By Jon Lorsch

Methods in Enzymology volumes offer an critical software for the researcher. every one quantity is thoroughly written and edited by way of specialists to comprise cutting-edge experiences and step by step protocols.

In this quantity, we have now introduced jointly a few middle protocols focusing on RNA, complementing the conventional content material that's present in prior, current and destiny Methods in Enzymology volumes.

  • Indispensable device for the researcher
  • Carefully written and edited via specialists to include step by step protocols
  • In this quantity we've got introduced jointly a few middle protocols targeting RNA

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Additional resources for Laboratory Methods in Enzymology: RNA

Example text

1. Theory It is possible to include data from various structure sensitive probes in the calculation of RNA secondary structure. , 2004) and also in the confidence of the predicted structure (Mathews, 2004). 2). 4 (a) RNAstructure predicted MFE structure for E. coli 5 S rRNA. The sequence is written and numbered 50 –30 . Base pairs are indicated by dashes. (b) Dot plot of secondary structure calculation for E. coli 5 S rRNA. The x and y axes are the nucleotide numbers of the sequence. The squares in the plot area represent a pair x–y, while the color indicates the DG range that contains the possible MFE fold given pair x–y (see color key in figure).

Laboratory Methods in Enzymology: RNA Edited by JON LORSCH CHAPTER ONE Computational Prediction of RNA Secondary Structure Walter N. edu Contents 1. 1 List of protocols 2. Equipment 3. 4 Duration 4. 4 Tip 5. 2 Duration 6. 4 Duration 7. 6 Tip 8. 00001-4 # 2013 Elsevier Inc. All rights reserved. 6 10 10 10 10 11 11 12 12 12 12 14 14 14 14 14 16 16 17 17 17 18 18 18 19 19 19 19 19 19 19 20 20 3 4 9. 4 Tip 10. 4 Duration 11. 3 Tip 12. Step 2(III) Submit Sequence to RNAstructure 13. Step 3(III) Viewing the Results of Secondary Structure Calculation 14.

In contrast to proteins, RNAs are ‘information poor’ molecules. There are only four types of residues in RNA, with fairly similar structural and chemical properties, versus 22 amino acids in proteins with strikingly different structure and chemistry. As well, even small RNA molecules have a very large number of possible secondary structures. 8 N possible secondary structures (Zuker and Sankoff, 1984): for example, a 100 nucleotide RNA has more possible secondary structures than the number of stars in the visible universe.

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