Linked Life Data

13130135

Source:http://linkedlifedata.com/resource/pubmed/id/13130135

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
10
pubmed:dateCreated
2003-9-17
pubmed:abstractText
We previously isolated from random sequences ribozymes able to form a glycosidic linkage between a ribose sugar and 4-thiouracil in a reaction that mimics protein-catalyzed nucleotide synthesis. Here we report on two serial in vitro selection experiments that defined the core motif of one of the nucleotide synthase ribozymes and provided improved versions of this ribozyme. The first selection experiment started from a degenerate sequence pool based on the previously isolated sequence and used a selection-amplification protocol that allowed the sequence requirements at the 3' terminus of the ribozyme to be interrogated. Comparing the active sequences identified in this experiment revealed the complicated secondary structure of the nucleotide synthase ribozyme. A second selection was then performed to remove nonessential sequence from the ribozyme. This selection started with a pool with variation introduced in both the sequence and the length of the nonconserved loops and joining regions. This pool was generated using a partial reblocking/deblocking strategy on a DNA synthesizer, allowing the combinatorial synthesis of both point deletions and point substitutions. The consensus ribozyme motif that emerged was an approximately 71 nt pseudoknot structure with five stems and two important joining segments. Comparative sequence analysis and a cross-linking experiment point to the probable location of nucleotide synthesis. The prototype isolate from the second selection was nearly 35 times more efficient than the initial isolate and at least 10(8) times more efficient than an upper limit of an as-yet undetectable uncatalyzed reaction, supporting the idea that RNA-catalyzed nucleotide synthesis might have been important in an RNA world.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-10360365, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-1697402, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-1934059, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-2271660, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-3044450, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-3684574, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-3741845, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-7505429, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-7567476, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-7667099, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-8555167, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-9375255, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-9751052, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-9759501, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-9846125, http://linkedlifedata.com/resource/pubmed/commentcorrection/13130135-9868373
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Oct
pubmed:issn
1355-8382
pubmed:author
pubmed:issnType
Print
pubmed:volume
9
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1208-20
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2003
pubmed:articleTitle
Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme.
pubmed:affiliation
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't