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Latest comment: 21 September 2013 by Omei in topic Double T Stacking Example

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<p>As for the poly(A) mystery, I've been having the wildest ideas myself for many weeks, T-shaped stacking was one of them. I never managed to model something that could come close to possibly explaining the observed phenomenon. Always a problem with the construct. Either some of the bases should appear reactive, or the construct would not have the terminal 6 reactive ones, etc. At this point, I really wish we could apply at least NMR. I suggested titration on the forum, but it would just tell us whether cations are involved or not. Sigh...</p>
<p>As for the poly(A) mystery, I've been having the wildest ideas myself for many weeks, T-shaped stacking was one of them. I never managed to model something that could come close to possibly explaining the observed phenomenon. Always a problem with the construct. Either some of the bases should appear reactive, or the construct would not have the terminal 6 reactive ones, etc. At this point, I really wish we could apply at least NMR. I suggested titration on the forum, but it would just tell us whether cations are involved or not. Sigh...</p>
<p>-- [[User:ElNando888|ElNando888]] ([[User talk:ElNando888|talk]]) 22:15, 20 September 2013 (UTC)</p>
<p>-- [[User:ElNando888|ElNando888]] ([[User talk:ElNando888|talk]]) 22:15, 20 September 2013 (UTC)</p>
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<p>FWIW, my interpretation of the 6 or so reactive ones is that the backbone of the poly(A) has such a radically different configuration (I'll call it the &zeta;-configuration) from the &alpha;-helix that there has to be a multiiple-nucleotide&nbsp; transition region from the &alpha;-helix of heterogeneous RNA to the &zeta;-configuration of the poly(A).</p>
<p>[[User:Omei|Omei]] ([[User talk:Omei|talk]]) 00:18, 21 September 2013 (UTC)</p>
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Revision as of 00:18, 21 September 2013

Double T Stacking Example

Nando, I find this extremely interesting.  What is the PDB entry and positions?

I've been thinking about how T stacking, in combination with more common stacking, might create enough energetic non-linearity in the poly(A) molecule to account for the fact that any particular lab sequence seems to form into a well-defined structure (i.e. not enough variation among the thousands of instances of that sequence to turn all the SHAPE values into "average" values), and yet the formations look so different for molecules with only slightly different sequences at the 3' end of the poly(A).

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Hi Omei,

I added the source information on the page itself, below the picture.

As for the poly(A) mystery, I've been having the wildest ideas myself for many weeks, T-shaped stacking was one of them. I never managed to model something that could come close to possibly explaining the observed phenomenon. Always a problem with the construct. Either some of the bases should appear reactive, or the construct would not have the terminal 6 reactive ones, etc. At this point, I really wish we could apply at least NMR. I suggested titration on the forum, but it would just tell us whether cations are involved or not. Sigh...

-- ElNando888 (talk) 22:15, 20 September 2013 (UTC)Reply[reply]

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FWIW, my interpretation of the 6 or so reactive ones is that the backbone of the poly(A) has such a radically different configuration (I'll call it the ζ-configuration) from the α-helix that there has to be a multiiple-nucleotide  transition region from the α-helix of heterogeneous RNA to the ζ-configuration of the poly(A).

Omei (talk) 00:18, 21 September 2013 (UTC)Reply[reply]

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