We have demonstrated that the aggregation of DNA-conjugated thermoresponsive polymer was inhibited by the formation of double strand DNA (dsDNA) from single strand DNA (ssDNA) by the change in the number of electric charges and hydrophilic states of DNA. The polymer was prepared by conjugation of short ssDNA with poly(N-isopropylacrylamide) (PNIPAM) and subsequent hybridization of the conjugated DNA with complementary DNA to form dsDNA. The ssDNA-conjugated PNIPAM highly aggregated with an increase in temperature, while the dsDNA-conjugated PNIPAM was inhibited from aggregation by the hybridization with fully matched complementary DNA and further prevented by hybridization with longer complementary DNA with a protruding sequence. Further characterizations suggest that the difference in the degree of aggregation between the ssDNA- and dsDNA-conjugated PNIPAM was mainly driven by the change in the number of electric charges associated with the conjugated DNA.