Secondary structures in RNA
I'm using mfold in order to determine the structure of an RNA sequence. However, I don't quite understand how to intrepret the thermodynamic results. Say, I'm looking at the helix with -4.70 gibbs energy. Using the two closing pairs, "closing pair g94-c99" and "external closing pair c22-g73" how do I trace that helix structure out on the predicted structure?
Structural element δG Information
External loop -1.50 12 ss bases & 1 closing helices.
Stack -2.50 External closing pair is g9-c126
Stack -1.50 External closing pair is u10-g125
Stack -2.10 External closing pair is c11-g124
Stack -1.30 External closing pair is u12-a123
Stack -2.20 External closing pair is a13-u122
Stack -1.40 External closing pair is c14-g121
Stack -2.10 External closing pair is g15-u120
Stack -3.40 External closing pair is g16-c119
Helix -16.50 9 base pairs.
Multi-loop 3.80 External closing pair is c17-g118
4 ss bases & 3 closing helices.
Stack -2.50 External closing pair is g74-u117
Stack -3.30 External closing pair is c75-g116
Stack -2.10 External closing pair is c76-g115
Stack -1.40 External closing pair is u77-g114
Stack -3.30 External closing pair is g78-c113
Stack -2.20 External closing pair is g79-c112
Helix -14.80 7 base pairs.
Interior loop 3.30 External closing pair is u80-a111
Stack -2.10 External closing pair is c86-g107
Helix -2.10 2 base pairs.
Interior loop -3.50 External closing pair is u87-g106
Interior loop 1.10 External closing pair is g90-c103
Stack -1.40 External closing pair is u92-g101
Stack -3.30 External closing pair is g93-c100
Helix -4.70 3 base pairs.
Hairpin loop 0.20 Closing pair is g94-c99
Stack -3.30 External closing pair is c22-g73
Helix -3.30 2 base pairs.
Bulge loop 1.70 External closing pair is c23-g72
Stack -2.20 External closing pair is a24-u70
Stack -3.30 External closing pair is c25-g69
Stack -3.30 External closing pair is c26-g68
Stack -2.10 External closing pair is c27-g67
Stack -2.10 External closing pair is u28-a66
Helix -13.00 6 base pairs.
Interior loop 1.60 External closing pair is g29-c65
Stack -3.40 External closing pair is g33-c60
Helix -3.40 2 base pairs.
Interior loop 0.70 External closing pair is c34-g59
Stack -3.30 External closing pair is c37-g56
Stack -2.40 External closing pair is c38-g55
Stack -2.40 External closing pair is g39-c54
Helix -8.10 4 base pairs.
Interior loop 2.20 External closing pair is a40-u53
Stack -2.40 External closing pair is u43-a50
Helix -2.40 2 base pairs.
Hairpin loop 4.50 Closing pair is c44-g49
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What exactly is your question?
@linus My question is what are external closing pairs, what are closing pairs, and what is the meaning the statement "3 base pairs" in this context. In the end I want to be able to understand/point out where the helix is in the predicted structure picture.
Okay maybe this helps:
g94 : Base G at position 94 in your sequence
c99: Base C at position 99 in your sequence
So your hairpin loop contains the sequence from 95-98 and is closed by the pair GC basepair.
(i can color it in the picture if you want.)
Ps: it is at the bottom next to the 100 ;)
Thank you! My other question is how does that relate to c22-g73 in the helix structure?
c22-g73 closes the right arm and is part of the interior loop.
maybe these slides help you to understand the basics:
https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&cad=rja&uact=8&ved=0CE8QFjAG&url=http%3A%2F%2Fmendel.informatics.indiana.edu%2F~yye%2Flab%2Fteaching%2Fgetfile.php%3Fwhat%3Dlecture%26name%3DI519-rnafolding1.pdf&ei=fGoIVPDDK-fy7AbruIDgDg&usg=AFQjCNFUOQBF83i7bzASJg3_P5xuo1jcYg&sig2=wc2ihgY0wVAsOH5vc8fv7A
Sorry for the google link