Introduction
After extensive research, we have found that information about circRNA is limited. Currently, there is not only a lack of effective methods for detecting circRNA, but also no standard protocol for synthesizing it. Therefore, we are providing a coherent platform for both the synthesis and detection of circRNA. Our platform includes following three sections:
1. CircRNA synthesis. (Figure 1)
2. Gold nanoparticle-based colorimetric assay. (Figure 2)
3. Lateral flow test. (Figure 3)
Figure 1. CircRNA synthesis process. We utilize restriction enzymes for traditional cloning (BBa_K4636040, BBa_K4636041), PCR primers (BBa_K4636001 - BBa_K4636006) for amplifying the target (BBa_K4636040, BBa_K4636041), a modified T7 promoter (BBa_K4636000) for efficient transcription of DNA to RNA. Finally, we use a splint (BBa_K4636013 - BBa_K4636018) to assist in the circularization procedure.
Figure 2. Process of gold nanoparticle-based colorimetric assay. We use RCA primers (BBa_K4636028 - BBa_K4636035) to conduct the RCA and generate long-repeated ssDNA for further detection using DNA probes (BBa_K4636007 - BBa_K4636012) on gold nanoparticles.
Figure 3. Process of lateral flow test. We utilize these modified RPA primers (BBa_K4636019 - BBa_K4636027, BBa_K4636042) to conduct RT-RPA, and the resulting amplicon can be detected using PCRD detection.
Basic parts
| Item | Number | Name | Description |
|---|---|---|---|
| 1 | BBa_K4636000 | Modified T7 promoter | The modified T7 promoter can be used to transcribe efficiency. |
| 2 | BBa_K4636001 | cDNA of 0101802 | cDNA of hsa_circ_0101802 |
| 3 | BBa_K4636002 | cDNA of 0004771 | cDNA of hsa_circ_0004771 |
| 4 | BBa_K4636003 | PCR_0101802fw | Insert_0004771 PCR forward primer |
| 5 | BBa_K4636004 | PCR_0101802rv | Insert_0004771 PCR reverse primer |
| 6 | BBa_K4636005 | PCR_0004771fw | Insert_0101802 PCR forward primer |
| 7 | BBa_K4636006 | PCR_0004771rv | Insert_0101802 PCR reverse primer |
| 8 | BBa_K4636007 | Probe_0101802_bsj | Probe recognizes back splicing junction of RCA product |
| 9 | BBa_K4636008 | Probe_0101802_10 | Probe for recognizing RCA product |
| 10 | BBa_K4636009 | Probe_0101802_11 | Probe for recognizing RCA product |
| 11 | BBa_K4636010 | Probe_0004771_bsj | Probe recognizes back splicing junction of RCA product |
| 12 | BBa_K4636011 | Probe_0004771_11 | Probe for recognizing RCA product |
| 13 | BBa_K4636012 | Probe_0004771_12 | Probe for recognizing RCA product |
| 14 | BBa_K4636013 | Splint_1802_18 | Splint helps the back splicing of linear RNA |
| 15 | BBa_K4636014 | Splint_1802_16 | Splint helps the back splicing of linear RNA |
| 16 | BBa_K4636015 | Splint_1802_14 | Splint helps the back splicing of linear RNA |
| 17 | BBa_K4636016 | Splint_4771_18 | Splint helps the back splicing of linear RNA |
| 18 | BBa_K4636017 | Splint_4771_16 | Splint helps the back splicing of linear RNA |
| 19 | BBa_K4636018 | Splint_4771_14 | Splint helps the back splicing of linear RNA |
| 20 | BBa_K4636019 | RPA_0101802fw_1 | With biotin modification, it can be used for lateral flow testing after RPA. |
| 21 | BBa_K4636020 | RPA_0101802rv_1 | With FAM modification, it can be used for lateral flow testing after RPA. |
| 22 | BBa_K4636021 | RPA_0101802fw_2 | With biotin modification, it can be used for lateral flow testing after RPA. |
| 23 | BBa_K4636022 | RPA_0101802rv_2 | With FAM modification, it can be used for lateral flow testing after RPA. |
| 24 | BBa_K4636023 | RPA_0004771fw_1 | With biotin modification, it can be used for lateral flow testing after RPA. |
| 25 | BBa_K4636024 | RPA_0004771rv_1 | With DIG modification, it can be used for lateral flow testing after RPA. |
| 26 | BBa_K4636025 | RPA_0004771fw_2 | With biotin modification, it can be used for lateral flow testing after RPA. |
| 27 | BBa_K4636026 | RPA_0004771rv_2 | With DIG modification, it can be used for lateral flow testing after RPA. |
| 28 | BBa_K4636027 | RPA_0004771fw_3 | With biotin modification, it can be used for lateral flow testing after RPA. |
| 29 | BBa_K4636042 | RPA_0004771rv_3 | With DIG modification, it can be used for lateral flow testing after RPA. |
| 30 | BBa_K4636028 | RCA_indu_1802_1 | RCA primers initiates the amplification process |
| 31 | BBa_K4636029 | RCA_indu_1802_2 | RCA primers initiates the amplification process |
| 32 | BBa_K4636030 | RCA_indu_4771_1 | RCA primers initiates the amplification process |
| 33 | BBa_K4636031 | RCA_indu_4771_2 | RCA primers initiates the amplification process |
| 34 | BBa_K4636032 | RCA_45_1802_1 | RCA primers initiates the amplification process |
| 35 | BBa_K4636033 | RCA_45_1802_2 | RCA primers initiates the amplification process |
| 36 | BBa_K4636034 | RCA_45_4771_1 | RCA primers initiates the amplification process |
| 37 | BBa_K4636035 | RCA_45_4771_2 | RCA primers initiates the amplification process |
| 38 | BBa_K4636036 | PCRforAELA_fw | Primer for AELA-PCR preparation |
| 39 | BBa_K4636037 | PCRforAELA_rv | Primer for AELA-PCR preparation |
| 40 | BBa_K4636038 | AELA_PCR_fw | Primer for AELA-PCR |
| 41 | BBa_K4636039 | AELA_PCR_rv | Primer for AELA-PCR |
Composite part
| Item | Number | Name | Composite |
|---|---|---|---|
| 1 | BBa_K4636040 | Insert_0101802 | Modified T7 promoter + cDNA of 0101802 |
| 2 | BBa_K4636041 | Insert_0004771 | Modified T7 promoter + cDNA of 0004771 |
| 3 | BBa_K4636052 | insert_ligation_0101802 | Insert_0101802 + Insert_0101802 |
| 4 | BBa_K4636053 | insert_ligation_0004771 | Insert_0004771 + Insert_0004771 |
| 5 | BBa_K4636054 | pUC19_insert_ligation_0101802 | puc19 vector + insert_ligation_0101802 |
| 6 | BBa_K4636055 | pUC19_insert_ligation_0004771 | puc19 vector + insert_ligation_0004771 |