When ligand are being immobilized onto the surface of the sensor chip, what causes the slight RU jump during the binding process? Is it due to the difference between the pre-buffer and conditioning solution?
If I understand correct you are talking about the injection of the ligand during immobilisation. If the pre-concentration is relatively high not all the ligand is directly covalent bound to the sensor surface. When the ligand injection stops some will detach the surface resulting in a jump down. In addition, the immobilisation buffer contains low ionic strength compared to the flow buffer and will therefore give a negative jump of about a 1000 RU.