The side-chain and backbone dynamics of two model polyamines, polylysine (PL) and poly(allylamine) (PAM), were examined with time-resolved fluorescence anisotropy (TRFA) in aqueous solution and when the polyamines were entrapped into sol-gel derived silica. Both polyamines were ionically labeled with fluorescein, causing the rotational characteristics of the probe to be interconnected to the dynamics of the polyamine chain. TRFA studies of the probe-polyamine complex could be fit to two rotational components reflecting motions of the side chains (ps component) and short segments (its component), respectively. The rate and amplitude of these motions were reproducibly higher for PL than PAM, indicative of a higher conformational flexibility in PL relative to PAM. This result was supported by molecular mechanics optimizations, which showed a much larger variance in the distance between adjacent amino groups in PL relative to PAM, consistent with more degrees of freedom in the more dynamic polyamine. When entrapped into sodium silicate (SS)derived hydrogels, PL unexpectedly showed a high degree of segmental flexibility, while PAM experienced a significant damping of all detectable motions, accompanied by a large increase in the residual anisotropy. Since the random coil of PL can be considered as a model of flexible or denatured proteins with a high affinity toward the silica surface, we would expect the presence of segmental motions in such proteins when entrapped into a SS network, even if these are bound to the silica surface, in agreement with previous studies of such proteins entrapped in sol-gel glasses. On the other hand, PAM provides a useful model of more rigid proteins, such as antibodies, which show significant losses in dynamic motion upon entrapment in silica. The results show that the dynamics of proteins entrapped in silica materials must be viewed with caution, as it is possible to have significant dynamic motion even when proteins interact with the matrix.