Abstract:
:Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in vivo mutation rate and high gene-specificity in Escherichia coli. eMutaT7, a cytidine deaminase fused to an orthogonal RNA polymerase, can introduce up to ∼4 mutations per 1 kb per day, rivalling the rate in typical in vitro mutagenesis for directed evolution of proteins, and promotes rapid continuous evolution of model proteins for antibiotic resistance and allosteric activation. eMutaT7 provides a very simple and tunable method for continuous directed evolution of proteins, and suggests that the fusion of new DNA-modifying enzymes to the orthogonal RNA polymerase is a promising strategy to explore the expanded sequence space without compromising gene specificity.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Park H,Kim Sdoi
10.1093/nar/gkaa1231subject
Has Abstractpub_date
2021-01-06 00:00:00eissn
0305-1048issn
1362-4962pii
6066637pub_type
杂志文章abstract::In Xenopus oocytes in vitro transcribed mouse U7 RNA is assembled into small nuclear ribonucleoproteins (snRNPs) that are functional in histone RNA 3' processing. If the special Sm binding site of U7 (AAUUUGUCUAG, U7 Sm WT) is converted into the canonical Sm sequence derived from the major snRNAs (AAUUUUUGGAG, U7 Sm O...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.16.3141
更新日期:1995-08-25 00:00:00
abstract::FIMM database (http://sdmc.krdl.org.sg:8080/fimm) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.226
更新日期:2002-01-01 00:00:00
abstract::Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl396
更新日期:2006-06-06 00:00:00
abstract::Fifteen years elapsed between the discovery of the double helix (1953) and the first DNA sequencing (1968). Modern DNA sequencing began in 1977, with development of the chemical method of Maxam and Gilbert and the dideoxy method of Sanger, Nicklen and Coulson, and with the first complete DNA sequence (phage X174), whi...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/gkm688
更新日期:2007-01-01 00:00:00
abstract::Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa427
更新日期:2020-07-09 00:00:00
abstract::The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the bi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.24.4792
更新日期:1999-12-15 00:00:00
abstract::During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt728
更新日期:2013-11-01 00:00:00
abstract::The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa969
更新日期:2021-01-08 00:00:00
abstract::DNA primase has been partially purified from wheat germ. This enzyme, like DNA primases characterized from many procaryotic and eucaryotic sources, catalyses the synthesis of primers involved in DNA replication. However, the wheat enzyme differs from animal DNA primase in that it is found partially associated with a D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.16.4867
更新日期:1990-08-25 00:00:00
abstract::The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm956
更新日期:2008-01-01 00:00:00
abstract::Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1177
更新日期:2019-01-10 00:00:00
abstract::Many cellular proteins are methylated on lysine residues and this has been most intensively studied for histone proteins. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx432
更新日期:2017-08-21 00:00:00
abstract::The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky977
更新日期:2019-01-08 00:00:00
abstract::Analysis of the human protein-tyrosine phosphatase (PTP) PTPRJ mRNA detected three in-frame AUGs at the 5'-end (starting at nt +14, +191 and +356) with no intervening stop codons. This tandem AUG arrangement is conserved between humans and the mouse and is unique among the genes of the classical PTPs. Until now it was...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn391
更新日期:2008-08-01 00:00:00
abstract::Mutations in human mitochondrial DNA are often associated with incurable human neuromuscular diseases. Among these mutations, an important number have been identified in tRNA genes, including 29 in the gene MT-TL1 coding for the tRNA(Leu(UUR)). The m.3243A>G mutation was described as the major cause of the MELAS syndr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr546
更新日期:2011-10-01 00:00:00
abstract::Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz474
更新日期:2019-09-05 00:00:00
abstract::Ethionamide is an antituberculous drug for the treatment of multidrug-resistant Mycobacterium tuberculosis. This antibiotic requires activation by the monooxygenase EthA to exert its activity. Production of EthA is controlled by the transcriptional repressor EthR, a member of the TetR family. The sensitivity of M. tub...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1113
更新日期:2012-04-01 00:00:00
abstract::We previously reported the isolation of PRP28, a gene in Saccharomyces cerevisiae whose activity is required for the first step of nuclear mRNA splicing in vivo. Sequence analysis revealed that PRP28 is included in the 'DEAD-box' gene family, members of which are thought to function as ATP-dependent RNA helicases. Gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3187
更新日期:1994-08-11 00:00:00
abstract::The use of the ammonia deprotection step to introduce (15)N labels at specific exocyclic amino positions of adenine, cytosine, guanine or 2-aminopurine of oligodeoxynucleotides is described. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.2982
更新日期:1994-08-11 00:00:00
abstract::The gene for human apolipoprotein (apo) A-II has been isolated from a human genomic DNA library. The cloned fragment was approximately 14 kilobase-pair (kb) long, and extended about 9.0 kb upstream as well as 3.5 kb downstream from the apoA-II gene, which was contained within a 3.1 kb HindIII fragment of human DNA. Th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.12.4597
更新日期:1985-06-25 00:00:00
abstract::We previously constructed a multiribozyme expression vector by combining cis- and trans-acting ribozymes and we showed that several ribozymes, each directed against a different target in the HIV genome and acting independently in a 'shotgun' manner, markedly increased the efficiency of cleavage of HIV RNA in vitro [Oh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.23.5060
更新日期:1994-11-25 00:00:00
abstract::Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1053
更新日期:2015-01-01 00:00:00
abstract::Anisotropic motions of DNA fragments in the size range 6-118 base pairs are studied by the steady-state fluorescence polarization of different excitation transitions in the intercalated ethidium cation. Calculated effective tumbling and twisting times are found to be shorter than predicted for overall motions of rigid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.9.3945
更新日期:1986-05-12 00:00:00
abstract::Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1071
更新日期:2012-01-01 00:00:00
abstract::Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered liga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl176
更新日期:2006-04-28 00:00:00
abstract::DNA breaks occur during many processes in mammalian cells, including recombination, repair, mutagenesis and apoptosis. Here we report a simple and rapid method for assaying DNA breaks and identifying DNA breaksites. Breaksites are first tagged and amplified by ligation-mediated PCR (LM-PCR), using nested PCR primers t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.6.e33
更新日期:2001-03-15 00:00:00
abstract::Many, if not all, mRNAs in T.brucei start with the same sequence of 35 nucleotides, separately encoded in clustered so-called mini-exon repeats. From these mini-exon repeats a 141-nt precursor RNA with the 35-nt sequence at its 5' end is transcribed. Indirect evidence suggests that this RNA is linked in a second step ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.24.9457
更新日期:1984-12-21 00:00:00
abstract::Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the oc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3778
更新日期:1995-09-25 00:00:00
abstract::Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1023
更新日期:2017-01-09 00:00:00
abstract::The budding yeast Saccharomyces cerevisiae is proving to be an useful and accurate model for eukaryotic DNA replication. It contains both DNA polymerase alpha (I) and delta (III). Recently, proliferating cell nuclear antigen (PCNA), which in mammalian cells is an auxiliary subunit of DNA polymerase delta and is essent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.2.261
更新日期:1990-01-25 00:00:00