Abstract:
:In 4M NaCl solutions (dC-dG)n (n = 3,4; approximately 9 mM) exist as a mixture o +/- B and Z forms. The low and high field components of two 31P NMR resonances originating from internal phosphodiester groups are assigned to the GpC and CpG linkages, respectively. Low temperatures stabilize the Z-forms, which completely disappear above 50 degrees C (n = 3) and 65 degrees C (n = 4). delta H = -44 and -17 kJ/mol for B to Z transition in the hexamer and octamer duplexes, respectively. Temperature dependent changes (0-50 degrees C range) in the spin-lattice relaxation times at 145.7 MHz are distinctly different for the 31P nuclei o +/- GpC and CpG groups. The relaxation data can be explained by assuming that the GpC phosphodiester groups undergo more local internal motion than do the CpG groups.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Holak TA,Borer PN,Levy GC,van Boom JH,Wang AHdoi
10.1093/nar/12.11.4625subject
Has Abstractpub_date
1984-06-11 00:00:00pages
4625-35issue
11eissn
0305-1048issn
1362-4962journal_volume
12pub_type
杂志文章abstract::Prokaryotic genomic DNA is generally negatively supercoiled in vivo. Many regulatory processes, including the initiation of transcription, are known to depend on the superhelical state of the DNA substrate. The stresses induced within DNA by negative superhelicity can destabilize the DNA duplex at specific sites. Vari...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj007
更新日期:2006-01-01 00:00:00
abstract::We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl170
更新日期:2006-07-01 00:00:00
abstract::Not I linking clones contain sequences flanking Not I recognition sites and were previously shown to be tightly associated with CpG islands and genes. To directly assess the value of Not I clones in genome research, high density grids with 50 000 Not I linking clones originating from six representative Not I linking l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.7.1635
更新日期:2000-04-01 00:00:00
abstract::The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki546
更新日期:2005-05-06 00:00:00
abstract::The mRNAs for different variant surface antigens of Trypanosoma brucei start with the same 35 nucleotides. This sequence is encoded by a separate mini-exon, located in a 1.35-kb repetitive element. We have reported that trypanosomes contain many transcripts that hybridize to mini-exon probes, even if they do not make ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3777
更新日期:1984-05-11 00:00:00
abstract::Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1685
更新日期:1992-04-11 00:00:00
abstract::EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm938
更新日期:2008-01-01 00:00:00
abstract::ID elements comprise a rodent SINE (short interspersed DNA repetitive element) family that has amplified by retroposition of a few master genes. In order to understand the important factors of SINE amplification, we investigated the transcription of rat ID elements. Three different size classes of ID transcripts, BC1,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.12.2245
更新日期:1995-06-25 00:00:00
abstract::Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky383
更新日期:2018-07-02 00:00:00
abstract::Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.8.3427
更新日期:1984-04-25 00:00:00
abstract::The positions of the trfA and trfB promoters of broad host range IncP plasmid RK2 (identical to RP1, RP4, R68 and R18 ) were identified by RNA polymerase protection studies, and the nucleotide sequences of the promoter regions determined. A mutation within the trfA promoter sequence is associated with loss of kilD act...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.8.3619
更新日期:1984-04-25 00:00:00
abstract::Type II restriction endonucleases Bam HI and Eco RI were covalently coupled to Sepharose. These insolubilized enzymes generated fragment patterns for several viral DNAs identical to those produced by the respective free enzymes. Conditions for optimal activity were similar for both bound and unbound forms of the enzym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.3.679
更新日期:1978-03-01 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.10.4083
更新日期:1984-05-25 00:00:00
abstract::The interactions of HIV-1 reverse transcriptase (HIV-1 RT) with a synthetic 53/19-mer DNA substrate was investigated. For this template-primer HIV-1 RT displayed a Km value of 20 nM. The 53/19-mer competitively inhibited DNA synthesis performed on poly (rC).oligo(dG) with Ki value of 260 nM. This corresponded well to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.17.3943
更新日期:1993-08-25 00:00:00
abstract::DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1189
更新日期:2019-01-10 00:00:00
abstract::Numerous RNA-binding proteins have modular structures, comprising one or several copies of a selective RNA-binding domain generally coupled to an auxiliary domain that binds RNA non-specifically. We have built and compared homology-based models of the cold-shock domain (CSD) of the Xenopus protein, FRGY2, and of the t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2223
更新日期:2001-06-01 00:00:00
abstract::Alu elements have repeatedly been found involved in gene rearrangements in humans. Although these elements have been suggested to stimulate gene rearrangements, sparse information is available for the possible mechanism(s) of these events. Here we present a compilation of Alu elements that have been involved in recomb...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.2.256
更新日期:1995-01-25 00:00:00
abstract::Histone post-translational modifications regulate chromatin structure and function largely through interactions with effector proteins that often contain multiple histone-binding domains. PHF1 [plant homeodomain (PHD) finger protein 1], which contains two kinds of histone reader modules, a Tudor domain and two PHD fin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky461
更新日期:2018-07-27 00:00:00
abstract::Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3843
更新日期:1984-05-11 00:00:00
abstract::We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2318
更新日期:1994-06-25 00:00:00
abstract::A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.19.7327
更新日期:1984-10-11 00:00:00
abstract::Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku137
更新日期:2014-04-01 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::NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1216
更新日期:2010-05-01 00:00:00
abstract::Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segmen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm245
更新日期:2007-01-01 00:00:00
abstract::Dlx homeobox genes are first expressed in embryonic retina at E11.5. The Dlx1/Dlx2 null retina has a reduced ganglion cell layer (GCL), with loss of late-born differentiated retinal ganglion cells (RGCs) due to increased apoptosis. TrkB signaling is proposed to regulate the dynamics of RGC apoptosis throughout develop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1099
更新日期:2008-02-01 00:00:00
abstract::The 'sandwich' binding format, which uses two reagents that can bind simultaneously to a given analyte, is the gold standard in diagnostics and many biochemical techniques. One of the bottlenecks in creating a sandwich assay is identifying pairs of reagents that bind non-competitively to the target. To bridge this gap...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx688
更新日期:2017-10-13 00:00:00
abstract::We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.1935
更新日期:2002-05-01 00:00:00
abstract::Transcription of the bacteriophage Mu mom operon requires transactivation by the phage-encoded C protein. DNase I footprinting showed that in the absence of C, Escherichia coli RNA polymerase E(sigma)70 (RNAP) binds to the mom promoter (Pmom) region at a site, P2 (from -64 to -11 with respect to the transcription star...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.20.4042
更新日期:1996-10-15 00:00:00