Difference between revisions of "Part:BBa K5102073"

Revision as of 12:08, 2 October 2024

pRAM_ProgRAM-recording-tape2.0

The composite part features several key elements within its modular design:

Mammalian promoter: promoter for plasmid expression of ProgRAM in a mammalian cell line. In the current instance, a CMV enhancer (<a href="https://parts.igem.org/Part:BBa_K5102067">BBa_K5102067</a>) and a CMV promotor (<a href="https://parts.igem.org/Part:BBa_K2217006">BBa_K2217006</a>). Alternative mammalian promoters driving the expression are possible, for instance, <a href="https://parts.igem.org/Part:BBa_J433025">BBa_J433025</a>, <a href="https://parts.igem.org/Part:BBa_J433001">BBa_J433001</a>, or <a href="https://parts.igem.org/Part:BBa_J433002">BBa_J433002</a>.
5'UTR (601–680): 5' untranslated region. In the current instance, CMV 5'UTR (<a href="https://parts.igem.org/Part:BBa_K5102068">BBa_K5102068</a>). This region can be substituted with synthetic alternatives, such as (<a href="https://parts.igem.org/Part:BBa_K5102079">BBa_K5102079</a> and <a href="https://parts.igem.org/Part:BBa_K5102080">BBa_K5102080</a>), offering customizable designs for modulation of RNA stability and ribosome recruitment as outlined on the <a href="https://2024.igem.wiki/munich/model/#synthetic-5-utr-design">iGEM Munich 2024 model page</a>.
T7 promoter (681–698): phage T7 promoter (<a href="https://parts.igem.org/Part:BBa_K3633015">BBa_K3633015</a>) for in vitro expression of the ProgRAM.
Recording tape (700–751): recording tape, functioning as a deamination target and translation initiation site. In the current instance, a 3.0 tape design (<a href="https://parts.igem.org/Part:BBa_K5102041">BBa_K5102041</a>). This is a recording tape based on the REPAIR system using 30 nt long gRNAs. Alternative designs based on a co-optimal length of 50 nt, are also provided (<a href="https://parts.igem.org/Part:BBa_K5102106">BBa_K5102106</a> and <a href="https://parts.igem.org/Part:BBa_K5102107">BBa_K5102107</a>). Alternative 30 nt-based design comprises parts <a href="https://parts.igem.org/Part:BBa_K5102072">BBa_K5102072</a> to <a href="https://parts.igem.org/Part:BBa_K5102078">BBa_K5102078</a> The deamination site (writing site), also known as the central base triplet (CBT), was chosen for its high deamination efficacy and fidelity to be at the +22 position. A sequence of 'CAU' was chosen for the CBT following the mammalian Kozak consensus sequence, which results in the deamination environment of moderate efficiency. The reading site was chosen for its high potency towards Cas13b binding disruption to be at the +12 position. The current instance of the tape features 3 intact START codons, corresponding to the initial 0th state, with each START codon having a +1 frame shift relative to its predecessor. The tape was constructed from these minimal sequence constraints, as highlighted on the <a href="https://2024.igem.wiki/munich/model/#tape-construction-algorithm">iGEM Munich 2024 model page</a>.
Coding region (753–4237): in vivo reporter system featuring a fluorescent proteins array. Each array element comprises T2A-XFP-P2A-eUnaG-STOP, with a +1 frame shift relative to its predecessor. The T2A (<a href="https://parts.igem.org/Part:BBa_K5102012">BBa_K5102012</a>, <a href="https://parts.igem.org/Part:BBa_K5102013">BBa_K5102013</a>, and <a href="https://parts.igem.org/Part:BBa_K5102014">BBa_K5102014</a>) site divides a near-native XFP from the upstream sequences, while the P2A (<a href="https://parts.igem.org/Part:BBa_K5102015">BBa_K5102015</a>, <a href="https://parts.igem.org/Part:BBa_K5102016">BBa_K5102016</a>, and <a href="https://parts.igem.org/Part:BBa_K5102017">BBa_K5102017</a>) site functions as a separator between the XFP and the eUnaG. This arrangement of 2A peptides was chosen to approach proportionality between expressed proteins. eUnaG (<a href="https://parts.igem.org/Part:BBa_K5102009">BBa_K5102009</a>, <a href="https://parts.igem.org/Part:BBa_K5102010">BBa_K5102010</a>, and <a href="https://parts.igem.org/Part:BBa_K5102011">BBa_K5102011</a>) is used as total protein expression control and is present in all 3 reading frames. The current instance features miRFP670nano3 (<a href="https://parts.igem.org/Part:BBa_K5102001">BBa_K5102001</a>), mScarlet3 (<a href="https://parts.igem.org/Part:BBa_K5102002">BBa_K5102002</a>), and mTagBFP2 (<a href="https://parts.igem.org/Part:BBa_K5102003">BBa_K5102003</a>) as switching fluorescent proteins indicating the current tape state. Alternative proteins may be utilized if they comply with sequence requirements. The sequence of the current array was enabled by removing hidden stop codons and optimizing for various other parameters, including codon adaptation, minimization of repeats, and exclusion of splice and polyadenylation sites, among others, which is explained in detail on the <a href="https://2024.igem.wiki/munich/model/#codon-optimization">iGEM Munich 2024 model page</a>.
3'UTR (4241–4284): 3' untranslated region. In the current instance, human beta-globin 3'UTR (<a href="https://parts.igem.org/Part:BBa_K5102053">BBa_K5102053</a>).
Aptamer (4295-4317): an RNA aptamer acting as an anchor, enabling tape pulldown or localization. In the current instance, PP7 phage aptamer (<a href="https://parts.igem.org/Part:BBa_K5102054">BBa_K5102054</a>).
T7 terminator (4334–4381): phage T7 transcriptional terminator (<a href="https://parts.igem.org/Part:BBa_K73172">BBa_K73172</a>) for in vitro expression of the ProgRAM.
WPRE (4382–4979): woodchuck hepatitis virus posttranscriptional regulatory element (<a href="https://parts.igem.org/Part:BBa_K5102069">BBa_K5102069</a>) for increasing transgene expression by minimizing readthrough transcription and improving termination.
polyA (4984–5105): a polyadenylation site for mammalian transcription termination and RNA polyadenylation. In the current instance, SV40 polyA (<a href="https://parts.igem.org/Part:BBa_K2217005">BBa_K2217005</a>). Alternative polyA sites could be used.

