Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog
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<div id="description_area"> | <div id="description_area"> | ||
<h2>Catalog for regulatory RNAs</h2> | <h2>Catalog for regulatory RNAs</h2> | ||
- | <p><font color="white"> Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them. | + | <p><font color="white"> Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them.Over the years, the number of non-coding RNAs in Part Registry has increased steadily over time and many have been made available to end users. More than 400 entries in the Part Registry are related to RNA devices (updated 25-12-2014). Based on different mode of actions and natures of non-coding RNAs (ncRNAs), they can be grouped under different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing ncRNAs. Some of them are simply grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them. For example, BBa_K145013, which is a part for antisense LuxI, could be used to add an extra layer of control to the widely utilized quorum sensing Lux pathway but it has not been extensively reused. It is likely that Part Registry users are unaware of its existence because there has yet to be an information hub for ncRNA. |
<br><br> | <br><br> | ||
- | We would like to solve this problem by designing a list of category tags as well as a guideline, so that automated display of | + | We would like to solve this problem by designing a list of category tags as well as a guideline, so that automated display of non-coding RNAs by the <parttable> function can be facilitated. By doing so, we hope that we can assist other users to find and use those parts efficiently. Ultimately we want to facilitate the implementation of the philosophy of Part Registry, which is to get and give (and share), through a better organization of ncRNA parts in the registry. |
<br><br> | <br><br> | ||
This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval, we will tag existing regulatory RNAs and complete the page. Being part of the cross-cohort "Project Riboregulator", the page is far from complete and is expected to take shape by Summer 2015. We welcome and encourage constant update and adoption of this page in the future.</font></p> | This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval, we will tag existing regulatory RNAs and complete the page. Being part of the cross-cohort "Project Riboregulator", the page is far from complete and is expected to take shape by Summer 2015. We welcome and encourage constant update and adoption of this page in the future.</font></p> | ||
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<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
<p> | <p> | ||
- | + | Riboregulators regulate translation by two elements: a cis-repressive sequence upstream of RBS, and a trans-activating RNA. In absence of the latter, the cis-repressive sequence promotes formation of a hairpin at the RBS. With the RBS locked up, translation cannot take place.. Trans-activating RNA, when introduced, can form complementary bases to cis-repressive sequence, promotes disassembly of the hairpin, and expose the RBS for ribosomal binding, allowing translation to occur. </p> | |
- | + | </p> | |
- | + | ||
</div> | </div> | ||
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<div class='content_1'><h3>RNA Aptamer</h3> | <div class='content_1'><h3>RNA Aptamer</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p>A RNA aptamer | + | <p>A RNA aptamer can fold into a tertiary confirmation that binds with strong affinity and high specificity to small molecules through non-Watson-Crick base pairing.</p> |
</p> | </p> | ||
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<!--end of catalog --> | <!--end of catalog --> | ||
<!--catalog --> | <!--catalog --> | ||
- | <div class='content_1'><h3> | + | <div class='content_1'><h3>CRISPR</h3> |
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p> | + | <p>CRISPR/Cas RNAs are guiding RNAs that direct Cas proteins to their spacers. They can be a 2-subunit RNA comprising CRISPR RNA (crRNA) and trans-acting crRNA (tracrRNA). They can also be a single guide RNA by fusing the above 2 functional domains together through RNA linkers. They associate with Cas proteins or their derivatives and guide them to DNA containing complementary sequence to crRNA./p> |
</p> | </p> | ||
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<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
<p> | <p> | ||
- | + | RNA-OUT is a small ncRNA that regulates translation on the RNA level. RNA-OUT will bind to 5'UTR, which include the RBS of mRNA and prevents the ribosome from binding to mRNA to inhibit translation of downstream gene. RNA-IN is also a ncRNA that is antisense to RNA-OUT and the binding of RNA-IN and RNA-OUT will prevent RNA-OUT from binding to mRNA, thus allowing ribosome to bind to mRNA and initiating translation. </p> | |
- | + | </p> | |
- | + | ||
</div> | </div> | ||
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<div class='content_1'><h3>RNA interference (RNAi)</h3> | <div class='content_1'><h3>RNA interference (RNAi)</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | + | <p> | |
