Hybridization Chain Reaction Amplification of MicroRNA Detection with a Tetrahedral DNA Nanostructure-based Electrochemical Biosensor Zhilei Ge1,†, Meihua Lin1,†, Ping Wang2, Hao Pei1, Juan Yan2, Jiye Shi3, Qing Huang1, Dannong He2, Chunhai Fan1, Xiaolei Zuo1,* 1
Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China 2 National Engineering research Center for Nanotechnology (NERCN), Shanghai, China 3 UCB Pharma, Slough, UK †
Zhilei Ge and Meihua Lin contributed equally to this work.
Email:
[email protected] S1
Table S1. The hairpin structures are stable enough to keep the “hairpins” without the initiator. Thermodynamic calculation through The DINAMelt Web Server Hosted by The RNA Institute, College of Arts and Sciences, State University of New York at Albany. Name
△G (kcal/mol)
Tm (℃ ℃)
H1
-21.81
89.9
H2
-22.22
93.1
microRNA-helper
-20.14
81.3
microRNA-H1
-19.03
87.6
microRNA-H2
-19.32
90.4
S2
Figure S1. We can easily detect the microRNA as low as 10 aM. The signal difference between 10 aM and 0 aM is significant. We calculated the binding energy of the microRNA target and probe via mfold. We obtained a free energy of -28.3 kcal/mol (corresponding to -118.3 kJ/mol).
700
600
500
N
400
300
2
N(a,t)= 2πNAC0D [at+2a (t/πD)^0.5] 200
100
0 0
10000 20000 30000 40000 50000 60000 70000 80000 90000 100000
t/s
Figure S2. A theoretical model has been employed to calculate the accumulation time of target molecules on the nanostructured surface (ACS Nano 2011, 5 (4), 3360-3366). Our sensing surface can be considered as nanostructured surface since our gold surface is S3
modified with DNA nanostructures. Based on this model, we calculated the time to accumulate one microRNA molecule on our DNA tetrahedron modified electrode is 3.85 s, which is fast. But, for samples with concentration of 10 aM, it will still need ~24hours to accumulate all 600 molecules that may be too long for usual detection. In the acceptable time scale (2h), the number of molecules binding on the surface is 79.
S4