The development of highly sensitive fluorescence molecular probes in combination with innovative optical techniques plays a pivotal role in the advancement of non-invasive optical imaging of human pathologic conditions. Fluorochromes attached to various ligands have been used for detection of nucleic acid hybridization, in drug discovery, detection of molecular interactions, and for deciphering biological pathways. To advance this technique to an application that could be relevant to clinical study requires the development of near-infrared (NIR) fluorescent dyes since imaging in this range of wavelength (700-900 nm) allows light to penetrate several centimeters into the tissue and reducing the interference from biological background. In addition, the wavelength of NIR optical probes lies in the oscillation wavelength of a semiconductor laser. Therefore, it is suitable for imaging using laser beam as a source of light. We describe herein the design and synthesis of specific peptide-based fluorescence beacons for detection of cancer. Besides the NIR feature, the dyes possess some other important properties for biological application such as stability in an array of chemical milieu, water solubility, good quantum yield, and a handle for bioconjugation. In order to increase the selectivity during bioconjugation, the cyclic polymethine cyanine dyes were developed using different approaches. The stability of these dyes was demonstrated by labeling a peptide epitope via solid phase peptide chemistry. The in vivo optical imaging showed potential and broad application of these dyes in developing molecular-based beacons for cancer detection.