Abstract:
:We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is similar for the two ribozymes. The delta(H)degrees' and delta(S)degrees' for pG binding to the Anabaena ribozyme--RNA substrate complex (E x S) are 3.4 +/- 4 kcal/mol and 27 +/- 10 e.u., respectively. The negligible enthalpic contribution and positive entropy change were found previously for the Tetrahymena ribozyme, and are considered remarkable for a hydrogen-bonding interaction between a nucleotide and a nucleic acid. These thermodynamic values may reflect conformational changes or water release upon pG binding that are comparable for the two ribozymes. In addition, the apparent chemical steps of the two ribozyme reactions share similar activation energies and a positive deltaS++. It now appears that such thermochemical values for guanosine binding and activation may be intrinsic properties of the group I intron catalytic center.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kuo LY,Cech TRdoi
10.1093/nar/24.19.3722subject
Has Abstractpub_date
1996-10-01 00:00:00pages
3722-7issue
19eissn
0305-1048issn
1362-4962pii
6t0335journal_volume
24pub_type
杂志文章abstract::The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp477
更新日期:2009-07-01 00:00:00
abstract::Period2 (Per2) is an essential component of the mammalian clock mechanism and robust circadian expression of Per2 is essential for the maintenance of circadian rhythms. Although recent studies have shown that the circadian E2 enhancer (a non-canonical E-box) accounts for most of the circadian transcriptional drive of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl868
更新日期:2007-01-01 00:00:00
abstract::The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1159
更新日期:2008-02-01 00:00:00
abstract::In eukaryotic cells, the shortening and removal of the poly(A) tail of cytoplasmic mRNA by deadenylase enzymes is a critical step in post-transcriptional gene regulation. The ribonuclease activity of deadenylase enzymes is attributed to either a DEDD (Asp-Glu-Asp-Asp) or an endonuclease-exonuclease-phosphatase domain....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt972
更新日期:2014-03-01 00:00:00
abstract::The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq747
更新日期:2010-11-01 00:00:00
abstract::The Escherichia coli fmu gene product has recently been determined to be the 16S rRNA m(5)C 967 methyltransferase. As such, Fmu represents the first protein identified as an S -adenosyl-L-methionine (AdoMet)- dependent RNA m(5)C methyltransferase whose amino acid sequence is known. Using the amino acid sequence of Fmu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.15.3138
更新日期:1999-08-01 00:00:00
abstract::Transcription of tRNA-encoding genes by RNA polymerase (Pol) III requires the six-subunit general transcription factor IIIC that uses subcomplexes τA and τB to recognize two gene-internal promoter elements named A- and B-box. The Schizosaccharomyces pombe τA subcomplex comprises subunits Sfc1, Sfc4 and Sfc7. The cryst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt664
更新日期:2013-10-01 00:00:00
abstract::Bcg I and Bcg I-like restriction endonucleases cleave double stranded DNA specifically on both sides of their asymmetric recognition sequences which are interrupted by several ambiguous base pairs. Their heterosubunit structure, bifunctionality and stimulation by AdoMet make them different from other classified restri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.22.4444
更新日期:1997-11-15 00:00:00
abstract::We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1008
更新日期:2009-03-01 00:00:00
abstract::DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz653
更新日期:2019-09-19 00:00:00
abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1072
更新日期:2017-01-04 00:00:00
abstract::Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm854
更新日期:2008-01-01 00:00:00
abstract::Benzo[c]phenanthrene dihydrodiol epoxide (B[c] PhDE) is well known as an important environmental chemical carcinogen that preferentially modifies DNA in adenine residues. However, the molecular mechanism by which B[c]PhDE induces tumorigenesis is not fully understood. In this report, we demonstrate that DNA mismatch r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg875
更新日期:2003-11-15 00:00:00
abstract::Mutant AraC proteins were selected for their ability to induce but not to repress, or their ability to repress but not to induce the araBAD operon. One such unusual mutant is able to bind to the araI site with an affinity only two to three-fold weaker than the wild type AraC protein, but the mutant protein was shown, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5019
更新日期:1985-07-25 00:00:00
abstract::GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg057
更新日期:2003-01-01 00:00:00
abstract::The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2801
更新日期:1978-08-01 00:00:00
abstract::A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite clos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.2.499
更新日期:2001-01-15 00:00:00
abstract::Tetrahymena thermophila mitochondrial DNA is a linear molecule with two tRNAs, large subunit beta (LSU beta) rRNA (21S rRNA) and LSU alpha rRNA (5.8S-like RNA) encoded near each terminus. The DNA sequence of approximately 550 bp of this region was determined in six species of Tetrahymena. In three species the LSU beta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.1.327
更新日期:1988-01-11 00:00:00
abstract::Synthesis of (p)ppRNA-DNA chains by purified HeLa cell DNA primase-DNA polymerase alpha (pol alpha-primase) was compared with those synthesized by a multiprotein form of DNA polymerase alpha (pol alpha 2) using unique single-stranded DNA templates containing the origin of replication for simian virus 40 (SV40) DNA. Th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.18.7305
更新日期:1986-09-25 00:00:00
abstract::The human thrombopoietin (TPO) gene, which codes for the principal cytokine involved in platelet maturation, shows a peculiar alternative splicing of its last exon, where an intra-exonic 116 nt alternative intron is spliced out in a fraction of its mRNA. To characterize the molecular mechanism underlying this alternat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.4.886
更新日期:2001-02-15 00:00:00
abstract::KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1142
更新日期:2018-01-25 00:00:00
abstract::Methyl carbon-13 NMR spectra of purified tRNA species are presented for the first time. In addition, these spectra of tRNA species specific for phenylalanine, tyrosine, and cysteine exhibited the first resolution of single methyl carbon resonances. Carbon-13 enriched methyl groups of ribothymidine (T) and 7-methylguan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.9.2085
更新日期:1980-05-10 00:00:00
abstract::An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq032
更新日期:2010-06-01 00:00:00
abstract::The role of thymine dimerization for previously reported U.V. induced conformational changes has been proved using acetophenone as sensitizer for the specific thymine dimerization upon irradiation at 313 nm. CD results demonstrate that formation of pyrimidine dimers cause typical conformational changes of the DNA B he...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.2.179
更新日期:1975-02-01 00:00:00
abstract::Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1270
更新日期:2021-01-12 00:00:00
abstract::When the function of origins of replication in yeast was compromised by placing ARS sequences downstream of strong promoters, ARS activity might have been affected either by transcription or by an altered chromatin configuration induced by the construct. To distinguish between these possibilities, derivatives of the y...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.19.3904
更新日期:1994-09-25 00:00:00
abstract::A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removin...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/28.12.e67
更新日期:2000-06-15 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::A 2.1-kb cDNA clone representing a new member of the protease inhibitor family was isolated from a human liver cDNA library. The inhibitor, named human Leuserpin 2 (hLS2), comprises 480 amino acids and contains a leucine residue at its putative reactive center. HLS2 is about 25-28% homologous to three human members of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.2.1073
更新日期:1986-01-24 00:00:00
abstract::In a recent paper we have estimated the total number of protein coding open reading frames (ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800. This number is much smaller than the 5800-6000 which is widely accepted. In this paper we analyse differences between the set of ORFs with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.17.3503
更新日期:1999-09-01 00:00:00