Abstract：
:During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive DNA replication. We determine the main kinetic parameters of the nucleotide incorporation cycle and their dependence on external load and nucleotide (dNTP) concentration. The data is inconsistent with power stroke models for translocation, instead supports a loose-coupling mechanism between chemical catalysis and mechanical translocation during DNA replication. According to this mechanism the DNA polymerase works by alternating between a dNTP/PPi-free state, which diffuses thermally between pre- and post-translocated states, and a dNTP/PPi-bound state where dNTP binding stabilizes the post-translocated state. We show how this thermal ratchet mechanism is used by the polymerase to generate work against large opposing loads (∼50 pN).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Morin JA,Cao FJ,Lázaro JM,Arias-Gonzalez JR,Valpuesta JM,Carrascosa JL,Salas M,Ibarra Bdoi
10.1093/nar/gkv204subject
Has Abstractpub_date
2015-04-20 00:00:00pages
3643-52issue
7eissn
0305-1048issn
1362-4962pii
gkv204journal_volume
43pub_type
杂志文章abstract：:Yeast uses nucleotide excision repair (NER) and photolyase (photoreactivation) to repair cyclobutane pyrimidine dimers (CPDs) generated by ultraviolet light. In active genes, NER preferentially repairs the transcribed strand (TS). In contrast, we recently showed that photolyase preferentially repairs the non-transcrib...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.19.3795
更新日期：1997-10-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2014-02-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2012-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku453
更新日期：2014-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.3.373
更新日期：1975-03-01 00:00:00
abstract：:We report the use of MonoQ FPLC (Fast Protein Liquid Chromatography) for the rapid purification of a novel Type II restriction endonuclease PmaCI, from Pseudomonas maltophila, which recognises the sequence 5'-CAC decreases GTG-3'. The resulting enzyme is free of other nucleases to a level suitable for its characterisa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.3.1293
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abstract：:The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1995-06-25 00:00:00
abstract：:Chromatin modulation at various cis-acting elements is critical for V(D)J recombination during T and B cell development. MARbeta, a matrix-associated region (MAR) located upstream of the T cell receptor beta (TCRbeta) enhancer (Ebeta), serves a crucial role in silencing Ebeta-mediated TCR activation. By DNaseI hyperse...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh807
更新日期：2004-09-15 00:00:00
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doi：10.1093/nar/gkx804
更新日期：2017-11-16 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq667
更新日期：2010-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.16.6711
更新日期：1986-08-26 00:00:00
abstract：:Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (posi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq341
更新日期：2010-09-01 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
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abstract：:The multiprotein complexes involved in active dis-ruption of chromatin structure, homologous to yeast SWI/SNF complex, have been described for human and Drosophila cells. In all SWI/SNF-class complexes characterised so far, one of the key components is the SNF5-type protein. Here we describe the isolation of a plant (...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.11.2393
更新日期：1999-06-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa417
更新日期：2020-07-09 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku432
更新日期：2014-07-01 00:00:00
abstract：:Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa826
更新日期：2020-11-04 00:00:00
abstract：:The availability of the complete sequence of the Saccharomyces cerevisiae genome has allowed a comprehensive analysis of the genes encoding cytoplasmic ribosomal proteins in this organism. On the basis of this complete inventory a new nomenclature for the yeast ribosomal proteins is presented. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.24.4872
更新日期：1997-12-15 00:00:00
abstract：:Chicken erythrocyte inner histones (H2A, H2B, H3 and H4) were associated with the two complementary homopolymeric polydeoxyribonucleotides and the two alternating copolymeric polydeoxyribonucleotides. No evidence for formation of chromatin-like structures was obtained for the complexes with poly(dG) . poly(dC) or poly...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.4.1387
更新日期：1979-04-01 00:00:00
abstract：:Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkn412
更新日期：2008-08-01 00:00:00
abstract：:In Xenopus oocytes, progesterone stimulates the cytoplasmic polyadenylation and resulting translational activation of c-mos mRNA, which is necessary for the induction of oocyte maturation. Although details of the biochemistry of polyadenylation are beginning to emerge, the mechanism by which 3' poly(A) addition stimul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.13.3208
更新日期：1998-07-01 00:00:00
abstract：:Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.21.4969
更新日期：1980-11-11 00:00:00
abstract：:Thiol-activated neocarzinostatin chromophore abstracts tritium from the 5', but not from the 1' or 2' positions of deoxyribose in DNA and incorporates it into a stable, non-exchangeable form. The abstracted tritium remains covalently associated with the chromophore or its degradation product after treatment with acid ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.5.1637
更新日期：1985-03-11 00:00:00
abstract：:Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.11.3855
更新日期：1977-11-01 00:00:00
abstract：:Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1's function has remaine...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt082
更新日期：2013-04-01 00:00:00
abstract：:Two CTAG-recognizing restriction and modification (R/M) systems, designated MthZI and MthFI, were identified in the thermophilic archaeon Methanobacterium thermoformicicum strains Z-245 and FTF, respectively. Further analysis revealed that the methyltransferase (MTase) genes are plasmid-located in both strains. The pl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.19.5047
更新日期：1992-10-11 00:00:00
abstract：:In the haploid genome of Xenopus laevis there are two genes coding for the r-protein L14. It is not known if they are located on the same chromosome. cDNA clones deriving from the transcripts of the two genes have been isolated from an oocyte messenger cDNA bank showing that they are both expressed. We have studied th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.19.7633
更新日期：1986-10-10 00:00:00
abstract：:The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.17.4239
更新日期：1981-09-11 00:00:00
abstract：:The TGGCA protein, the chicken homologue of HeLa cell NF-I, was purified to homogeneity from liver tissue by a procedure which includes preparative mobility shift electrophoresis (PMSE) as the final step. PMSE was here adjusted for the isolation of the TGGCA protein, but can be used as a general method to characterize...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.23.9707
更新日期：1987-12-10 00:00:00
abstract：:ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from a green alga and the atpF gene product from Bradyrhizobium, that ymf39 might code for subunit b of mitochondrial F(0)F(...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg326
更新日期：2003-05-01 00:00:00
