A method of detecting nucleic acids with an amplified signal utilizes first and second amplification nanoparticles. The method includes hybridizing a first segment and a second segment of a target sequence with a first capture probe on capture particles and a second capture probe on first amplification nanoparticles, respectively, and forming a capture particle-target-first amplification nanoparticle complex; adding second amplification nanoparticles and hybridizing the second linker probes on second amplification nanoparticles with first linker probes on the first amplification nanoparticles in the complex, wherein a ratio of the first linker probes to the second capture probes on first amplification particles is from about 1:1 to 50:1; hybridizing reporter probes with third linker probes on the second amplification nanoparticles, wherein a ratio of the third linker probes to the second linker probes on the second amplification particles is from about 3:1 to 20:1; and detecting signals from the reporter probes.