Difference between revisions of "Part:BBa K3897005"

 
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pH-sensitive HR2 aptamer.
  
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=Design=
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===Usage and Biology===
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Based on the design in previous literature<sup>[1]</sup>, we adopted a similar design by switching out ATP aptamer with HR2 aptamer<sup>[2]</sup>.
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pHs-HR2 consists of 3 parts:
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- HR2 aptamer
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- pH-sensitive DNA switch
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- Complementary strand for HR2 aptamer
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The 5' end of the DNA switch connects the HR2 aptamer and the 3' end connects the complementary strand.
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When at normal pH (7.1), the DNA switch will form a duplex shape, which places the two ends together. Thus, HR2 aptamer is inhibited by complementary strand. When the aptamer is placed in low pH (6.5), protonation of the bases occurs and stabilizes C·G Hoogsteen base pairing, which folds the ssDNA chain into a triplex. The triplex shape separates the two ends so the aptamer functions normally.
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[[File:T--GreatBay_SCIE--Design Basis.png|800px|thumb|center|<b>Figure 1 The design basis of pH-sensitive HR2 aptamer<sup>[1]</sup>.</b>]]
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=Sequence and Features=
  
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<span class='h3bb'>Sequence and Features</span>
 
 
<partinfo>BBa_K3897005 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3897005 SequenceAndFeatures</partinfo>
  
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=Reference=
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<ol>
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li>Thompson, I., Zheng, L., Eisenstein, M., &amp; Soh, H. T. (2020). Rational design of aptamer switches with programmable pH response. <em>Nature communications</em>, <em>11</em>(1), 2946. https://doi.org/10.1038/s41467-020-16808-</li>
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<li>Liu, Z., Duan, J. H., Song, Y. M., Ma, J., Wang, F. D., Lu, X., &amp; Yang, X. D. (2012). Novel HER2 aptamer selectively delivers cytotoxic drug to HER2-positive breast cancer cells in vitro. <em>Journal of translational medicine</em>, <em>10</em>, 148.https://doi.org/10.1186/1479-5876-10-148</li>
  
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</ol>
 
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===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K3897005 parameters</partinfo>
 
<partinfo>BBa_K3897005 parameters</partinfo>
 
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Revision as of 02:31, 9 October 2021


pH-sensitive HR2 Aptamer, allows high affinity for HER2 receptor under low pH

pH-sensitive HR2 aptamer.

Design

Based on the design in previous literature[1], we adopted a similar design by switching out ATP aptamer with HR2 aptamer[2]. pHs-HR2 consists of 3 parts: - HR2 aptamer - pH-sensitive DNA switch - Complementary strand for HR2 aptamer The 5' end of the DNA switch connects the HR2 aptamer and the 3' end connects the complementary strand. When at normal pH (7.1), the DNA switch will form a duplex shape, which places the two ends together. Thus, HR2 aptamer is inhibited by complementary strand. When the aptamer is placed in low pH (6.5), protonation of the bases occurs and stabilizes C·G Hoogsteen base pairing, which folds the ssDNA chain into a triplex. The triplex shape separates the two ends so the aptamer functions normally.

Figure 1 The design basis of pH-sensitive HR2 aptamer[1].

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]

Reference

    li>Thompson, I., Zheng, L., Eisenstein, M., & Soh, H. T. (2020). Rational design of aptamer switches with programmable pH response. Nature communications, 11(1), 2946. https://doi.org/10.1038/s41467-020-16808-
  1. Liu, Z., Duan, J. H., Song, Y. M., Ma, J., Wang, F. D., Lu, X., & Yang, X. D. (2012). Novel HER2 aptamer selectively delivers cytotoxic drug to HER2-positive breast cancer cells in vitro. Journal of translational medicine, 10, 148.https://doi.org/10.1186/1479-5876-10-148