The use of gold nanoparticles for the colorimetric detection of single nucleotide mutations associated with cancer in liquid biopsies is a promising strategy for early cancer diagnosis. To realize this technology, the sensor must discriminate mutations in double stranded dsDNA with an average length of ∼140 bp. Here, we compared ssDNA and dsDNA of differing lengths (70 and 140 bp) and the effect of chemical modifications (2′-OMe vs 2′-F) on the DNA probe sequence stabilizing gold nanoparticles of either 25 or 53 nm. We confirmed that the performance of the single nucleotide polymorphism (SNP) detection decreases with both the increase of the length of the sequences and the incorporation of dsDNA architecture. We found that for the larger particles the sensitivity of the assay increases, while the selectivity is better for smaller particles. Finally, the presence of 2′-F modification improves the detection of SNP in ssDNA, while 2′-OMe modification is better for SNP detection in dsDNA.