Effect of rotor type on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation

Separation of differentially isotope-labeled bacterial RNA by isopycnic density gradient centrifugation is a critical step in RNA-based stable isotope probing (RNA-SIP) analyses, which allow to link the structure and function of complex microbial communities. Using isotope-labeled Escherichia coli RNA, we could show that an 8 mL near-vertical rotor performed better than a 2 mL fixed angel rotor, thereby corroborating current recommendations. Neither increased concentrations of formamide nor urea in the medium improved the separation results using the fixed angel rotor.