The presence or absence and nature of the free patchy ends in DNA sequences has a decisive effect on the performance of colorimetric sensors based on the use of gold nanoparticles (Au NPs). The authors have designed two unmodified gene probes (probe 1: a 19-mer; probe 2: an 18-mer). They are complementary to either half of a 37-mer target derived from the conserved region of Hepatitis C Virus (HCV) RNA. Each probe has further been modified with 10-mer poly(A) and thiol-functionalized 10-mer poly(A) at the 5′ positions. Nine combinations of probe and HCV RNA were then designed to investigate the effect of free patchy ends on the stability of citrate-modified Au NPs against salt-induced aggregation which lead to color change from red to blue. The aggregation of Au NPs can be monitored by ratiometric spectroscopy at wavelengths of 520 and 700 nm. The differentiation between HCV RNA and control has also been studied by varying the concentration of probe and analyte. The particle size and zeta potentials were determined before and after aggregation. It is demonstrated that the change in surface charge density of the Au NPs governs the critical coagulation concentration of NaCl. The method presented here can be used to quantify HCV RNA in the 370 nM to 3 μM concentration range, and the detection limit is 500 nM. The results obtained with Au NPs that are chemically non-conjugated with the oligonucleotides have been found to be valuable in rationally devising the design rules for rapid and efficient colorimetric sensing of oligonucleotides. Graphical abstractSchematic representation of the nine combinatorial pairs of oligonucleotides that vary in the length of patchy ends and their position to unearth their effect in rapid gold nanoparticle-based colorimetric gene sensing without time-consuming and expensive thiol-conjugation step.