Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: The role of loop stacking in the dynamics of DNA hairpin formation   We study the dynamics of DNA hairpin formation using oxDNA, a
nucleotide-level coarse-grained model of DNA. In particular, we explore the
effects of the loop stacking interactions and non-native base pairing on the
hairpin closing times. We find a non-monotonic variation of the hairpin closing
time with temperature, in agreement with the experimental work of Wallace et
al. [Proc. Nat. Acad. Sci. USA 2001, 98, 5584-5589]. The hairpin closing
process involves the formation of an initial nucleus of one or two bonds
between the stems followed by a rapid zippering of the stem. At high
temperatures, typically above the hairpin melting temperature, an effective
negative activation enthalpy is observed because the nucleus has a lower
enthalpy than the open state. By contrast, at low temperatures, the activation
enthalpy becomes positive mainly due to the increasing energetic cost of
bending a loop that becomes increasingly highly stacked as the temperature
decreases. We show that stacking must be very strong to induce this
experimentally observed behavior, and that the existence of just a few weak
stacking points along the loop can substantially suppress it. Non-native base
pairs are observed to have only a small effect, slightly accelerating hairpin
formation.

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The categories of this paper are: eess
24
The categories of this paper are: dg-ga
18
The categories of this paper are: econ
8
The categories of this paper are: hep-ex
25
The categories of this paper are: patt-sol
14
The categories of this paper are: math-ph
0
The categories of this paper are: hep-ph
23
The categories of this paper are: solv-int
7
The categories of this paper are: hep-th
27
The categories of this paper are: comp-gas
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The categories of this paper are: q-alg
1
The categories of this paper are: cs
35
The categories of this paper are: mtrl-th
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The categories of this paper are: hep-lat
13
The categories of this paper are: quant-ph
31
The categories of this paper are: ao-sci