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定性3文字 <ref>T7 phage factor required for managing RpoS in Escherichia coli. Tabib-Salazar A,  Liu B,  Barker D,  Burchell L,  Qimron U,  Matthews SJ,  Wigneshweraraj S. Proc Natl Acad Sci U S A, 2018 Jun 5;115(23):E5353-E5362.  PMID:29789383</ref>. 又一个参考文献在一对尖括号内，例子里的参考文献格式是pubmed直接copy的
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[[File:T--Fudan--定性3图片不要用中文做文件名.png|400px|thumb|none|'''Figure 3. 图标题.''' 图注 引用的不要忘了写某某人某某年的出处]]

Revision as of 11:18, 11 October 2022


Hammerhead ribozyme


Introduction

2021 Fudan

Hammerhead ribozyme was first found in the genome of viruses and viroids. It involved in the processing of RNA transcripts based on rolling-circle replication. The tandem copy of RNA sequence will be generated in the roll ring replication, and the self-cleaving activity of ribozyme can ensure the generation of RNA copy of unit length.[1]

The secondary structure of hammerhead ribozyme resembles a hammer. According to different open helix tips, hammerhead ribozymes can be divided into three types: TypeⅠ, Type II and Type III. The catalytic center of ribozyme consists of 15 highly conserved bases surrounded by three helixs(HelixⅠ, Helix II and Helix III). The long-range interaction between HelixⅠ and Helix II can help stabilize the conformation of the catalytic center of the enzyme and improve the catalytic efficiency (Figure 1).[2] While working, ribozymes utilize a network of defined hydrogen bonds, ionic and hydrophobic interactions to generate catalytic pockets, which capitalize on steric constraints to generate in-line cleavage alignments and general acid-base chemistry to catalyze site-specific cleavage of the phosphodiester backbone.[3]

Figure 1. Overall tertiary structure of different types of hammerhead ribozymes.Blue marks highly conserved bases. The black arrow marks the digestion site. Red marks the long-range interaction between HelixⅠand Helix II.(Jimenez, Randi M et al. 2015)

Usage and Biology

Hammerhead ribozyme can perform self-cleaving efficiently. While constructing polycistrons in E. coli, ribozyme sequence should be inserted between two coding sequences. After the transcription of CDS is completed, the ribozyme will conduct self-cleaving and separate the long piece of mRNA into segments corresponding to each CDS. Therefore, the translation process of target proteins will depend on their respective RBS strength.

Characterization

定性1标题

定性1文字

File:T--Fudan--定性1图片不要用中文做文件名.png
Figure 1. 图标题. 图注 引用的不要忘了写某某人某某年的出处

定性1小结

定性2标题

定性2文字

File:T--Fudan--定性2图片不要用中文做文件名.png
Figure 2. 图标题. 图注 引用的不要忘了写某某人某某年的出处

定性2小结


定性3标题

定性3文字

File:T--Fudan--定性3图片不要用中文做文件名.png
Figure 3. 图标题. 图注 引用的不要忘了写某某人某某年的出处

定性3小结

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]



References

  1. ↑ Ferré-D'Amaré, A. R., & Scott, W. G. (2010). Small self-cleaving ribozymes. Cold Spring Harbor perspectives in biology, 2(10), a003574. https://doi.org/10.1101/cshperspect.a003574
  2. ↑ Jimenez, R. M., Polanco, J. A., & Lupták, A. (2015). Chemistry and Biology of Self-Cleaving Ribozymes. Trends in biochemical sciences, 40(11), 648–661. https://doi.org/10.1016/j.tibs.2015.09.001
  3. ↑ Ren, A., Micura, R., & Patel, D. J. (2017). Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes. *Current opinion in chemical biology*, *41*, 71–83.