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New_Concert_4315 t1_iy14l2p wrote

Doesn't the 5 prime of initial A that gets decapped bind to the 3 prime of the T? If not, why?

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corknut1 t1_iy1setu wrote

The initial end is bonded to a "support" (glass beads called cpg are typical) and only cleaved from the support once the entire chain is grown. The cleaving process also caps this end.

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Germanofthebored t1_iy1cfcb wrote

Good question - one reason is that the chain isn't flexible enough to make such a tight turn. Still, a free nucleotide building block could hydrogen bond to a growing chain. But that would only be 2 or 3 H bonds, and thus much too weak to stabilize the complex

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heresacorrection t1_iy1ez3m wrote

The “cap” only allows 3’ additions OP probably simplified the wording it’s not an actual 5’ cap (as you hear about in mRNA), it’s a chemical blocking done by modifying the 3’ end of the chain. The 5’ is never exposed.

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