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We report a gold-nanoparticle-based miniaturized, inexpensive and battery-operated ultra-sensitive fluorescence resonance energy transfer (FRET) probe for screening biological agents DNA at the femtomolar level. We demonstrate a hybridization detection method using multicolor oligonucleotide-functionalized organic dyes and gold nanoparticles as nanoprobes. In the presence of various target sequences, detection of sequence-specific DNA is possible via an independent hybridization process. As proof of concept, multiplexed detection of two target sequences, (1) oligonucleotide sequence associated with the anthrax lethal factor and (2) sequence related to positions 1027-1057 of the E. coli 23S rDNA, have been demonstrated with high sensitivity and specificity. The quenching efficiency as a function of distance is investigated. The mechanism of distant dependence fluorescence quenching has been discussed. [ABSTRACT FROM AUTHOR]