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We present a promising approach for the label-free characterization of genetic material. Time-resolved terahertz (THz) transmission analysis of polynucleotides demonstrate a strong dependence of the complex refractive index on the binding state (hybridized/denatured) of deoxyribonucleic acid (DNA) molecules. By monitoring THz transients, one can thus infer the binding state of oligo- and polynucleotides, and hence identify polynucleotides by detecting the binding of unknown polynucleotide DNA sequences to known probe molecules. A broadband experimental demonstration in a free-space configuration, as well as a discussion of the potential application for next generation gene chips is presented. © 2000 American Institute of Physics.