3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: bciezah1 on November 08, 2017, 10:44:13 am

Title: human telomeric g quadruplex - base stacking energy
Post by: bciezah1 on November 08, 2017, 10:44:13 am: 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.
Title: Re: human telomeric g quadruplex - base stacking energy
Post by: xiangjun on November 08, 2017, 11:01:14 am: Hi Basilio,

Try the latest DSSR v1.7.1-2017nov01 which has a section does just that. See below for an example (1xav (http://www.rcsb.org/pdb/explore/explore.do?structureId=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
Title: Re: human telomeric g quadruplex - base stacking energy
Post by: bciezah1 on November 13, 2017, 08:58:12 am: Dear xiangjun,

I will right now. Thank you a lot!

Best wishes,

Basilio.