Difference between revisions of "Part:BBa K3593005"

 
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__NOTOC__
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<partinfo>BBa_K3593005 short</partinfo>
  
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The capture strand composes the control line of our test strip, which is complementary to the reporter probe on Au nanoparticle. This allows the capture of Au particle at any time with a toxin or not, to verify the function of lateral flow assay.
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=Sequence and features=
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<partinfo>BBa_K3593005 SequenceAndFeatures</partinfo>
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=Characterisation of this part=
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==Design==
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Besides aptamers, we have some short single stranded DNA known as 'probes', which binds to other single stranded DNA. BBa_K3593005 is one of those so-called 'probes' in our design, and play important roles in our hardware, in which it binds and immobilizes the aptamer, as the aptamer amplicon has a single strand DNA of poly A resembling the real process in organism during DNA transcription. this sequence is reserved from primer of amplification due to a C3 spacer preventing elongation. That's because poly A can hardly form secondary structure on its own, thus it will not affect the function of aptamer.BBa_K3593005 is completely consisted of thymines, which can bind strongly with our aptamer with a complementary strand to it. The use of 'Poly T' is used in several articles.[1][2][3] Its 5' end is conjugated to biotin[4] to bind with streptavidin.
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=References=
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1.Chao Zhu, Guilan Zhang, Yafei Huang, Shuming Yang, Shuyue Ren, Zhixian Gao, Ailiang Chen, Dual-competitive lateral flow aptasensor for detection of aflatoxin B1 in food and feedstuffs, Journal of Hazardous Materials https://doi.org/10.1016/j.jhazmat.2017.10.026 <br>
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2.Wu, S., Liu, L., Duan, N. et al. A test strip for ochratoxin A based on the use of aptamer-modified fluorescence upconversion nanoparticles. Microchim Acta 185, 497 (2018). https://doi.org/10.1007/s00604-018-3022-0<br>
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3.Delley CL, Liu L, Sarhan MF, Abate AR. Combined aptamer and transcriptome sequencing of single cells. Sci Rep. 2018 Feb 13;8(1):2919. doi: 10.1038/s41598-018-21153-y. PMID: 29440771; PMCID: PMC5811598.<br>
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4.Jauset-Rubio M, Svobodová M, Mairal T, et al. Aptamer Lateral Flow Assays for Ultrasensitive Detection of β-Conglutin Combining Recombinase Polymerase Amplification and Tailed Primers. Anal Chem. 2016;88(21):10701-10709. doi:10.1021/acs.analchem.6b03256<br>
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<!-- Add more about the biology of this part here
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===Usage and Biology===
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<!-- Uncomment this to enable Functional Parameter display
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===Functional Parameters===
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<partinfo>BBa_K3593005 parameters</partinfo>
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Latest revision as of 03:34, 28 October 2020

ssDNA, capture probe of test line for RPA method

The capture strand composes the control line of our test strip, which is complementary to the reporter probe on Au nanoparticle. This allows the capture of Au particle at any time with a toxin or not, to verify the function of lateral flow assay.

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]

Characterisation of this part

Design

Besides aptamers, we have some short single stranded DNA known as 'probes', which binds to other single stranded DNA. BBa_K3593005 is one of those so-called 'probes' in our design, and play important roles in our hardware, in which it binds and immobilizes the aptamer, as the aptamer amplicon has a single strand DNA of poly A resembling the real process in organism during DNA transcription. this sequence is reserved from primer of amplification due to a C3 spacer preventing elongation. That's because poly A can hardly form secondary structure on its own, thus it will not affect the function of aptamer.BBa_K3593005 is completely consisted of thymines, which can bind strongly with our aptamer with a complementary strand to it. The use of 'Poly T' is used in several articles.[1][2][3] Its 5' end is conjugated to biotin[4] to bind with streptavidin.

References

1.Chao Zhu, Guilan Zhang, Yafei Huang, Shuming Yang, Shuyue Ren, Zhixian Gao, Ailiang Chen, Dual-competitive lateral flow aptasensor for detection of aflatoxin B1 in food and feedstuffs, Journal of Hazardous Materials https://doi.org/10.1016/j.jhazmat.2017.10.026
2.Wu, S., Liu, L., Duan, N. et al. A test strip for ochratoxin A based on the use of aptamer-modified fluorescence upconversion nanoparticles. Microchim Acta 185, 497 (2018). https://doi.org/10.1007/s00604-018-3022-0
3.Delley CL, Liu L, Sarhan MF, Abate AR. Combined aptamer and transcriptome sequencing of single cells. Sci Rep. 2018 Feb 13;8(1):2919. doi: 10.1038/s41598-018-21153-y. PMID: 29440771; PMCID: PMC5811598.
4.Jauset-Rubio M, Svobodová M, Mairal T, et al. Aptamer Lateral Flow Assays for Ultrasensitive Detection of β-Conglutin Combining Recombinase Polymerase Amplification and Tailed Primers. Anal Chem. 2016;88(21):10701-10709. doi:10.1021/acs.analchem.6b03256