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RNA Secondary Structure Prediction Using High-throughput SHAPE
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JoVE Journal Biology
RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

DOI:
10.3791/50243-v

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13:42 min

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May 31, 2013

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, , , ,
1RT Biochemistry Section, HIV Drug Resistance Program,Frederick National Laboratory for Cancer Research

Chapters

  • 00:05Title
  • 01:40RNA Folding
  • 03:09Chemical Modification of the RNA
  • 04:33Reverse Transcription
  • 07:08Preparation of Sequencing Ladder and Capillary Electrophoresis
  • 09:55ShapeFinder Software
  • 11:15Data Normalization
  • 11:51Results: RNA Structure Determination using RNA Structure Software
  • 12:53Conclusion

Summary

Automatic Translation

Automatic Translation

High-throughput selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) utilizes a novel chemical probing technology, reverse transcription, capillary electrophoresis and secondary structure prediction software to determine the structures of RNAs from several hundred to several thousand nucleotides at single nucleotide resolution.

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Keywords: RNA Secondary StructureHigh-throughput SHAPEChemical ProbingReverse TranscriptionCapillary ElectrophoresisShapeFinderRNAStructureIn Silico PredictionSingle Nucleotide Resolution

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