Assay design considerations for use of affinity aptamer amplification in ultra-sensitive protein assays using capillary electrophoresis

Affinity probe capillary electrophoresis (APCE) holds promise to be a powerful tool in diagnostic applications that rely on the selective and sensitive detection of proteins. Aptamers can serve to unlock the full potential of the technology since their use opens up possibilities to unite the immuno-sensing and separating strength of capillary electrophoresis with the signal enhancement power of nucleic acid amplification. To enable routine use of aptamer APCE, careful selection of the experimental conditions is crucial. Here it is shown how customization and careful consideration of the experimental parameters can significantly improve assay performance.

[1]  J. Schrooten,et al.  Probing the osteoinductive effect of calcium phosphate by using an in vitro biomimetic model. , 2011, Tissue engineering. Part A.

[2]  M. Israel,et al.  A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. , 1979, The Journal of biological chemistry.

[3]  D. Whitcombe,et al.  The elimination of primer-dimer accumulation in PCR. , 1997, Nucleic acids research.

[4]  Il-Hyun Kim,et al.  An alternative to Western blot analysis using RNA aptamer-functionalized quantum dots. , 2010, Bioorganic & medicinal chemistry letters.

[5]  Christof M Niemeyer,et al.  Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification. , 2005, Trends in biotechnology.

[6]  Xiluan Yan,et al.  DNA aptamer folding on magnetic beads for sequential detection of adenosine and cocaine by substrate-resolved chemiluminescence technology. , 2010, The Analyst.

[7]  P. Doty,et al.  Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. , 1962, Journal of molecular biology.

[8]  D. Drolet,et al.  An enzyme-linked oligonucleotide assay , 1996, Nature Biotechnology.

[9]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[10]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Clive Brown,et al.  Toward clinical proteomics on a next-generation sequencing platform. , 2011, Analytical chemistry.

[13]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[14]  N. Sugimoto,et al.  Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. , 1996, Nucleic acids research.

[15]  C. Y. Lin,et al.  Primer Design Assistant (PDA): a web-based primer design tool , 2003, Nucleic Acids Res..

[16]  H. Schluesener,et al.  Systematic Evolution of a DNA Aptamer Binding to Rat Brain Tumor Microvessels , 2001, The Journal of Biological Chemistry.

[17]  J. Kinet,et al.  High-affinity oligonucleotide ligands to human IgE inhibit binding to Fc epsilon receptor I. , 1996, Journal of immunology.

[18]  Weihong Tan,et al.  Aptamer-based microfluidic device for enrichment, sorting, and detection of multiple cancer cells. , 2009, Analytical chemistry.

[19]  X Chris Le,et al.  Ultrasensitive detection of proteins by amplification of affinity aptamers. , 2006, Angewandte Chemie.

[20]  Francisco Melo,et al.  Comparison of different melting temperature calculation methods for short DNA sequences , 2005, Bioinform..

[21]  M. Bowser,et al.  In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis. , 2004, Analytical chemistry.

[22]  C. O’Sullivan.  Aptasensors – the future of biosensing? , 2002, Analytical and bioanalytical chemistry.

[23]  X Chris Le,et al.  Tunable aptamer capillary electrophoresis and its application to protein analysis. , 2008, Journal of the American Chemical Society.

[24]  Jeffrey B.-H. Tok,et al.  Massively Parallel Interrogation of Aptamer Sequence, Structure and Function , 2008, PloS one.