3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: hume on January 07, 2015, 12:08:21 am

Title: How 3DNA-DSSR define RNA junctions?
Post by: hume on January 07, 2015, 12:08:21 am: Dear developer,

Hello! I am using 3DNA-DSSR to find junctions in RNA structures, but I am just curious about the criteria for the RNA structure elements to be a junction so that appears in the PDB file:

1) The length of each stem
2) Do other structure elements that do not belong to the junction on the secondary structure level but is close to the junction on the tertiary structure level count?

I do appreciate your help!

Thank you so much,
Chen
Title: Re: How 3DNA-DSSR define RNA junctions?
Post by: xiangjun on January 07, 2015, 09:55:36 am: Hi Chen,

DSSR identifies junctions (and other types of loops, such as hairpin loop, internal loop or bulge) as one would expect when looking at the secondary structure representation. For example, the cover image of the DSSR User Manual for the yeast phenylalanine tRNA (1ehz) shows the 4-way junction in the middle and three hairpin loops at the peripheral. The length of stems do not matter, and a (junction) loop forms a 'topological' circle -- see the DSSR output of the 4-way junction for 1ehz:

Code: [Select]
List of 1 junction 1 4-way junction: nts=16; [2,1,5,0]; linked by [#1,#2,#3,#4] nts=16 UUAgCgCGAGgUCcGA A.U7,A.U8,A.A9,A.2MG10,A.C25,A.M2G26,A.C27,A.G43,A.A44,A.G45,A.7MG46,A.U47,A.C48,A.5MC49,A.G65,A.A66 nts=2 UA A.U8,A.A9 nts=1 g A.M2G26 nts=5 AGgUC A.A44,A.G45,A.7MG46,A.U47,A.C48 nts=0
More details about the underlying algorithms will be described in the DSSR manuscript I have been focusing on. Stay tuned.

HTH,

Xiang-Jun
Title: Re: How 3DNA-DSSR define RNA junctions?
Post by: hume on January 07, 2015, 11:54:33 am: Dear Xiangjun,

Thank you for your reply and your information! Then in my case I can only test several models and analyze the output. I am looking forward to seeing the details in the coming paper.

Thank you so much,
Chen