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki291
更新日期:2005-03-03 00:00:00
abstract::Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.4.889
更新日期:1992-02-25 00:00:00
abstract::DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1142
更新日期:2011-04-01 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::Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm788
更新日期:2008-01-01 00:00:00
abstract::We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1293
更新日期:2011-03-01 00:00:00
abstract::In previous studies, we reported that fractionation of HeLa cell nuclear extracts on glycerol gradients revealed an endogenous ∼10S particle that contained galectin-3 and U1 snRNP and this particle was sufficient to load the galectin polypeptide onto a pre-mRNA substrate. We now document that this interaction between ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw303
更新日期:2016-07-27 00:00:00
abstract::The U1 snRNP-specific protein C contains an N-terminal zinc finger-like CH motif which is required for the binding of the U1C protein to the U1 snRNP particle. Recently a similar motif was reported to be essential for in vivo homodimerization of the yeast splicing factor PRP9. In the present study we demonstrate that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.23.4864
更新日期:1995-12-11 00:00:00
abstract::The 16S ribosomal RNA mutation database (16SMDB) provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenoty...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.166
更新日期:1996-01-01 00:00:00