Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Observation of a Change in Bend of an RNA Kissing Complex Using the
  Angular Dependence of Fluorescence Resonance Energy Transfer   We report on the observation of a change in the bend angle of an RNA kissing
complex upon Rop binding using single-molecular-pair FRET. The angular
relationship between the dyes, rather than the distance between them, is shown
to be responsible for the observed change in energy transfer. It has long been
thought that Rop increases the bend angle of the R1inv-R2inv complex upon
binding, but this has never been directly observed. In contrast, we find an
increase in FRET upon the addition of Rop that is shown via modeling to be
consistent with a decrease in the bend angle of the complex of
$-15^{\circ}\pm7^{\circ}$. The model predicts FRET from dye trajectories
generated using molecular dynamics simulations of Cy3 and Cy5 attached to $5'$
terminal cytosine or guanosine on RNA. While FRET is commonly used to observe
global changes in molecular structure attributed to changes in the distance
between dyes, it is rarely, if ever, used to elucidate angular changes. Subtle
global changes in molecular structure upon binding are generally difficult to
discern using NMR or crystallography, but FRET is well suited to observe these
changes because of its sensitivity at interdye distance around the F\"orster
radius, $R_F\approx5$ nm. While FRET is often referred to and used as a
"molecular ruler" for distances around $R_F$, for dye pairs that have minimal
rotational freedom, FRET can also be used to observe changes in structure for
which there is no significant change in distance between the dyes. This is the
case for the R1inv-R2inv kissing complex studied here. This complex is derived
from the RNA I - RNA II complex in E. coli. RNA II is a primer for replication
of the ColE1 plasmid, its function is modulated by interaction with RNA II. Rop
is known to stabilize the complex, and it is also known to bind kissing
complexes in a structure, but not sequence, dependent fashion.

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The categories of this paper are: chao-dyn
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The categories of this paper are: funct-an
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The categories of this paper are: astro-ph
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The categories of this paper are: atom-ph
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The categories of this paper are: cond-mat
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The categories of this paper are: quant-ph
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The categories of this paper are: dg-ga
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The categories of this paper are: alg-geom
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The categories of this paper are: q-alg
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The categories of this paper are: hep-th
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The categories of this paper are: gr-qc
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The categories of this paper are: hep-lat
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The categories of this paper are: stat
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The categories of this paper are: hep-ph
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The categories of this paper are: econ
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The categories of this paper are: bayes-an