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.
authors.affiliation: Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States; Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, United States; Bindley Bioscience Center at Discovery Park, West Lafayette, IN 47907, United States.
authors.forename: Ulhas S
authors.initials: US
authors.lastname: Kadam
authors.affiliation: Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, United States.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Schulz
authors.affiliation: Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States; Bindley Bioscience Center at Discovery Park, West Lafayette, IN 47907, United States. Electronic address: josephi@purdue.edu.
authors.forename: Joseph
authors.initials: J
authors.lastname: Irudayaraj
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000235:genetics* / Q000378:metabolism; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics; D006046:Gold / Q000737:chemistry; D057230:Limit of Detection; D053768:Metal Nanoparticles / Q000737:chemistry; D009693:Nucleic Acid Hybridization; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D013059:Spectrum Analysis, Raman
chemical_list: D029681:Arabidopsis Proteins; D018797:Cell Cycle Proteins; D015342:DNA Probes; D004277:DNA, Single-Stranded; D020033:Protein Isoforms; D022821:RNA Splice Sites; D012333:RNA, Messenger; D018749:RNA, Plant; D006046:Gold; C511919:DCL2 protein, Arabidopsis; D043244:Ribonuclease III
keywords: Alternative splicing; Arabidopsis thaliana; Gold-nanoprobe; Raman spectroscopy; mRNA