- | + | Small interfering RNAs (siRNAs) and micro RNAs (miRNAs) function through the RNA interference (RNAi) pathway. siRNAs are usually produced by "dicing" exogenous, long double stranded RNA into 21-nucleotides small fragments. Whereas miRNAs usually have an endogenous origin and started as hairpin transcripts. Processed siRNAs or miRNAs associates with Argonaute in the RNA-induced silencing complex (RISC). The complex then search for RNA targets using the siRNA/miRNA, and in most cases degrades the latter, resulting in inhibition or reduction of gene expression. | |
- | + | </p> | |
</div> | </div> | ||
<div class = "catalog_table_area"> | <div class = "catalog_table_area"> | ||
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<div class='content_1'><h3>Riboswitch</h3> | <div class='content_1'><h3>Riboswitch</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p>A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an on or off manner. Riboswitches usually contain sensor domains for binding of small molecules and regulatory domains for gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation. </p> | + | <p>A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an on or off manner. Riboswitches usually contain sensor domains that bind small molecules and regulatory domains that regulate gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation. on or off manner. Riboswitches usually contain sensor domains for binding of small molecules and regulatory domains for gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation. </p> |
- | + | </p> | |
</div> | </div> | ||
<div class = "catalog_table_area"> | <div class = "catalog_table_area"> | ||
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<div class='content_1'><h3>Ribozyme</h3> | <div class='content_1'><h3>Ribozyme</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p>A ribozyme is a RNA molecule with intrinsic catalytic activity, usually cleavage | + | <p>A ribozyme is a RNA molecule with intrinsic catalytic activity, which are usually cleavage or ligation activities.</p> |
</div> | </div> | ||
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<div class='content_1'><h3>Aptazyme</h3> | <div class='content_1'><h3>Aptazyme</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p> | + | <p>RNA aptazymes, as the name suggests, are RNAs that carry properties o both aptamers and ribozymes. They are capable of sensing small molecules. Ribozyme-mediated cleavage is triggered upon ligand binding.</p> |
- | <p> | + | <p>• For a part to be qualified as an apatazyme, the aptamer domain and the ribozyme domain should be functionally coupled. A RNA that contains aptamer domains and ribozyme domains without functional relationships is merely a composite RNA device. </p> |
</div> | </div> | ||
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<div class='content_1'><h3>pT181</h3> | <div class='content_1'><h3>pT181</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | + | <p> | |
- | + | The pT181-RNAI is a special class of ncRNAs derived from elements in the Staphylococcus aureus pathogenicity plasmid pT181. A specific 5’ UTR region would normally form an anti-termination loop. pT181-RNAI, when introduced, induces formation of a premature terminator loop instead, which results in early termination an incompletely transcribed mRNA. | |
+ | </p> | ||
</div> | </div> | ||
<div class = "catalog_table_area"> | <div class = "catalog_table_area"> | ||
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<div class='content_1'><h3>Complex</h3> | <div class='content_1'><h3>Complex</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p>This | + | <p>This tag describes ncRNA BioBricks containing 2 or more ncRNAs..</p> |
</div> | </div> | ||
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<div class='content_1'><h3>Target sequence</h3> | <div class='content_1'><h3>Target sequence</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p>This | + | <p>This tag describes with segments of ncRNAs that are purposefully designed to serve as recognizable targets by other ncRNAs.</p> |
</div> | </div> | ||
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<div class='content_1'><h3>Other</h3> | <div class='content_1'><h3>Other</h3> | ||
<div class= "catalog_description_area"> | <div class= "catalog_description_area"> | ||
- | <p> | + | <p>This tag describes ncRNAs that do not belong to any types of ncRNA listed above</p> |
</div> | </div> |
Revision as of 05:04, 29 January 2015
Catalog for regulatory RNAs
Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them.Over the years, the number of non-coding RNAs in Part Registry has increased steadily over time and many have been made available to end users. More than 400 entries in the Part Registry are related to RNA devices (updated 25-12-2014). Based on different mode of actions and natures of non-coding RNAs (ncRNAs), they can be grouped under different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing ncRNAs. Some of them are simply grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them. For example, BBa_K145013, which is a part for antisense LuxI, could be used to add an extra layer of control to the widely utilized quorum sensing Lux pathway but it has not been extensively reused. It is likely that Part Registry users are unaware of its existence because there has yet to be an information hub for ncRNA.
