Thermodynamic design audit of a 17-mer DNA probe for EGFR T790M discrimination before immobilization on a carboxylated CNT–Fe3O4 nanocomposite

The 17-nucleotide DNA probe 5′-ATGAGCTGCATGATGAG-3′ was assessed for predicted discrimination of the EGFR T790M variant before immobilization on a carboxylated CNT–Fe 3 O 4 nanocomposite. Nearest-neighbor calculations were independently re-summed and compared across four published parameter sets. The fully matched T790M duplex was more stable than the wild-type A·C-mismatched duplex (ΔΔ G ° 37 = −3.86 to − 4.51 kcal mol −1 ; Δ T m = 6.81–9.29 °C across parameter sets). At 150 mM Na + , the corrected two-state model identified 53–55 °C as a candidate range for experimental testing. Sequence-level screening found no perfect 17-base transcriptome match but identified a 15-base contiguous off-target with predicted stability greater than the wild-type duplex. The calculations describe solution-phase sequence thermodynamics; they do not model the nanocomposite surface or establish assay performance. The results provide a testable basis for probe-condition optimization, while highlighting the need to evaluate the off-target experimentally and validate the immobilized assay.