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This homework comes in three parts.

Hammerhead ribozyme YES gate

Verify the properties of the YES-1 gate in Figure 2 of the RNA logic gates paper by Breaker and Penchovsky, covered in class:

NB: the relevant RNA sequence is given in Figure 2.

You should report the following for both the OFF and ON positions of the switch (NB these are exactly the results reported for Fig2a of the Breaker-Penchovsky paper):

  1. Predicted MFE structure;
  2. Base-pairing probability plot;
  3. Status of stems I, II and III from the hammerhead structure, and accessibility of the cleavage site.

Hint: in the ON configuration, part of the YES-1 sequence (the Oligonucleotide Binding Site, or OBS) is base-paired with an external, complementary sequence (the DNA-1 sequence). If you removed DNA-1 without changing the structure of YES-1, then the OBS part of YES-1 would be single-stranded. (Contrast this with the OFF configuration, where OBS folds back on itself and an adjacent part of YES-1, forming stem IV.)

In other words, the change in structure when DNA-1 is introduced as a binding partner to OBS may be considered as a two-step process: first OBS becomes single-stranded, then it binds to DNA-1. You only really need to consider the first step (i.e. OBS becoming single-stranded). How might you force this outcome when predicting the structure of the ON state?

Write up your entire analysis on your biowiki page (or on a separate homework page, linked to from your biowiki page). Include details of every program that you run and the command-line options that you used for that program, to sufficient detail that someone could reproduce your analysis EXACTLY.

Software for verifying YES gate

Outline the design for a Python program that verifies the correctness of a YES gate of the form given in the previous part of the homework.

You don't need to actually write the program, but you should describe all the key steps, giving code snippets where appropriate.

The program should take as inputs:

  1. an RNA sequence (corresponding to the YES-1 sequence from the Penchovsky-Breaker example);
  2. the co-ordinates of the oligonucleotide binding site (the OBS subsequence from the P-B example).

The output of the program should be the truth table of the logic gate.

Hammerhead ribozyme structure

Predict the MFE structure of the AF404053.1 hammerhead ribozyme sequence and compare to the structure given in Rfam.


-- IanHolmes - 15 Sep 2009

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