Nuclease protection of RNAs containing site-specific labels: a rapid method for mapping RNA-protein interactions.
This report describes a method that combines nuclease protection and site-specific labeling to determine sites and extents of RNA-protein interactions. The utility of the method is demonstrated by the analysis of the binding of factors to the 3' splice site region of a pre-mRNA labeled at three specific positions. This "reverse footprinting" technique should be widely applicable to a variety of questions concerning RNA-protein interactions.
Maroney
P A
PA
Center for RNA Molecular Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.
Romfo
C M
CM
Nilsen
T W
TW
D001665:Binding Sites; D006868:Hydrolysis; D007553:Isotope Labeling / Q000379:methods*; D011485:Protein Binding; D012313:RNA / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D012322:RNA Precursors / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D012326:RNA Splicing; D016601:RNA-Binding Proteins / Q000378:metabolism*; D016914:Ribonuclease H / Q000378:metabolism*; D017411:Ribonucleoproteins, Small Nuclear / Q000378:metabolism
D012322:RNA Precursors; D016601:RNA-Binding Proteins; D017411:Ribonucleoproteins, Small Nuclear; D012313:RNA; D016914:Ribonuclease H