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Questions and answers > RNA structures (DSSR)
human telomeric g quadruplex - base stacking energy
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bciezah1:
Dear Xiang-Jun,
I wonder if 3DNA has an option to calculate the base pair stacking energy (projected area) for g-quadruplex RNA. I know 3DNA can do it for a dsDNA, but I wonder if there is the same option for g-quadruplex.
Thanks you,
Basilio.
xiangjun:
Hi Basilio,
Try the latest DSSR v1.7.1-2017nov01 which has a section does just that. See below for an example (1xav).
--- Code: ---List of 1 G4-stem
Note: a G4-stem is defined as a G4-helix with backbone connectivity.
Bulges are also allowed along each of the four strands.
stem#1[#1] layers=3 loops=3 INTRA-molecular parallel
1 syn=---- WC-->Major area=11.75 rise=3.73 twist=30.20 nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
2 syn=---- WC-->Major area=17.06 rise=3.74 twist=23.28 nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
3 syn=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
strand#1 +1 DNA syn=--- nts=3 GGG A.DG4,A.DG5,A.DG6
strand#2 +1 DNA syn=--- nts=3 GGG A.DG8,A.DG9,A.DG10
strand#3 +1 DNA syn=--- nts=3 GGG A.DG13,A.DG14,A.DG15
strand#4 +1 DNA syn=--- nts=3 GGG A.DG17,A.DG18,A.DG19
loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT11,A.DA12
loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT16
--- End code ---
Note that the identification and characterization of G-quadruplexes is a new feature of DSSR from v1.7.0. I welcome user feedback, as always.
Xiang-Jun
bciezah1:
Dear xiangjun,
I will right now. Thank you a lot!
Best wishes,
Basilio.
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.