We would like to solve this problem by designing a list of category tags as well as a guideline, so that automated display of non-coding RNAs by the
This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval, we will tag existing regulatory RNAs and complete the page. Being part of the cross-cohort "Project Riboregulator", the page is far from complete and is expected to take shape by Summer 2015. We welcome and encourage constant update and adoption of this page in the future.
Riboregulator
Riboregulators regulate translation by two elements: a cis-repressive sequence upstream of RBS, and a trans-activating RNA. In absence of the latter, the cis-repressive sequence promotes formation of a hairpin at the RBS. With the RBS locked up, translation cannot take place.. Trans-activating RNA, when introduced, can form complementary bases to cis-repressive sequence, promotes disassembly of the hairpin, and expose the RBS for ribosomal binding, allowing translation to occur.
Designer | Part Number | Description |
---|---|---|
Delft 2009 | BBa_K175029 | Weak lock |
Delft 2009 | BBa_K175030 | Key for lcok of weak RBS |
Delft 2009 | BBa_K175030 | Medium lock |
Delft 2009 | BBa_K175030 | Key for Medium lock |
Delft 2009 | BBa_K175034 | (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030 |
Delft 2009 | BBa_K175034 | Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032 |
Caltech 2007 | BBa_I759015 | cis3-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759016 | cis4-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759020 | cis8-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759027 | cis3-repressed, tet-regulated Q |
Caltech 2007 | BBa_I759028 | cis4-repressed, tet-regulated Q |
Caltech 2007 | BBa_I759014 | (cis2-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759017 | cis5-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759018 | cis6-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759019 | cis7-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759013 | cis1-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759032 | Ptet_cis1_YFP |
Caltech 2007 | BBa_I759034 | Ptet_cis2_YFP |
Caltech 2007 | BBa_I759036 | Ptet_cis3_YFP |
Caltech 2007 | BBa_I759038 | Ptet_cis4_YFP |
Caltech 2007 | BBa_I759040 | Ptet_cis5_YFP |
Caltech 2007 | BBa_I759042 | Ptet_cis6_YFP |
Caltech 2007 | BBa_I759044 | Ptet_cis7_YFP |
Caltech 2007 | BBa_I759046 | Ptet_cis8_YFP |
Caltech 2007 | BBa_I759023 | pBAD-trans2 |
Caltech 2007 | BBa_I759022 | pBAD-trans1 |
Caltech 2007 | BBa_I759024 | pBAD-trans3 |
Caltech 2007 | BBa_I759025 | pBAD-trans4 |
Caltech 2007 | BBa_I759026 | pBAD-trans5 |
Peking 2007 | BBa_I714070 | R0040-J23078-pTet-Lock3 |
Peking 2007 | BBa_I714080 | [R0040][J23078][E0040][B0015] |
Peking 2007 | BBa_I714081 | R0040-J01010-E0040-B0015 |
Peking 2007 | BBa_I714037 | R751+ C600 E.coli cells with traI-R751 knockout |
Peking 2007 | BBa_I714074 | R0010-J23066-pLac-Key3-DblTerm Uses Lock and Key 3 from berkeley |
K.U. Leuven 2008 | BBa_K145215 | FILTER Key (TetR promoter + key) |
K.U. Leuven 2008 | BBa_K145216 | FILTER T7 RNA pol Lock from berkeley |
K.U. Leuven 2008 | BBa_K145217 | FILTER Complete The two previous together |
K.U. Leuven 2008 | BBa_K145220 | INVERTED TIMER |
K.U. Leuven 2008 | BBa_K145225 | RESET lactonase |
K.U. Leuven 2008 | BBa_K145300 | Lactonase controlled by key/lock |
K.U. Leuven 2008 | BBa_K145301 | lacI controlled by key/lock |
