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SUMMARY:Shinnosuke Seki (University of Electro-Communications\, Tokyo)
DTSTART:20241120T140000Z
DTEND:20241120T150000Z
DTSTAMP:20260423T035754Z
UID:FLAT/8
DESCRIPTION:Title: <a href="https://researchseminars.org/talk/FLAT/8/">RNA
  co-transcriptionality - A platform for in vivo programming of molecular m
 achines</a>\nby Shinnosuke Seki (University of Electro-Communications\, To
 kyo) as part of One FLAT World Seminar\n\n\nAbstract\nTranscription is a p
 rocess in which an RNA sequence (of bases of 4 types $A$\, $C$\, $G$\, $U$
 ) is synthesized from a DNA template sequence (of $A$\, $C$\, $G$\, $T$) a
 ccording to the loss-less mapping $A \\to U$\, $C \\to G$\, $G \\to C$\, a
 nd $T \\to A$. The resulting RNA sequence\, called transcript\, folds upon
  itself while being transcribed. This co-transcriptional folding (CF) is d
 riven primarily by having helices form between complementary domains (fact
 ors)\, which bind with each other in the anti-parallel manner via base pai
 rs $A-U$\, $C-G$\, and $G-U$ and then twist\, and secondly by having helic
 es stacked coaxially. This platform has proven programmable in vitro by Ge
 ary\, Rothemund\, and Andersen\; indeed\, they demonstrated how to program
  a quasi-planar rectangular RNA tile into a transcript (in fact\, into its
  DNA template) and a single CF-pathway any other of which is hardly taken\
 , guaranteeing a high success rate.\n\nThis “Hello World” program has 
 brought up the following two problems among others:\n\n1. How can we progr
 am a computation on this platform\, that is\, how to design a transcript t
 hat accommodates multiple CF-pathways and takes one of them depending on a
 n input and what has folded so far?\n\n2. How can we maximize success rate
  by choosing a CF-pathway properly?\n\nThis talk will devote its first hal
 f to motivating these problems by providing background information on mole
 cular programming\, and particularly on helix-based RNA structures such as
  hairpin and pseudoknot\, coaxial stacking among them\, CF-kinetics\, and 
 RNA triple (not double) helix. Its second half is on programming of a Turi
 ng-universal computation on this platform by using a model of CF-driven co
 mputation called oritatami.\n
LOCATION:https://researchseminars.org/talk/FLAT/8/
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