RNA Detection

a(Toehold)

b(Stem)

c(Loop)

b

c

b

a

b

Hairpin set (^) Triggers chain
reaction
Cascade chain
reaction
...
Target (initiator)^
a
b
a
b
c
b
a
b
c
b
a
b
c
b
a
b
Nicked double strand
b a
H1 H2
Fig. 1Linear hybridization chain reaction in solution. All hairpin probes have a structure of toehold-stem-loop.
Letters marked with asteriskare complementary to the correspondingunmarked letter. Target DNA hybridizes
with hairpin in H1 via base pairing to single-stranded toehold “a”, mediating a branch migration that opens the
stem of the hairpin, exposing a “c-b” sticky end. This complex further opens hairpin H2 by base pairing to
“c” to form a new complex containing a “b-a*” sticky end, which is the same to the target. Thus, a cascade
chain reaction is generated to form a nicked double strand polymer. Figure adapted from [5] with permission
from Elsevier
Fig. 2Effect of initiator concentration on HCR amplification.Lanes 1and 2 :1μM A1 and 1μM A2,
respectively.Lane 3: DL2000 DNA marker.Lanes 4–7: four different concentrations of initiator (100, 50,
10, and 0 nM) in a 1μM mixture of A1 and A2. Figure adapted from [5] with permission from Elsevier