Difference between revisions of "Part:BBa K4586023"

 
 
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<partinfo>BBa_K4586023 short</partinfo>
 
<partinfo>BBa_K4586023 short</partinfo>
  
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C\D Box or kink turn is a single stranded RNA that form 3D hairpin structure which have an affinity to L7Ae.
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==Part Description==
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C\D Box or kink turn is a single stranded RNA that form 3D hairpin structure which have an affinity to L7Ae. Therefore, C\D box and L7Ae are used in multiple biological circuit due to their ability to perform variable functions.
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==Usage==
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we implemented this part in our design to mediate the loading of our therapeutic agent into exosomes selectively and efficiently, through adding C\D box in the 3` end of our cargo.
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==Literature Characterization==
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NORD27 is a class of c/d box, and the study used a soluble nuclear fraction where fibrillarin is not detected and a portion of SNORD27 is present.
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<html><div align="center"style="border:solid #17252A; width:50%;float:center;"><img style="                              max-width:850px;
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width:75%;
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height:auto;
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position: relative;
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top: 50%;
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left: 35%;
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transform: translate( -50%);
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padding-bottom:25px;
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padding-top:25px;
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"src="https://static.igem.wiki/teams/4586/wiki/literature-characterisation-parts/cd-box.png">
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<p class=MsoNormal align=center style='text-align:left;border:none;width:98% ;justify-content:center;'><span
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lang=EN style='font-size:11.0pt;line-height:115%'>((A) The diagram represents HeLa cell fractionation under the original circumstances. (b) It is Western blot analysis, as 5% of the total volume of each fraction prepared was analyzed by Western blot-specific antibodies used to assess The components of spliceosomes (PRP8 and PRPF39), splicing regulators (CBP80/NCBP1 and hnRNPG), and constitutive SNORD binding proteins (NHP2L1/15.5K, NOP56, NOP58, and fibrillarin) (c) The arrow indicates SNORD27, and boxes refer to hosting exons. RPA was used to assess the distribution of SNORD27 in cellular fractions. The RPA probe covered the specified SNORD27 sequence as well as 5 nucleotides from the next intron. (d) Nuclear supernatant (C) was separated on a 10-45% glycerol gradient, which was subdivided into 20 fractions, and then RPA with an SNORD27 antisense probe was used to analyze and isolate RNA from 50% of each fraction. (E) Western blotting used antibodies recognizing markers for pre-mRNA processing (CBP80, hnRNPG, and SRSF6) to assess individual glycerol gradient fractions. (F) RPA determined The distribution of U1, U2, and U4 snRNAs in the fractions obtained by HeLa cell fractionation (A) (G)SNORD27's association with naturally occurring SNORD-binding proteins NHP2L1, NOP58, and NOP56 that were flag-tagged as well as endogenous fibrillarin were immunoprecipitated and purified together. Then, RT-PCR was used to find SNORD27. GFP-transfected cells were employed as a control.
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</span></p></div></html>
  
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==References==
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Falaleeva, M., Pages, A., Matuszek, Z., Hidmi, S., Agranat-Tamir, L., Korotkov, K., ... & Stamm, S. (2016). Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing. Proceedings of the National Academy of Sciences, 113(12), E1625-E1634.
 
<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
===Usage and Biology===

Latest revision as of 04:21, 25 September 2023


C\D Box

Part Description

C\D Box or kink turn is a single stranded RNA that form 3D hairpin structure which have an affinity to L7Ae. Therefore, C\D box and L7Ae are used in multiple biological circuit due to their ability to perform variable functions.

Usage

we implemented this part in our design to mediate the loading of our therapeutic agent into exosomes selectively and efficiently, through adding C\D box in the 3` end of our cargo.

Literature Characterization

NORD27 is a class of c/d box, and the study used a soluble nuclear fraction where fibrillarin is not detected and a portion of SNORD27 is present.

((A) The diagram represents HeLa cell fractionation under the original circumstances. (b) It is Western blot analysis, as 5% of the total volume of each fraction prepared was analyzed by Western blot-specific antibodies used to assess The components of spliceosomes (PRP8 and PRPF39), splicing regulators (CBP80/NCBP1 and hnRNPG), and constitutive SNORD binding proteins (NHP2L1/15.5K, NOP56, NOP58, and fibrillarin) (c) The arrow indicates SNORD27, and boxes refer to hosting exons. RPA was used to assess the distribution of SNORD27 in cellular fractions. The RPA probe covered the specified SNORD27 sequence as well as 5 nucleotides from the next intron. (d) Nuclear supernatant (C) was separated on a 10-45% glycerol gradient, which was subdivided into 20 fractions, and then RPA with an SNORD27 antisense probe was used to analyze and isolate RNA from 50% of each fraction. (E) Western blotting used antibodies recognizing markers for pre-mRNA processing (CBP80, hnRNPG, and SRSF6) to assess individual glycerol gradient fractions. (F) RPA determined The distribution of U1, U2, and U4 snRNAs in the fractions obtained by HeLa cell fractionation (A) (G)SNORD27's association with naturally occurring SNORD-binding proteins NHP2L1, NOP58, and NOP56 that were flag-tagged as well as endogenous fibrillarin were immunoprecipitated and purified together. Then, RT-PCR was used to find SNORD27. GFP-transfected cells were employed as a control.

References

Falaleeva, M., Pages, A., Matuszek, Z., Hidmi, S., Agranat-Tamir, L., Korotkov, K., ... & Stamm, S. (2016). Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing. Proceedings of the National Academy of Sciences, 113(12), E1625-E1634. 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]