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal SpeI site found at 18
12
INCOMPATIBLE WITH RFC[12]
Illegal SpeI site found at 18
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 2494
Illegal BamHI site found at 3554
Illegal XhoI site found at 2563
23
INCOMPATIBLE WITH RFC[23]
Illegal SpeI site found at 18
25
INCOMPATIBLE WITH RFC[25]
Illegal SpeI site found at 18
Illegal NgoMIV site found at 4899
Illegal AgeI site found at 3645
1000
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K5102073 short</partinfo>
-The composite part features several key elements within its modular design:
+<p>The composite part features several key elements within its modular design:</p>
-- **Mammalian promoter**: promoter for plasmid expression of ProgRAM in a mammalian cell line. In the current instance, a CMV enhancer ([BBa_K5102067](https://parts.igem.org/Part:BBa_K5102067)) and a CMV promotor ([BBa_K2217006](https://parts.igem.org/Part:BBa_K2217006)). Alternative mammalian promoters driving the expression are possible, for instance, [BBa_J433025](https://parts.igem.org/Part:BBa_J433025), [BBa_J433001](https://parts.igem.org/Part:BBa_J433001), or [BBa_J433002](https://parts.igem.org/Part:BBa_J433002).
+<ul>
-- **5'UTR** (601–680): 5' untranslated region. In the current instance, CMV 5'UTR ([BBa_K5102068](https://parts.igem.org/Part:BBa_K5102068)). This region can be substituted with synthetic alternatives, such as ([BBa_K5102079](https://parts.igem.org/Part:BBa_K5102079) and [BBa_K5102080](https://parts.igem.org/Part:BBa_K5102080)), offering customizable designs for modulation of RNA stability and ribosome recruitment as outlined on the [iGEM Munich 2024 model page](https://2024.igem.wiki/munich/model/#synthetic-5-utr-design).
+<li><strong>Mammalian promoter</strong>: promoter for plasmid expression of ProgRAM in a mammalian cell line. In the current instance, a CMV enhancer (<a href="https://parts.igem.org/Part:BBa_K5102067">BBa_K5102067</a>) and a CMV promotor (<a href="https://parts.igem.org/Part:BBa_K2217006">BBa_K2217006</a>). Alternative mammalian promoters driving the expression are possible, for instance, <a href="https://parts.igem.org/Part:BBa_J433025">BBa_J433025</a>, <a href="https://parts.igem.org/Part:BBa_J433001">BBa_J433001</a>, or <a href="https://parts.igem.org/Part:BBa_J433002">BBa_J433002</a>.</li>
-- **T7 promoter** (681–698):  phage T7 promoter ([BBa_K3633015](https://parts.igem.org/Part:BBa_K3633015)) for *in vitro* expression of the ProgRAM.
+<li><strong>5&#39;UTR</strong> (601–680): 5&#39; untranslated region. In the current instance, CMV 5&#39;UTR (<a href="https://parts.igem.org/Part:BBa_K5102068">BBa_K5102068</a>). This region can be substituted with synthetic alternatives, such as (<a href="https://parts.igem.org/Part:BBa_K5102079">BBa_K5102079</a> and <a href="https://parts.igem.org/Part:BBa_K5102080">BBa_K5102080</a>), offering customizable designs for modulation of RNA stability and ribosome recruitment as outlined on the <a href="https://2024.igem.wiki/munich/model/#synthetic-5-utr-design">iGEM Munich 2024 model page</a>.</li>
