Identification of proteins bound to a thioaptamer probe on a proteomics array

He Wang; Xianbin Yang; Gavin C. Bowick; Norbert K. Herzog; Bruce A. Luxon; Lee O. Lomas; David G. Gorenstein

doi:10.1016/j.bbrc.2006.06.132

Identification of proteins bound to a thioaptamer probe on a proteomics array

He Wang, Xianbin Yang, Gavin C. Bowick, Norbert K. Herzog, Bruce A. Luxon, Lee O. Lomas, David G. Gorenstein

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

A rapid method to screen and identify unknown bound proteins to specific nucleic acid probes anchored on ProteinChip array surfaces from crude biological samples has been developed in this paper. It was demonstrated with screening specific binding proteins from LPS-stimulated mouse 70Z/3 pre-B cell nuclear extracts by direct coupling of thioaptamer XBY-S2 to the pre-activated ProteinChip array surfaces. With pre-fractionation of crude nuclear extracts by ion exchange method, specific "on-chip" captured proteins have been obtained that were pure enough to do "on-chip" digestion and the subsequent identification of the "on-chip" bound proteins by microsequencing of the trypsin digested peptide fragments through tandem MS. Five mouse heterogeneous nuclear ribonucleoproteins (hnRNPs) A1, A2/B1, A3, A/B, and D0 were identified. To verify those bound hnRNPs, a novel thioaptamer/antibody sandwich assay provides highly sensitive and selective identification of proteins on ProteinChip arrays.

Original language	English (US)
Pages (from-to)	586-593
Number of pages	8
Journal	Biochemical and Biophysical Research Communications
Volume	347
Issue number	3
DOIs	https://doi.org/10.1016/j.bbrc.2006.06.132
State	Published - Sep 1 2006
Externally published	Yes

Keywords

Aptamer array
DNA-binding
Fractionation
Proteomics
SELDI-TOF-MS
Sandwich assay
Thioaptamer
Transcription factor AP-1
hnRNPs

ASJC Scopus subject areas

Biophysics
Biochemistry
Molecular Biology
Cell Biology

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10.1016/j.bbrc.2006.06.132

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title = "Identification of proteins bound to a thioaptamer probe on a proteomics array",

abstract = "A rapid method to screen and identify unknown bound proteins to specific nucleic acid probes anchored on ProteinChip array surfaces from crude biological samples has been developed in this paper. It was demonstrated with screening specific binding proteins from LPS-stimulated mouse 70Z/3 pre-B cell nuclear extracts by direct coupling of thioaptamer XBY-S2 to the pre-activated ProteinChip array surfaces. With pre-fractionation of crude nuclear extracts by ion exchange method, specific {"}on-chip{"} captured proteins have been obtained that were pure enough to do {"}on-chip{"} digestion and the subsequent identification of the {"}on-chip{"} bound proteins by microsequencing of the trypsin digested peptide fragments through tandem MS. Five mouse heterogeneous nuclear ribonucleoproteins (hnRNPs) A1, A2/B1, A3, A/B, and D0 were identified. To verify those bound hnRNPs, a novel thioaptamer/antibody sandwich assay provides highly sensitive and selective identification of proteins on ProteinChip arrays.",

keywords = "Aptamer array, DNA-binding, Fractionation, Proteomics, SELDI-TOF-MS, Sandwich assay, Thioaptamer, Transcription factor AP-1, hnRNPs",

author = "He Wang and Xianbin Yang and Bowick, {Gavin C.} and Herzog, {Norbert K.} and Luxon, {Bruce A.} and Lomas, {Lee O.} and Gorenstein, {David G.}",

note = "Funding Information: This research was supported by DARPA (P42296LS0000), NIH (AI27744, U01 A1054827, IP30 ES06676, N01-HV-28184), DoD (DADD13-02-C-007, DAAD19011037 and DAAD17-01-D-0001), the Welch Foundation (H-1296), and the State of Texas Advanced Technology Program (004952-0038-2003). He Wang is thankful to Tu Duc Ngo for providing PU ProteinChip arrays at Ciphergen and to Barry Elsom for providing stimulated 70Z/3 nuclear extracts from UTMB. We are also grateful to Amin Mohammad at UTMB and to TuAnh T. Dang, from Ciphergen, for their advice and assistance.",

year = "2006",

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doi = "10.1016/j.bbrc.2006.06.132",

language = "English (US)",

volume = "347",

pages = "586--593",

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T1 - Identification of proteins bound to a thioaptamer probe on a proteomics array

