BDB -BiopanningDataSet Details

Biopanning Data

BiopanningDataSet ID: 1663

Peptides:

Sequences

GCGSCPVCHGYPC(1)
GCGGTEGHIGRGC(1)
GCCWTAAMAGTSC(1)
KCSRGIRCAGVLC(15)
KCSRGIRCAGVRC(1)
KCSRGIRCAGVLX(1)
GCTACDRMYLVCC(1)
GCRVCNRMEGVLC(1)
GCLYLWRQGGLAC(1)
RCIDHQYSWLCYC(1)
ECGCSHPVFLCYC(1)
RCWESYVDHLDLC(1)
GCQSYGPGDLCLC(1)
GCVGYSRIGLSVC(1)
GCWISISACFKSC(1)
GCVYSRLKVFADC(1)
GCWVEMRGSWKRC(1)
GCWGCMLSPEFRC(1)
ECIASSGRAGGVC(1)
GCRAASSVSWMWC(1)
KCKKPGSARWSKC(1)
RCNKSLIAIRYDC(1)
ECGYRKIARMVMC(1)
RCPSEGYHRRTGC(1)
ECCQSGRPRDGGC(1)
GCSGVGAARTWGC(1)
GCTFGTQPRHWCC(1)
ECHVTQHPYSRAC(1)
KCKGFVGFFSRAC(1)
ECTDCYLALSSYC(1)
ECRRCFAELSYAC(1)
ECLCYSYAGSCRC(1)
KCTLFKAAGGPFC(1)
RYGSFDDMSCGEC(1)
GCYDRMPGGTHSC(1)
GCGLGRARTDVAC(1)
RCEGCVHYMGLSC(1)
GCDRWSAGCVVC(1)
RCAFCDFLTRXLC(1)

Sequences Features:

Motif:

Unique Sequence Number:

Experimental Method:

mRNA display (competitive panning)

Sequencing Platform:

Sequencing Method:

Sanger sequencing

Rounds of Panning:

Reference:

PMID: 18824687

Target Name:

Internal ribosomal entry site, IRES

Template Name:

Not determined.

Structure of Target-Template Complex:

Not determined.

Structure of Target-Peptide Complex:

Not determined.

Library Name:

[RKEDG]-C-X(10)-C mRNA display library

Affinity Measurement Method:

Affinity Measurement Description:

Brief Description:

Rounds 1 and 2 were designed to decrease the complexity of the starting library while retaining all possible IRES binders. During these rounds Torula yeast RNA (TYR) was used as a binding competitor, and all column matrix bound material was eluted nonspecifically with NaOH and 8 M urea. Rounds 3-7 were designed to select more specifically for IRES binders by eluting column bound mRNA-peptide fusions competitively with soluble IRES. Following seven rounds of selection, ≈50% of the input library was eluted from IRES column with soluble IRES RNA in 2 h. Authors then further increased the stringency of the selection by using additional selection steps in rounds 8-11, aimed at the selection of peptides with slower dissociation rates, and improved IRES selectivity.

BiopanningDataSet Comments:

Cloning and sequencing of the library after round 11 revealed that the sequence 6B4, encoding the peptide MKCSRGIRCAGVLCGSVGHHHHHHHRL, accounted for >30% of the clones. The best peptide binds the IRES with subnanomolar affinity, and a specificity of at least 100-fold relative to binding to several other RNAs of similar length. The peptide specifically inhibits HCV IRES-initiated translation in vitro with no detectable effect on normal cap-dependent translation initiation.

Curator:

Curation Date:

0000-00-00

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