Abstract：
:During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted by an individual peptide is determined by co-translational events, such as secondary structure formation and peptide-tunnel interactions. To obtain information on these individual events, the measured ensemble fluorescence signal has to be decomposed into position-dependent intensities. Here, we describe mRNA translation as a Markov process with specific fluorescence intensities assigned to the different states of the process. Combining the computed stochastic time evolution of the translation process with a sequence of observed ensemble fluorescence time courses, we compute the unknown position-specific intensities and obtain detailed information on the kinetics of the translation process. In particular, we find that translation of poly(U) mRNAs dramatically slows down at the fourth UUU codon. The method presented here detects subtle differences in the position-specific fluorescence intensities and thus provides a novel approach to study translation kinetics in ensemble experiments.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Haase N,Holtkamp W,Lipowsky R,Rodnina M,Rudorf Sdoi
10.1093/nar/gky740subject
Has Abstractpub_date
2018-12-14 00:00:00pages
e130issue
22eissn
0305-1048issn
1362-4962pii
5068901journal_volume
46pub_type
杂志文章abstract：:A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.767
更新日期：1984-01-11 00:00:00
abstract：:New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx674
更新日期：2017-09-29 00:00:00
abstract：:Recombinant plasmids which contain EcoRI fragments of tobacco chloroplast DNA carrying tRNA genes were constructed. Plasmids pTC211 and pTC293 contain the base sequences for tRNAAsn in their 1.4 and 1.1 Md EcoRI fragments, respectively. These two tRNA sequences are identical and are; 5'-TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGC...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.21.5601
更新日期：1981-11-11 00:00:00
abstract：:Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5' end of the tetraloop. The(1)H resonances of this hairpin hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.9.1906
更新日期：2000-05-01 00:00:00
abstract：:A new way of studying RNA-protein complexes, using neutron small angle scattering in solution, is described and was applied in the case of the system, yeast valyl-tRNA synthetase, interacting with its cognate and non cognate yeast tRNAs. It was shown that, when limited amounts of tRNA (either cognate or non cognate) a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.7.2421
更新日期：1977-07-01 00:00:00
abstract：:We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in B:acillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.3.683
更新日期：2001-02-01 00:00:00
abstract：:We have synthesized a family of double-stranded cDNAs (ds cDNAs) using as a template the family of highly purified protamine mRNAs from rainbow trout testis. Individual pure protamine cDNA components were isolated by cloning this family of protamine ds cDNAs in a plasmid vector (pMB9). Clones containing protamine sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.6.1463
更新日期：1981-03-25 00:00:00
abstract：:The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.23.4698
更新日期：2000-12-01 00:00:00
abstract：:An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucle...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.8.1941
更新日期：1993-04-25 00:00:00
abstract：:Loop length and its composition are important for the structural and functional versatility of quadruplexes. To date studies on the loops have mainly concerned model sequences compared with naturally occurring quadruplex sequences which have diverse loop lengths and compositions. Herein, we have characterized 36 quadr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn543
更新日期：2008-10-01 00:00:00
abstract：:Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, her...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx407
更新日期：2017-07-03 00:00:00
abstract：:The 4.5S rRNA was isolated from the chloroplast ribosomes from Dryopteris acuminata. The complete nucleotide sequence was determined to be: OHUAAGGUCACGGCAAGACGAGCCGUUUAUCACCACGAUAGGUGCUAAGUGGAGGUGCAGUAAUGUAUGCAGCUGAGGC AUCCUAAUAGACCGAGAGGUUUGAACOH. The 4.5S rRNA is composed of 103 nucleotides and shows strong homolog...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.7.2257
更新日期：1982-04-10 00:00:00
abstract：:The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and mai...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks968
更新日期：2013-01-07 00:00:00
abstract：:In phytohemagglutinin stimulated human lymphocytes the time relationship was determined between induction of the parameters mentioned. The results indicate that the induction occurred in a specific sequence. Thus, a simultaneous increase in the activity of DNA polymerase and thymidinekinase occurred after 15 h of incu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.8.2713
更新日期：1977-08-01 00:00:00
abstract：:Sas2p is a histone acetyltransferase implicated in the regulation of transcriptional silencing, and ORC is the six-subunit origin recognition complex involved in the initiation of DNA replication and the establishment of transcriptionally silent chromatin by silencers in yeast. We show here that SAS2 deletion (sas2Del...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn465
更新日期：2008-09-01 00:00:00
abstract：:Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple he...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1222
更新日期：2020-04-06 00:00:00
abstract：:The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.19.5199
更新日期：1991-10-11 00:00:00
abstract：:Proper DNA double-strand break (DSB) repair is essential for maintaining genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism, which introduces mutations at break sites and contributes to chromosomal translocations and telomere fusions, thus driving carcinogenesis. Mitotic kin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky810
更新日期：2018-11-16 00:00:00
abstract：:The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathwa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt516
更新日期：2013-07-01 00:00:00
abstract：:Nucleotide sequences of large T1 ribonuclease fragments of 18S ribosomal RNA of Novikoff rat ascites hepatoma cells and chicken lymphoblastoid cells were determined and compared. Among the 19 large T1 ribonuclease fragments examined of rat 18S ribosomal RNA, 12 fragments were found to be the same in chicken 18S riboso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.5.1131
更新日期：1979-11-10 00:00:00
abstract：:Inspection of the structure of the C-terminal domain of ribosomal protein L7/L12 (1) reveals a helix-turn-helix motif similar to the one found in many DNA-binding regulatory proteins (2-5). The 19 alpha-carbon atoms of the L7/L12 alpha-helices superimpose on the DNA binding helices of CAP and cro with root-mean-square...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.10.3757
更新日期：1989-05-25 00:00:00
abstract：:Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional proper...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw217
更新日期：2016-06-20 00:00:00
abstract：:Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt961
更新日期：2014-01-01 00:00:00
abstract：:The chicken c-myb gene and the v-myb oncogene transduced by avian myeloblastosis virus (AMV) encode DNA binding transcription activators. The DNA binding domain of AMV v-Myb displays a number of amino acid changes relative to c-Myb; v-Myb proteins in which one or more of three crucial residues in the DNA binding domai...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.12.3043
更新日期：1992-06-25 00:00:00
abstract：:In order to further elucidate the mechanism of tRNA methylase-tRNA intreaction the methylation of some individual tRNAs separately and by pairs was performed. In conditions of tRNA excess the methylation rates of positionally analogous nucleotides in tRNA molecules are not summed up when two substrates are simultaneou...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.8.2079
更新日期：1976-08-01 00:00:00
abstract：:cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni184
更新日期：2005-12-02 00:00:00
abstract：:Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.12.3331
更新日期：1991-06-25 00:00:00
abstract：:Polyadenylation of nascent transcripts is one of the key mRNA processing events in eukaryotic cells. A large number of human and mouse genes have alternative polyadenylation sites, or poly(A) sites, leading to mRNA variants with different protein products and/or 3'-untranslated regions (3'-UTRs). PolyA_DB 2 contains p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl870
更新日期：2007-01-01 00:00:00
abstract：:Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.18.4537
更新日期：1981-09-25 00:00:00
abstract：:PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.304
更新日期：1998-01-01 00:00:00
