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Messages - kogucior

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RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 28, 2021, 11:35:38 am »
Ok, I'll check these structures, but it looks like our discussion goes beyond the canonical G-quadruplex structures (think in Webb da Silva's convention), hence the problems.
I look forward to the update if everything will be clearly explain in the publication. However, I hope that the "new convention" will be consistent with eg interpretations of CD spectra.
Unfortunately I am using the basic version of DSSR,  I have to think about buying the PRO version.

RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 27, 2021, 10:56:19 am »
loop#1 type=propeller strands=[#1,#4] nts=1 C A.DC5
    loop#2 type=propeller strands=[#4,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
    loop#3 type=propeller strands=[#3,#2] nts=1 A A.DA17

I still have doubts about assigning strand numbers, e.g. loop #1 in my opinion occurs between strand #1 and #2. Until now I thought that the order of the strands is due to their relative arrangement in the space and that the counting starts at the 5'-end and goes counterclockwise.

RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 27, 2021, 07:10:42 am »
As long the first G is in syn conformation, you will observe the same behavior for other G4 structures in DSSR-G4DB. The results should be self-consistent.

I don't understand why the anti/syn conformation is having an effect on this. Theoretically, according to the Webba da Silva formalism [Geometric Formalism for DNA QuadruplexFolding] -P-P-P and +P+P+P topology may have a composition of fully syn or anti G-tetrad.

If the topology determination is based on the syn/anti  composition of 4 guanines in G-tetrad then I would expect +/-(LPP) topology for 2kqg. While the identical structure (2kqh) has a -P-P-P topology.

I expected that the order of the guanines in the planes is based on the order in sequence and the interaction edge (WC or H) with the other adjacent guanines.

RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 27, 2021, 07:01:39 am »
As another concrete example, what do you think the descriptor for PDB entry 6r9k should be?

I believe it should be as it is currently described as: +L+P+P.

RNA structures (DSSR) / Incorrect topology assignment
« on: May 26, 2021, 10:57:27 am »
Dear Dr. Xiang-Jun Lu,

I was browsing prepared by you the G-quadruplex database (DSSR-G4DB) and I
encountered an error.
I think that for "" the
"+P+P+P" topology is wrongly assigned, it should be "-P-P-P".
I discovered that maybe this is due to a mis-ordering of G-strands
(#1-#4-#3-#2), where the first plane has a composition:
1 glyco-bond = s --- groove = w - n Major -> WC nts = 4 GGGG A.DG2,
A.DG18, A.DG14, A.DG6

and it should have:

1 glyco-bond = s --- groove = w - n Major -> WC nts = 4 GGGG A.DG2, A.DG6,
A.DG14, A.DG18

It is possible that there are more mistakes. I am curious what they come
from and I am looking forward to the revised version of the database.

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.