human telomeric g quadruplex - base stacking energy

[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: [Select]

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

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.