Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: The effect of base pair mismatch on DNA strand displacement   DNA strand displacement is a key reaction in DNA homologous recombination and
DNA mismatch repair and is also heavily utilized in DNA-based computation and
locomotion. Despite its ubiquity in science and engineering, sequence-dependent
effects of displacement kinetics have not been extensively characterized. Here,
we measured toehold-mediated strand displacement kinetics using single-molecule
fluorescence in the presence of a single base pair mismatch. The apparent
displacement rate varied significantly when the mismatch was introduced in the
invading DNA strand. The rate generally decreased as the mismatch in the
invader was encountered earlier in displacement. Our data indicate that a
single base pair mismatch in the invader stalls branch migration, and
displacement occurs via direct dissociation of the destabilized incumbent
strand from the substrate strand. We combined both branch migration and direct
dissociation into a model, which we term, the concurrent displacement model,
and used the first passage time approach to quantitatively explain the salient
features of the observed relationship. We also introduce the concept of
splitting probabilities to justify that the concurrent model can be simplified
into a three-step sequential model in the presence of an invader mismatch. We
expect our model to become a powerful tool to design DNA-based reaction schemes
with broad functionality.

31
The categories of this paper are: ao-sci
14
The categories of this paper are: math-ph
9
The categories of this paper are: nlin
21
The categories of this paper are: adap-org
17
The categories of this paper are: q-fin
20
The categories of this paper are: acc-phys
37
The categories of this paper are: supr-con
26
The categories of this paper are: bayes-an
0
The categories of this paper are: hep-ph
19
The categories of this paper are: eess
32
The categories of this paper are: atom-ph
33
The categories of this paper are: plasm-ph
1
The categories of this paper are: cs
13
The categories of this paper are: quant-ph
2
The categories of this paper are: math
24
The categories of this paper are: dg-ga