An alternative will be 8M Urea, works as well as Guanidine HCl but it doesn't affect the binding on the NiNTA. Remember to prepare always fresh Urea and don't overheat while dissolving as it ruins it.

Hi, here you have a protocol that I believe that could be useful

https://www.gelifesciences.co.jp/catalog/pdf/18113437ac.pdf

Neither 8 M urea nor 6 M G-HCl would affect binding to nickel ions. If you see this then you have something in your sample competing or partially blocking the adsorption sites. Are you washing the inclusion bodies? For how long do you allow solubilization of inclusion bodies? There is no general strategy for refolding, it largely depends on the hydrophobicity of your protein.

Here are some suggestions for refolding, but the best method will depend on what works best for your specific protein:

Rapid Dilution: Dilute your protein in high urea into a buffer without urea. The volume of the final buffer should be large enough to make a low final concentration of Urea (I usually go for less than 0.5M)

Dialysis: This is similar to rapid dilution, but will happen over a longer time period. Dialyze your protein into a final buffer without urea. A good rule of thumb is to do a 10X buffer exchange at least 2 times.

Refolding on column: This method is the most controlled, but also the most difficult. You can load your protein onto your Nickel column in a high urea buffer, then wash with a linear gradient of a buffer without urea, then elute with imidazole. The linear gradient should be very slow. I have done this with a 1mL column at 0.2mL/min with a 20CV gradient.

Guanidine should not affect the ability of your protein to bind the nickel column, however it will make problems with your SDS-PAGE samples.

Qiagen has good protocols for nickel-NTA protein purification under denaturing conditions: https://www.qiagen.com/us/resources/resourcedetail?id=79ca2f7d-42fe-4d62-8676-4cfa948c9435&lang=en