Difference between revisions of "Part:BBa K5036015"

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lang=EN style='padding-bottom:30px;font-size:11.0pt;line-height:115%'>This figure shows that NB1 and NB3 have higher affinity over the NB2 which make them candidates to be used in our switch
 
lang=EN style='padding-bottom:30px;font-size:11.0pt;line-height:115%'>This figure shows that NB1 and NB3 have higher affinity over the NB2 which make them candidates to be used in our switch
 
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==Characterization by Mathematical Modeling==
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The model provides the interaction kinetics of MMP-9 to Nanobody-1 that can be connected to MCP or NSP3 to mediate our TID switch circulation. The result shows an increase in the binding complex upon MMP-9 interaction based on parametric values from literature
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lang=EN style='padding-bottom:30px;font-size:11.0pt;line-height:115%'>Graph(1). Illustrates the relation between decreasing free MMP-9 (Blue line) upon their binding to MMP-9 nanobody (orange line) that results forming a binding complex ( Green line)
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==Reference==
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Lee DW, Kochenderfer JN, Stetler-Stevenson M, Cui YK, Delbrook C, Feldman SA, Fry TJ, Orentas R, Sabatino M, Shah NN, Steinberg SM. T cells expressing CD19 chimeric antigen receptors for acute lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial. The Lancet. 2015 Feb 7;385(9967):517-28.
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Shin YJ, Park SK, Jung YJ, Kim YN, Kim KS, Park OK, Kwon SH, Jeon SH, Trinh le A, Fraser SE, Kee Y, Hwang BJ. Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Sci Rep. 2015 Sep 16;5:14269. doi: 10.1038/srep14269. PMID: 26373678; PMCID: PMC4571616.
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 14:36, 26 September 2024


Nanobody1

Part Description

nanobodies are a unique type of antibody derived from camelids. These single-domain antibodies are significantly smaller and more stable, making them ideal for applications in diagnostics and therapeutics. Nanobodies can be used to develop highly sensitive and specific tests for a variety of diseases, including cancer and autoimmune disorders. Their compact size and stability also make them promising candidates for targeted drug delivery and other biomedical applications

Usage

we insert nanobodies to reach the conditioned circular RNA by mediating the attachment between NSP3 and the MCP of the aptamer

Dry lab Characterization

We Started by making a decision about which Nanobodies are candidates to be used in our project. We had to nominate 2 of 3 available nanobodies for the MMP-9 so we started by validating the nanobodies binding affinity to the MMP-9

MMP9-NB1 complex

This figure confirmed that The first nanobody-MMP9 interaction scored a binding stability (ΔG) of -12.3 kcal mol-1 which is considered a high binding stability .

Then we compared the binding stability between different nanobodies to MMP9

This figure shows that NB1 and NB3 have higher affinity over the NB2 which make them candidates to be used in our switch .

Characterization by Mathematical Modeling

The model provides the interaction kinetics of MMP-9 to Nanobody-1 that can be connected to MCP or NSP3 to mediate our TID switch circulation. The result shows an increase in the binding complex upon MMP-9 interaction based on parametric values from literature

Graph(1). Illustrates the relation between decreasing free MMP-9 (Blue line) upon their binding to MMP-9 nanobody (orange line) that results forming a binding complex ( Green line) .

Reference

Lee DW, Kochenderfer JN, Stetler-Stevenson M, Cui YK, Delbrook C, Feldman SA, Fry TJ, Orentas R, Sabatino M, Shah NN, Steinberg SM. T cells expressing CD19 chimeric antigen receptors for acute lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial. The Lancet. 2015 Feb 7;385(9967):517-28.

Shin YJ, Park SK, Jung YJ, Kim YN, Kim KS, Park OK, Kwon SH, Jeon SH, Trinh le A, Fraser SE, Kee Y, Hwang BJ. Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Sci Rep. 2015 Sep 16;5:14269. doi: 10.1038/srep14269. PMID: 26373678; PMCID: PMC4571616.


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]