K.U. Leuven 2008 | BBa_K145302 | luxI generator controlled by key/lock |
K.U. Leuven 2008 | BBa_K145303 | GFP generator controlled by key/lock |
K.U. Leuven 2008 | BBa_K145003 | T7 PoPS -> RiboKey 3d |
K.U. Leuven 2008 | BBa_K145004 | T7 PoPS + RiboLock |> LuxI |
K.U. Leuven 2008 | BBa_K145005 | T7 PoPS + PR -> cI |
K.U. Leuven 2008 | BBa_K145216 | FILTER T7 RNA pol |
K.U. Leuven 2008 | BBa_K145251 | OLD RESET lactonase |
K.U. Leuven 2008 | BBa_K145253 | OLD INVERTIMER Part 1 |
K.U. Leuven 2008 | BBa_K145255 | NEW INVERTIMER part 1 |
K.U. Leuven 2008 | BBa_K145264 | test FILTER (new) |
K.U. Leuven 2008 | BBa_K145265 | test FILTER (old) |
K.U. Leuven 2008 | BBa_K145271 | GFP regulated by AND-gate |
K.U. Leuven 2008 | BBa_K145272 | GFP regulated by AND-gate |
K.U. Leuven 2008 | BBa_K145275 | T7 polymerase generator under TetR repressible promoter (filter) |
K.U. Leuven 2008 | BBa_K145276 | T7 polymerase generator under TetR repressible promoter |
K.U. Leuven 2008 | BBa_K145277 | T7 DNA polymerase regulated by lock |
K.U. Leuven 2008 | BBa_K145278 | T7 DNA polymerase regulated by [lock3d] |
K.U. Leuven 2009 | BBa_K238004 | Vanillin synthesis |
K.U. Leuven 2009 | BBa_K238006 | Short version of vanillin synthesis |
K.U. Leuven 2009 | BBa_K238012 | short version II of vanillin synthesis |
Groningen 2011 | BBa_K607005 | short version II of vanillin synthesis |
Groningen 2011 | BBa_K607000 | PhybB_taRNA |
VictoriaBC 2009 | BBa_K235010 | [K145303] (ribokey-controlled GFP generator) |
VictoriaBC 2009 | BBa_K235000 | [R0010][J23066] (pLac+ribokey+stop) |
VictoriaBC 2009 | BBa_K235001 | [J23102][J23066] (constitutive promoter+ribokey+stop) |
VictoriaBC 2009 | BBa_K235009 | [J23102][J23032] (constitutive promoter+ribolocked RBS) |
VictoriaBC 2009 | BBa_K235011 | [K235009][K235005] (ribokey-controlled mCherry generator) |
VictoriaBC 2009 | BBa_K235013 | [K145303][K235000] (ribokey-mediated pLac-controlled GFP reporter) |
VictoriaBC 2009 | BBa_K235014 | [K145303][K235001] (ribokey-mediated GFP generator) |
VictoriaBC 2009 | BBa_K235016 | [I0500][J23032] (pAra+ribolocked RBS) |
VictoriaBC 2009 | BBa_K235019 | [K235016][K235003] (ribokey-mediated pAra-controlled lambda repressor generator) |
VictoriaBC 2009 | BBa_K235021 | [K235009][K235003] (ribokey-mediated lambda repressor generator) |
VictoriaBC 2009 | BBa_K235022 | [K235018][K235019] (mCherry generator, pAra-controlled ribokey-mediated signal inversion) |
VictoriaBC 2009 | BBa_K235024 | [K235018][K235021] (mCherry generator, ribokey-mediated signal inversion) |
VictoriaBC 2009 | BBa_K235025 | [K235022][K235000] (NAND gate, pAra and pLac input signal control, mCherry output signal) |
VictoriaBC 2009 | BBa_K235026 | [K235022][K235001] (NAND gate control test, pLac positive control) |
VictoriaBC 2009 | BBa_K235027 | [K235024][K235000] (NAND gate control test, arabinose positive control) |
VictoriaBC 2009 | BBa_K235028 | [K235024][K235001] (NAND gate control test, positive control) |
Melborne2008 | BBa_K085000 | (lacI)promoter->key3c |
Melborne2008 | BBa_K085002 | pTet->lock3d->GFP |
Calgary 2007 | BBa_I737003 | OmpF controlled RNA Key |
Calgary 2007 | BBa_I737006 | Temperature induced repression/activation of an RNA key |
Calgary 2007 | BBa_I737005 | AHL and RNA lock controlled AraC |
RNA Aptamer
A RNA aptamer can fold into a tertiary confirmation that binds with strong affinity and high specificity to small molecules through non-Watson-Crick base pairing.
