Novel probes for label-free detection of neurodegenerative GGGGCC repeats associated with amyotrophic lateral sclerosis

• Published in: Analytical and bioanalytical chemistry 2019-10, Vol.411 (26), p.6995-7003
• Main Authors: Taki, Motahareh, Rohilla, Kushal J., Barton, Maria, Funneman, Madison, Benzabeh, Najiyah, Naphade, Swati, Ellerby, Lisa M., Gagnon, Keith T., Shamsi, Mohtashim H.
• Format: Article
• Language: English
• Subjects: Amyotrophic lateral sclerosis; Amyotrophic Lateral Sclerosis - genetics; Analytical Chemistry; Base Sequence; Biochemistry; Biosensing Techniques - methods; Characterization and Evaluation of Materials; Charge transfer; Chemistry; Chemistry and Materials Science; Dementia disorders; Density; Deoxyribonucleic acid; Dielectric Spectroscopy - methods; Disease control; DNA; DNA probes; DNA Repeat Expansion; Electric properties; Electrochemical impedance spectroscopy; Electrochemistry; Enzymes; Ethylenediaminetetraacetic acid; Food Science; Frontotemporal dementia; Gene sequencing; Humans; Huntington Disease - genetics; Impedance; Laboratory Medicine; Monitoring/Environmental Analysis; Nervous system diseases; Neurological diseases; Nucleotide sequence; Oligonucleotide Probes - genetics; Oligonucleotides; Polyglutamine; Probes; Research Paper; RNA - genetics; Sensitivity; Spectroscopy; Strands; Target detection; Trinucleotide repeat diseases; Trinucleotide repeats
• ISSN: 1618-2642; 1618-2650
• DOI: 10.1007/s00216-019-02075-8

DNA repeat expansion sequences cause a myriad of neurological diseases when they expand beyond a critical threshold. Previous electrochemical approaches focused on the detection of trinucleotide repeats (CAG, CGG, and GAA) and relied on labeling of the probe and/or target strands or enzyme-linked assays. However, detection of expanded GC-rich sequences is challenging because they are prone to forming secondary structures such as cruciforms and quadruplexes. Here, we present label-free detection of hexanucleotide GGGGCC repeat sequences, which cause the leading genetic form of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). The approach relies on capturing targets by surface-bound oligonucleotide probes with a different number of complementary repeats, which proportionately translates the length of the target strands into charge transfer resistance (R CT ) signal measured by electrochemical impedance spectroscopy. The probe carrying three tandem repeats transduces the number of repeats into R CT with a 3× higher calibration sensitivity and detection limit. Chronocoulometric measurements show a decrease in surface density with increasing repeat length, which is opposite of the impedance trend. This implies that the length of the target itself can contribute to amplification of the impedance signal independent of the surface density. Moreover, the probe can distinguish between a control and patient sequences while remaining insensitive to non-specific Huntington’s disease (CAG) repeats in the presence of a complementary target. This label-free strategy might be applied to detect the length of other neurodegenerative repeat sequences using short probes with a few complementary repeats. Graphical abstract Short oligomeric probes with multiple complementary repeats detect long neurodegenerative targets with high sensitivity and transduce into higher impedance signal.