Table 1.
Binding conditions used to measure the interaction between FMRP and RNA.
| Publication | Assay | Conditions |
|---|---|---|
| Ashley et al. (1993) [51] | Pull-down | 16 mM HEPES-KOH pH 7.9, 120 mM KCI, 0.04% Nonidet P-40, 1 mg/mL BSA, 0.16 mM dithioerythritol, 0.4 mM phenylmethylsulfonyl fluoride |
|
| ||
| Brown et al. (1998) [49] | Pull-down | 10 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 100 mM NaCl, 2.5% Trition X100, 1 mg/mL heparin |
|
| ||
| Price et al. (1996) [52] | Pull-down | 20 mM Hepes, pH 7.9, 2 mM MgCl2, 10 mM ZnCl2, 70 mM NH4Cl, 0.02% Nonidet P-40, 5 mg/mL yeast tRNA |
|
| ||
| Sung et al. (2000) [21] | Pull-down Filter-Binding | 20 mM Hepes, pH 7.9, 2 mM MgCl2, 10 mM ZnCl2, 70 mM NH4Cl, 0.02% Nonidet P-40, 5 mg/mL yeast tRNA |
|
| ||
| Denman and Sung (2002) [57] | Pull-down | 20 mM Hepes, pH 7.9, 2 mM MgCl2, 10 mM ZnCl2, 70 mM NH4Cl, 0.02% Nonidet P-40, 5 mg/mL yeast tRNA |
|
| ||
| Schaeffer et al. (2001) [26] | EMSA | 50 mM Tris-HCl pH 7.4, 1 mM MgCl2, 1 mM EDTA, 150 mM KCl, 1 mM DTT, 0.25 mg/mL of E.coli tRNA, 0.01% BSA, 8 U of RNasin |
|
| ||
| Sung et al. (2003) [17] | Pull-down EMSA |
50 mM Tris-HCl, pH 7.0, 2 mM MgCl2, 150 mM NaCl, 1 mM DTT, 0.25 mg/mL E.coli tRNA, 0.25 mg/mL BSA |
|
| ||
| Bechara et al. (2006) [61] | EMSA | 50 mM Tris-HCl pH 7.4, 1 mM MgCl2, 1 mM EDTA, 150 mM KCl, 1 mM DTT, 0.25 mg/mL of E.coli tRNA, 0.01% BSA, 8 U of RNasin |
|
| ||
| Didiot et al. (2008) [54] | EMSA | 50 mM Tris-HCl pH 7.4, 1 mM MgCl2, 1 mM EDTA, 150 mM KCl, 1 mM DTT, 0.25 mg/mL of E. coli tRNA, 0.01% BSA, 8 U of RNasin |
|
| ||
| Zalfa et al. (2003) [36] | EMSA | 10 mM HEPES pH 7.9, 3 mM MgCl2, 10 mM DTT, 100 mM KCl, 750 mM NaCl, 5% glycerol, 7 mM β-Mercaptoethanol, 1 mg/mL Albumin, 1.3 mg/mL Heparin |
|
| ||
| Zalfa et al. (2005) [40] | EMSA | 20 mM HEPES-KOH, pH 7.6, 5 mM MgCl2, 300 mM KCl, 2 mM DTT, 5% glycerol, and 500 ng of total yeast tRNA or 20 μg of heparin. |
|
| ||
| Darnell et al. (2001) [22] | Filter-Binding | 10 mM Tris-OAc pH 7.7, 200 mM KOAc, 5 mM MgOAc2 |
|
| ||
| Darnell et al. (2005) [30] | Filter-Binding | 50 mM Tris-OAc at pH 7.7, 50 mM KOAc, 10 mM DTT, 5 mM Mg(OAc)2, 30 μg/mL tRNA |
|
| ||
| Gabus et al. (2004) [42] | EMSA | 20 mM Tris-HCl pH 7.5, 30 mM NaCl, 0.2 mM MgCl2, 5 mM DTT, 10 μM ZnCl2 |
|
| ||
| Laggerbauer et al. (2001) [16] | Pull-down | PBS, 0.02% IGEPAL, 1% BSA |
|
| ||
| Siomi et al. (1993) [15] | Pulldown | 10 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 0.5% Triton X-100, 100–1000 mM NaCl |
|
| ||
| Stetler et al. (2005) [56] | Pulldown | 2 M KOAc, 100 mM Tris-OAc pH 7.7 and 50 mM MgOAc2, 1 μL of yeast tRNA, 1 μL of RNAsin |
|
| ||
| Menon and Mihailescu (2007) [62] | EMSA | 50 mM Tris-HCl pH 7.5, 150 mM NaCl and protease inhibitors |
|
| ||
| Fahling et al. (2009) [20] | EMSA | 10 mM Hepes pH 7.2, 3 mM MgCl2, 5% glycerol, 1 mM DTT, 150 mM KCl, 2 U/μL RNaseOUT, 0.5 μg/μL rabbit rRNA |
|
| ||
| Zou et al. (2008) [63] | AGESA | 20 mM Tris-HCl pH 7.2, 150 mM NaCl |
|
| ||
| Iacoangeli et al. (2008) [47] | EMSA | 50 mM Tris-HCl pH 7.6, 150 mM KCl, 1 mM MgCl2, 1 mM EDTA, 1 mM DTT, 0.2 U/μL RNase inhibitor, 100 ng/μL total yeast tRNA, and 100 ng/μL BSA |
Sets of binding conditions are grouped by the different laboratories that used them. Each set of conditions is differentiated from the next by a dotted line. In some instances the same group used multiple sets of binding conditions in multiple publications.