Part:BBa_K3060002

RCA&MCA ssDNA for DNA hydrogel

This part is a ssDNA, using the primer 3 (BBa_K3060005) to form a circular template for the rolling circle amplification (RCA, or R). After the RCA completed, adding primer2 (BBa_K3060004) and primer3 (BBa_K3060005) to start the multi-primed chain amplification (MCA, or M). Hence, the hydrogel can be formed.

Usage

This part is a ssDNA, using the primer 3 (BBa_K3060005) to form a circular template for the rolling circle amplification (RCA, or R). After the RCA completed, adding primer2 (BBa_K3060004) and primer3 (BBa_K3060005) to start the multi-primed chain amplification (MCA, or M). Hence, the hydrogel can be formed. The preparation method can be found in 2019 DUT_China_A（https://2019.igem.org/Team:DUT_China_A/Protocols）
Note: It is important to confirm before using that the 5' terminal is a phosphate group and the 3' terminal is a hydroxyl group.

Characterization

The formation of circular template

In order to examine the successful preparation of the circular template, different samples were characterized by polyacrylamide gel electrophoresis (PAGE) As shown in Fig. 1, ligation products of ssDNA (Lane 2) exhibited a series of dispersive bands with slower migration than that of ssDNA (lane 1), indicating the formation of circular templates and other byproducts. After the ligation products were treated with Exo I and Exo III, only one bright and well-defined band still existed, proving the complete digestion of ligation byproducts and successful preparation of the circular template (lane 3).

Figure 1. PAGE image analysis of ssDNA (Lane 1), ligation products of ssDNA by reaction with Primer 3 and T4 DNA ligase (Lane 2), purified circular template by digesting above-mentioned ligation products with Exo I, and Exo III (Lane 3).

The formation of DNA Hydrogel.

Then, the circular template we preparation is used for the RCA and MCA processes to form the DNA hydrogel. The method can be found in 2019 DUT_China_A. （https://2019.igem.org/Team:DUT_China_A/Protocols） We use a variety of methods to characterize the formation of DNA hydrogel.

a.Agarose Gel Electrophoresis

Agarose gel electrophoresis was used to evaluate the formation of DNA hydrogel. DNA hydrogel is difficult to migrate through the agarose gel and remain the retention in home position.

Figure 2. AGE image analysis of phi29(+) (Lane 1), phi29(-) (Lane 2).M1, DL2000 DNA size marker. M2, DL500 DNA size marker.

b.SEM

Scanning electron microscopy (SEM) was used to obtain the morphology of theDNA hydrogel. As shown in Fig. 3, there are a large number of hydrogel particles with a diameter of about 2 μm in the buffer.

Figure 3. SEM images showing structures of DNA hydrogel particles.

c.DLS

We dynamic light scattering (DLS) analysis to get the size of the DNA hydrogel. As shown in Fig. 4, the size of hydrogel particles is between 100 nm and 3000 nm.

Figure 4. DLS size distribution of DNA hydrogel particle.

References

[1] Song P, Ye D, Zuo X, et al. DNA hydrogel with aptamer-toehold-based recognition, cloaking, and decloaking of circulating tumor cells for live cell analysis[J]. Nano letters, 2017, 17(9): 5193-5198.
[2] Lee J B, Peng S, Yang D, et al. A mechanical metamaterial made from a DNA hydrogel[J]. Nature Nanotechnology, 2012, 7(12): 816.
[3] Joosse S A, Gorges T M, Pantel K. Biology, detection, and clinical implications of circulating tumor cells[J]. EMBO molecular medicine, 2015, 7(1): 1-11.
[4] Dean F B, Nelson J R, Giesler T L, et al. Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification[J]. Genome research, 2001, 11(6): 1095-1099.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]