Question: Secondary structures in RNA
1
gravatar for usketch
5.3 years ago by
usketch10
United States
usketch10 wrote:

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
structure mfold • 1.4k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 5.3 years ago by usketch10
1

What exactly is your question?

  • How does Mfold in general computes the energy?
  • Or how does Mfold calculate explicitly the closing loops?
ADD REPLYlink written 5.3 years ago by linus330

@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.

ADD REPLYlink written 5.3 years ago by usketch10

Okay maybe this helps:

g94 : Base G at position 94 in your sequence

c99: Base C at position 99 in your sequence

So your hairpinloop 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 ;)

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by linus330

Thank you! My other question is how does that relate to c22-g73 in the helix structure?

ADD REPLYlink written 5.3 years ago by usketch10
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