Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes

Ulhas S. Kadam; Burkhard Schulz; Joseph Lrudayaraj

doi:10.1016/j.febslet.2014.02.061

Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes

Ulhas S. Kadam, Burkhard Schulz, Joseph Lrudayaraj

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

Abstract

Alternative splicing (AS) increases the size of the transcriptome and proteome to enhance the physiological capacity of cells. We demonstrate surface enhanced Raman spectroscopy (SERS) in combination with a DNA hybridization analytical platform to identify and quantify AS genes in plants. AS in AtDCL2 and AtPTB2 were investigated using non-fluorescent Raman probes using a 'sandwich assay'. Utilizing Raman probes conjugated to gold nanoparticles we demonstrate the recognition of RNA sequences specific to AtDCL2 and AtPTB2 splice junction variants with detection sensitivity of up to 0.1 fM.

Original language	English (US)
Pages (from-to)	1637-1643
Number of pages	7
Journal	FEBS Letters
Volume	588
Issue number	9
DOIs	https://doi.org/10.1016/j.febslet.2014.02.061
State	Published - May 2 2014
Externally published	Yes

Keywords

Alternative splicing
Arabidopsis thaliana
Gold-nanoprobe
Raman spectroscopy
mRNA

ASJC Scopus subject areas

Biophysics
Structural Biology
Biochemistry
Molecular Biology
Genetics
Cell Biology

Online availability

10.1016/j.febslet.2014.02.061

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title = "Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes",

abstract = "Alternative splicing (AS) increases the size of the transcriptome and proteome to enhance the physiological capacity of cells. We demonstrate surface enhanced Raman spectroscopy (SERS) in combination with a DNA hybridization analytical platform to identify and quantify AS genes in plants. AS in AtDCL2 and AtPTB2 were investigated using non-fluorescent Raman probes using a 'sandwich assay'. Utilizing Raman probes conjugated to gold nanoparticles we demonstrate the recognition of RNA sequences specific to AtDCL2 and AtPTB2 splice junction variants with detection sensitivity of up to 0.1 fM.",

keywords = "Alternative splicing, Arabidopsis thaliana, Gold-nanoprobe, Raman spectroscopy, mRNA",

author = "Kadam, {Ulhas S.} and Burkhard Schulz and Joseph Lrudayaraj",

note = "Funding Information: Authors gratefully acknowledge the funding from NSF-EAGER DBI-0939906 Award to B.S. and J.l. The Bilsland Dissertation Fellowship was awarded to UK from Purdue University. We thank Rosanne Altstatt for copy-editing. ",

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doi = "10.1016/j.febslet.2014.02.061",

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AU - Kadam, Ulhas S.

AU - Schulz, Burkhard

AU - Lrudayaraj, Joseph

N1 - Funding Information: Authors gratefully acknowledge the funding from NSF-EAGER DBI-0939906 Award to B.S. and J.l. The Bilsland Dissertation Fellowship was awarded to UK from Purdue University. We thank Rosanne Altstatt for copy-editing.

PY - 2014/5/2

Y1 - 2014/5/2

N2 - Alternative splicing (AS) increases the size of the transcriptome and proteome to enhance the physiological capacity of cells. We demonstrate surface enhanced Raman spectroscopy (SERS) in combination with a DNA hybridization analytical platform to identify and quantify AS genes in plants. AS in AtDCL2 and AtPTB2 were investigated using non-fluorescent Raman probes using a 'sandwich assay'. Utilizing Raman probes conjugated to gold nanoparticles we demonstrate the recognition of RNA sequences specific to AtDCL2 and AtPTB2 splice junction variants with detection sensitivity of up to 0.1 fM.

AB - Alternative splicing (AS) increases the size of the transcriptome and proteome to enhance the physiological capacity of cells. We demonstrate surface enhanced Raman spectroscopy (SERS) in combination with a DNA hybridization analytical platform to identify and quantify AS genes in plants. AS in AtDCL2 and AtPTB2 were investigated using non-fluorescent Raman probes using a 'sandwich assay'. Utilizing Raman probes conjugated to gold nanoparticles we demonstrate the recognition of RNA sequences specific to AtDCL2 and AtPTB2 splice junction variants with detection sensitivity of up to 0.1 fM.

KW - Alternative splicing

KW - Arabidopsis thaliana

KW - Gold-nanoprobe

KW - Raman spectroscopy

KW - mRNA

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Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes

Abstract

Keywords

ASJC Scopus subject areas

Online availability

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