AU - Wang, He

AU - Yang, Xianbin

AU - Bowick, Gavin C.

AU - Herzog, Norbert K.

AU - Luxon, Bruce A.

AU - Lomas, Lee O.

AU - Gorenstein, David G.

N1 - Funding Information: This research was supported by DARPA (P42296LS0000), NIH (AI27744, U01 A1054827, IP30 ES06676, N01-HV-28184), DoD (DADD13-02-C-007, DAAD19011037 and DAAD17-01-D-0001), the Welch Foundation (H-1296), and the State of Texas Advanced Technology Program (004952-0038-2003). He Wang is thankful to Tu Duc Ngo for providing PU ProteinChip arrays at Ciphergen and to Barry Elsom for providing stimulated 70Z/3 nuclear extracts from UTMB. We are also grateful to Amin Mohammad at UTMB and to TuAnh T. Dang, from Ciphergen, for their advice and assistance.

PY - 2006/9/1

Y1 - 2006/9/1

N2 - A rapid method to screen and identify unknown bound proteins to specific nucleic acid probes anchored on ProteinChip array surfaces from crude biological samples has been developed in this paper. It was demonstrated with screening specific binding proteins from LPS-stimulated mouse 70Z/3 pre-B cell nuclear extracts by direct coupling of thioaptamer XBY-S2 to the pre-activated ProteinChip array surfaces. With pre-fractionation of crude nuclear extracts by ion exchange method, specific "on-chip" captured proteins have been obtained that were pure enough to do "on-chip" digestion and the subsequent identification of the "on-chip" bound proteins by microsequencing of the trypsin digested peptide fragments through tandem MS. Five mouse heterogeneous nuclear ribonucleoproteins (hnRNPs) A1, A2/B1, A3, A/B, and D0 were identified. To verify those bound hnRNPs, a novel thioaptamer/antibody sandwich assay provides highly sensitive and selective identification of proteins on ProteinChip arrays.

AB - A rapid method to screen and identify unknown bound proteins to specific nucleic acid probes anchored on ProteinChip array surfaces from crude biological samples has been developed in this paper. It was demonstrated with screening specific binding proteins from LPS-stimulated mouse 70Z/3 pre-B cell nuclear extracts by direct coupling of thioaptamer XBY-S2 to the pre-activated ProteinChip array surfaces. With pre-fractionation of crude nuclear extracts by ion exchange method, specific "on-chip" captured proteins have been obtained that were pure enough to do "on-chip" digestion and the subsequent identification of the "on-chip" bound proteins by microsequencing of the trypsin digested peptide fragments through tandem MS. Five mouse heterogeneous nuclear ribonucleoproteins (hnRNPs) A1, A2/B1, A3, A/B, and D0 were identified. To verify those bound hnRNPs, a novel thioaptamer/antibody sandwich assay provides highly sensitive and selective identification of proteins on ProteinChip arrays.

KW - Aptamer array

KW - DNA-binding

KW - Fractionation

KW - Proteomics

KW - SELDI-TOF-MS

KW - Sandwich assay

KW - Thioaptamer

KW - Transcription factor AP-1

KW - hnRNPs

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U2 - 10.1016/j.bbrc.2006.06.132

DO - 10.1016/j.bbrc.2006.06.132

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AN - SCOPUS:33746214654

SN - 0006-291X

VL - 347

SP - 586

EP - 593

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

IS - 3

ER -

Identification of proteins bound to a thioaptamer probe on a proteomics array

Abstract

Keywords

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