Designer | Part Number | Description |
---|
CRISPR
CRISPR/Cas RNAs are guiding RNAs that direct Cas proteins to their spacers. They can be a 2-subunit RNA comprising CRISPR RNA (crRNA) and trans-acting crRNA (tracrRNA). They can also be a single guide RNA by fusing the above 2 functional domains together through RNA linkers. They associate with Cas proteins or their derivatives and guide them to DNA containing complementary sequence to crRNA./p>
Designer | Part Number | Description |
---|
RNA-IN / RNA-OUT
RNA-OUT is a small ncRNA that regulates translation on the RNA level. RNA-OUT will bind to 5'UTR, which include the RBS of mRNA and prevents the ribosome from binding to mRNA to inhibit translation of downstream gene. RNA-IN is also a ncRNA that is antisense to RNA-OUT and the binding of RNA-IN and RNA-OUT will prevent RNA-OUT from binding to mRNA, thus allowing ribosome to bind to mRNA and initiating translation.
Designer | Part Number | Description |
---|
RNA interference (RNAi)
Small interfering RNAs (siRNAs) and micro RNAs (miRNAs) function through the RNA interference (RNAi) pathway. siRNAs are usually produced by "dicing" exogenous, long double stranded RNA into 21-nucleotides small fragments. Whereas miRNAs usually have an endogenous origin and started as hairpin transcripts. Processed siRNAs or miRNAs associates with Argonaute in the RNA-induced silencing complex (RISC). The complex then search for RNA targets using the siRNA/miRNA, and in most cases degrades the latter, resulting in inhibition or reduction of gene expression.
Designer | Part Number | Description |
---|
Riboswitch
A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an on or off manner. Riboswitches usually contain sensor domains that bind small molecules and regulatory domains that regulate gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation. on or off manner. Riboswitches usually contain sensor domains for binding of small molecules and regulatory domains for gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation.
Designer | Part Number | Description |
---|
Ribozyme
A ribozyme is a RNA molecule with intrinsic catalytic activity, which are usually cleavage or ligation activities.
Designer | Part Number | Description |
---|
Aptazyme
RNA aptazymes, as the name suggests, are RNAs that carry properties o both aptamers and ribozymes. They are capable of sensing small molecules. Ribozyme-mediated cleavage is triggered upon ligand binding.
• For a part to be qualified as an apatazyme, the aptamer domain and the ribozyme domain should be functionally coupled. A RNA that contains aptamer domains and ribozyme domains without functional relationships is merely a composite RNA device.
Designer | Part Number | Description |
---|
pT181
The pT181-RNAI is a special class of ncRNAs derived from elements in the Staphylococcus aureus pathogenicity plasmid pT181. A specific 5’ UTR region would normally form an anti-termination loop. pT181-RNAI, when introduced, induces formation of a premature terminator loop instead, which results in early termination an incompletely transcribed mRNA.
Designer | Part Number | Description |
---|
Complex
This tag describes ncRNA BioBricks containing 2 or more ncRNAs..
Designer | Part Number | Description |
---|
Target sequence
This tag describes with segments of ncRNAs that are purposefully designed to serve as recognizable targets by other ncRNAs.
Designer | Part Number | Description |
---|
Other
This tag describes ncRNAs that do not belong to any types of ncRNA listed above
Designer | Part Number | Description |
---|
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