Abstract:
:Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with selection of the target phenotype. The model population is composed of 857 DNAzyme clones representing 215 discrete sequence classes, which had previously been identified from two parallel selection experiments, conducted under an increasingly stringent, or permissive and constant selection time pressure. In this report, we determined the principal phenotypic properties (i.e. k(obs), maximum cleavage yield and PCR efficiency) from a sample of 58 clones representing 46 different major and minor sequence classes from various rounds of each selection experiment. Interestingly, a positive correlation between the catalytic rate constant and the corresponding frequency and temporal position of a given DNAzyme was not consistently observed; however, the strength of the correlation was qualitatively higher under conditions of more stringent selection time pressure. These results suggest that the selective sampling paradigm on which in vitro selection is based, may underestimate the true functional capacity of any given random-sequence library.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schlosser K,Lam JC,Li Ydoi
10.1093/nar/gkp222subject
Has Abstractpub_date
2009-06-01 00:00:00pages
3545-57issue
11eissn
0305-1048issn
1362-4962pii
gkp222journal_volume
37pub_type
杂志文章abstract::The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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更新日期:2016-07-27 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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更新日期:2017-05-05 00:00:00
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journal_title:Nucleic acids research
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更新日期:2008-04-01 00:00:00
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journal_title:Nucleic acids research
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doi:10.1093/nar/8.17.3757
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abstract::By subtractive screening of a library made from mRNA of lipopolysaccharide (LPS)-stimulated mouse B lymphocytes we isolated cDNA-clones encoding the ribosomal protein L7. Human L7 mRNA was cloned from activated T-lymphocytes. Although no specific function of L7 in the translation apparatus is known as yet, it should b...
journal_title:Nucleic acids research
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更新日期:1993-01-25 00:00:00
abstract::We have compared the properties of the poly(rA).oligo(dT) complex with those of the poly(rU).oligo(dA)n complex. Three main differences were found. First, poly(rA) and oligo(dT)n do not form a complex in concentrations of CsCl exceeding 2 M because the poly(rA) is insoluble in high salt. If the complex is made in low ...
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更新日期:1976-04-01 00:00:00
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journal_title:Nucleic acids research
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doi:10.1093/nar/gkz419
更新日期:2019-07-09 00:00:00
abstract::Reverse gyrase is a peculiar DNA topoisomerase, specific of hyperthermophilic Archaea and Bacteria, which has the unique ability of introducing positive supercoiling into DNA molecules. Although the function of the enzyme has not been established directly, it has been suggested to be involved in DNA protection and rep...
journal_title:Nucleic acids research
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更新日期:2006-04-14 00:00:00
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journal_title:Nucleic acids research
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更新日期:1987-06-25 00:00:00
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journal_title:Nucleic acids research
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更新日期:1990-03-25 00:00:00
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journal_title:Nucleic acids research
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doi:
更新日期:1990-08-25 00:00:00
abstract::To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated i...
journal_title:Nucleic acids research
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更新日期:2016-12-15 00:00:00
abstract::Gap closure is a challenging phase in microbial random shotgun genome sequencing projects, particularly since genome assemblies are often complicated by the presence of repeat elements, insertion sequences and other similar factors that contribute to sequence misassemblies. While it is well recognized that the conserv...
journal_title:Nucleic acids research
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更新日期:2003-09-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1984-03-12 00:00:00
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journal_title:Nucleic acids research
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更新日期:2010-08-01 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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doi:10.1093/nar/15.8.3385
更新日期:1987-04-24 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...
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pub_type: 历史文章,杂志文章
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更新日期:2000-06-15 00:00:00