i made one nanorod with AuNR@CuS composition. I use layer-by-layer method to coat SDS and chitosan oligosaccharide sequentially on the surface of nanoparticles. After doing the DLS measurement, i found the nanoparticle have hydrodynamic size at ~135nm, and zeta potential near 39.0mV. But in the electrophoresis experiment, no siRNA binding. Can anyone explain the possible reason for me?
I'm not familiar with the exact system you are making but one thing comes to mind:
SDS typically gives you a negative zeta potential and the NH2 groups of the chitosan will generally be positive. But this depends on the pH so the overall zeta potential of your particles is likely to be influenced strongly by the pH. So, what pH are you measuring the zeta potential at and what are the pH conditions of your electrophoresis experiment (I assume you are referring to gel electrophoresis)?
I'm not familiar with the exact system you are making but one thing comes to mind:
SDS typically gives you a negative zeta potential and the NH2 groups of the chitosan will generally be positive. But this depends on the pH so the overall zeta potential of your particles is likely to be influenced strongly by the pH. So, what pH are you measuring the zeta potential at and what are the pH conditions of your electrophoresis experiment (I assume you are referring to gel electrophoresis)?
Salt concentration or conductivity can affect zeta potential (masking surface charge of either nanorods or RNA). Lack of surface charge on either of the solutes at high salt conc. can also explain no binding.
Zeta potential is relative to pH. You need to mantain your system in an adequate pH in order to bind and to evaluate siRNA binding. Moreover, maybe you need to vary your concentration of siRNA or actual positive charges to perform interaction. Maybe they are to far from each other and they do not interact with the polyanion. Have you calculated encapsulation efficiency directly?
How exactly did you perform the gel electrophoresis experiment? Did you try some kind of nucleic acid dose titration? Maybe the overall nucleic acid binding capacity of your nanoparticle is rather low under your experimental conditions and you are using too much nucleic acid to actually see a change in band intensity on the gel. I am also wondering, did you use a buffered system to determine the zeta in order to exclude pH effects?
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