Many viruses bind multivalently to their target. The understanding of these binding processes can be beneficial for the development of effective treatments. Here we describe a protocol for measuring the oligovalent binding interaction of an influenza A virus X31 and a DNA nanostructure presenting one or several specifically designed binding peptides. The DNA nanostructure with its coupled binding peptides is complementary to the binding sites of the target protein hemagglutinin on the viral membrane. A detailed description of the sample preparation and the use of a DRX2 device to measure the interaction is given. The device allows for real-time measurement of the binding interaction without the necessity of labeling the virus or the peptide.