Abstract：
:To investigate the mechanisms by which oligonucleotides hybridize to target molecules, the binding of two oligodeoxynucleotide probes to RNA targets was measured over a broad range of temperatures. Mutations were then scanned across each DNA/RNA hybrid to map, at single base resolution, sequences important for hybridization. Despite being unrelated in sequence, each hybrid formed by a similar mechanism. In the absence of secondary structure, two stretches of bases, termed nucleation regions, cooperated with one another by a looping mechanism to nucleate hybridization. Mutations inside each nucleation region strongly decreased hybridization rates, even at temperatures well below the melting temperature (T(m)) of the hybridized duplex. Surprisingly, nucleation regions were detected in a RNA target but not a corresponding DNA target. When either nucleation region was sequestered in secondary structure, the hybridization rate fell and the mechanism of hybridization changed. Single-stranded bases within the nucleation region of the probe and target first collided to form a double helix. If sufficiently G + C rich, the double helix then propagated throughout the oligonucleotide by a strand invasion process. On the basis of these results, general mechanisms for the hybridization of oligonucleotides to complementary and mutant targets are proposed.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Majlessi M,Becker MMdoi
10.1093/nar/gkn134subject
Has Abstractpub_date
2008-05-01 00:00:00pages
2981-9issue
9eissn
0305-1048issn
1362-4962pii
gkn134journal_volume
36pub_type
杂志文章abstract：:HIV-1 reverse transcriptase (RT) is a primary target for anti-AIDS drugs. Structures of HIV-1 RT, usually determined at approximately 2.5-3.0 A resolution, are important for understanding enzyme function and mechanisms of drug resistance in addition to being helpful in the design of RT inhibitors. Despite hundreds of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn464
更新日期：2008-09-01 00:00:00
abstract：:The complete nucleotide sequences of the various precursor 5S RNA species occurring in Bacillus licheniformis have been elucidated. The B. licheniformis precursors contain a 5'-precursor-specific segment of 95 nucleotides which is four times as long as the corresponding segment of the p5S RNAs from the closely related...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.19.4535
更新日期：1980-10-10 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
abstract：:We have determined the DNA sequence surrounding the transcription terminator following rpoC, the gene that codes for the beta' subunit of RNA polymerase in E. coli K12. The 2044 bp sequence obtained contains the distal 335 codons of rpoC followed by a 212 bp non-coding region and a second open reading frame (ORFa) of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.24.6827
更新日期：1981-12-21 00:00:00
abstract：:Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz296
更新日期：2019-06-20 00:00:00
abstract：:The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.22.6043
更新日期：1992-11-25 00:00:00
abstract：:A DNA methylase has been purified 270-fold from HeLa cell nuclei by chromatography on DEAE-cellulose, phosphocellulose, and hydroxyapatite. The enzyme transfers methyl groups from S-adenosyl-L-methionine to cytosine residues in DNA. The sole product of the reaction has been identified as 5-methylcytosine. The enzyme i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.10.1669
更新日期：1975-10-01 00:00:00
abstract：:The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outco...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg096
更新日期：2003-01-01 00:00:00
abstract：:Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifyin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz457
更新日期：2019-07-02 00:00:00
abstract：:Mature chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength are enriched in beta-globin DNA sequences. Vitellogenin chromatin, which is not expressed in this tissue, is found in aggregation prone, salt insoluble chromatin. There is a direct correlation between the size of soluble fragm...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.1081
更新日期：1987-02-11 00:00:00
abstract：:Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.6.1635
更新日期：1983-03-25 00:00:00
abstract：:Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku107
更新日期：2014-04-01 00:00:00
abstract：:Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt718
更新日期：2013-11-01 00:00:00
abstract：:Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.11.2723
更新日期：1998-06-01 00:00:00
abstract：:The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki209
更新日期：2005-01-26 00:00:00
abstract：:Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (I...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.3.331
更新日期：1974-03-01 00:00:00
abstract：:The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj004
更新日期：2006-01-01 00:00:00
abstract：T:Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄- GAG CA-3΄ or 5΄- GAG CA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx057
更新日期：2017-03-17 00:00:00
abstract：:The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.15.3467
更新日期：1980-08-11 00:00:00
abstract：:Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt153
更新日期：2013-04-01 00:00:00
abstract：:The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt977
更新日期：2014-01-01 00:00:00
abstract：:A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.12.4857
更新日期：1987-06-25 00:00:00
abstract：:Abasic substitutions in the non-template strand and promoter sequence changes were made to assess the roles of various promoter features in sigma70 holoenzyme interactions with fork junction probes. Removal of -10 element non-template single strand bases, leaving the phosphodiester backbone intact, did not interfere w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg400
更新日期：2003-06-01 00:00:00
abstract：:During DNA double-strand break and replication fork repair by homologous recombination, the RAD51 recombinase catalyzes the DNA strand exchange reaction via a helical polymer assembled on single-stranded DNA, termed the presynaptic filament. Our published work has demonstrated a dual function of the SWI5-SFR1 complex ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw375
更新日期：2016-07-27 00:00:00
abstract：:Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa324
更新日期：2020-06-19 00:00:00
abstract：:Wybutine (Ywye), situated next to the 3'-side of the anticodon of tRNAPhe from Saccharomyces cerevisiae, can be photo-crosslinked to mRNA when bound to Escherichia coli ribosomes. Crosslinking can be obtained with poly(U) as well as with oligonucleotides such as pAUGUUU or p(U)6. In order to identify the site of react...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.21.8181
更新日期：1984-11-12 00:00:00
abstract：:Purified UvrA, UvrB, UvrC, UvrD, PolA and Lig proteins from Escherichia coli have been used to assess the effect of nucleotide excision repair on the conformation of native negatively supercoiled plasmid DNA in an in vitro test system. The analysis of labeled reaction products on specific gel systems suggests that the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.24.10337
更新日期：1989-12-25 00:00:00
abstract：:The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration wi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1001
更新日期：2017-01-04 00:00:00
abstract：:Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the replication terminator protein (RTP) and DNA terminator sites. While determination of the crystal structure of RTP has facilitated our understanding of how a single RTP dimer inte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.3.590
更新日期：1997-02-01 00:00:00
abstract：:PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set com...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.61
更新日期：2001-01-01 00:00:00
