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Interaction of RNA with phage display selected peptides analyzed by capillary electrophoresis mobility shift assay.
- Source :
-
RNA (New York, N.Y.) [RNA] 2002 May; Vol. 8 (5), pp. 698-704. - Publication Year :
- 2002
-
Abstract
- A sensitive capillary electrophoresis mobility shift assay (CEMSA) to analyze RNA/peptide interactions has been developed. Capillary electrophoresis (CE) has been adapted for investigating the interaction between variously methylated 17-nt analogs of the yeast tRNAPhe anticodon stem and loop domain (ASL(Phe)) and 15-amino-acid peptides selected from a random phage display library (RPL). A peptide-concentration-dependent formation of RNA/peptide complex was clearly visible during CEMSA. In the presence of peptide, the UV-monitored CE peak for ASLPhe with three of the five naturally occurring modifications (2'-O-methylcytidine (Cm32), 2'-O-methylguanine (Gm34) and 5-methylcytidine (m5C40) shifted from 18.16 to 20.90 min. The mobility shift was observed only for methylated RNA. The negative effects of diffusion, electroosmotic flow and adhesion of molecules to the capillary internal wall were suppressed by using a buffer containing a sieving polymer and a polyacrylamide-coated capillary. Under these conditions, well-shaped peaks and resolution of RNA free and bound to peptide were achieved. Peptide tF2, the most populated ligand in the RPL, specifically bound triply methylated ASLPhe in a methylated nucleoside-dependent manner. CE was found to be an efficient and sensitive method for the qualitative analysis of RNA-peptide interaction and should be generally applicable to the study of RNA-peptide (protein) interactions.
- Subjects :
- Amino Acid Sequence
Anticodon chemistry
Anticodon genetics
Anticodon metabolism
Base Sequence
In Vitro Techniques
Molecular Sequence Data
Nucleic Acid Conformation
Peptide Library
Peptides chemistry
RNA, Transfer, Phe chemistry
RNA, Transfer, Phe genetics
Electrophoresis, Capillary methods
Peptides metabolism
RNA, Transfer, Phe metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1355-8382
- Volume :
- 8
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- RNA (New York, N.Y.)
- Publication Type :
- Academic Journal
- Accession number :
- 12022235
- Full Text :
- https://doi.org/10.1017/s1355838202020319