-- **Recording tape** (700–751): recording tape, functioning as a deamination target and translation initiation site. In the current instance, a 3.0 tape design ([BBa_K5102041](https://parts.igem.org/Part:BBa_K5102041)). This is a recording tape based on the REPAIR system using 30 nt long gRNAs. Alternative designs based on a co-optimal length of 50 nt, are also provided ([BBa_K5102106](https://parts.igem.org/Part:BBa_K5102106) and [BBa_K5102107](https://parts.igem.org/Part:BBa_K5102107)). Alternative 30 nt-based design comprises parts [BBa_K5102072](https://parts.igem.org/Part:BBa_K5102072) to [BBa_K5102078](https://parts.igem.org/Part:BBa_K5102078) The deamination site (writing site), also known as the central base triplet (CBT), was chosen for its high deamination efficacy and fidelity to be at the +22 position. A sequence of 'CAU' was chosen for the CBT following the mammalian Kozak consensus sequence, which results in the deamination environment of moderate efficiency. The reading site was chosen for its high potency towards Cas13b binding disruption to be at the +12 position. The current instance of the tape features 3 intact START codons, corresponding to the initial 0th state, with each START codon having a +1 frame shift relative to its predecessor. The tape was constructed from these minimal sequence constraints, as highlighted on the [iGEM Munich 2024 model page](https://2024.igem.wiki/munich/model/#tape-construction-algorithm).
+<li><strong>T7 promoter</strong> (681–698):  phage T7 promoter (<a href="https://parts.igem.org/Part:BBa_K3633015">BBa_K3633015</a>) for <em>in vitro</em> expression of the ProgRAM.</li>
-- **Coding region** (753–4237): *in vivo* reporter system featuring a fluorescent proteins array. Each array element comprises T2A-XFP-P2A-eUnaG-STOP, with a +1 frame shift relative to its predecessor. The T2A ([BBa_K5102012](https://parts.igem.org/Part:BBa_K5102012), [BBa_K5102013](https://parts.igem.org/Part:BBa_K5102013), and [BBa_K5102014](https://parts.igem.org/Part:BBa_K5102014)) site divides a near-native XFP from the upstream sequences, while the P2A ([BBa_K5102015](https://parts.igem.org/Part:BBa_K5102015), [BBa_K5102016](https://parts.igem.org/Part:BBa_K5102016), and [BBa_K5102017](https://parts.igem.org/Part:BBa_K5102017)) site functions as a separator between the XFP and the eUnaG. This arrangement of 2A peptides was chosen to approach proportionality between expressed proteins. eUnaG ([BBa_K5102009](https://parts.igem.org/Part:BBa_K5102009), [BBa_K5102010](https://parts.igem.org/Part:BBa_K5102010), and [BBa_K5102011](https://parts.igem.org/Part:BBa_K5102011)) is used as total protein expression control and is present in all 3 reading frames. The current instance features miRFP670nano3 ([BBa_K5102001](https://parts.igem.org/Part:BBa_K5102001)),  mScarlet3 ([BBa_K5102002](https://parts.igem.org/Part:BBa_K5102002)), and mTagBFP2 ([BBa_K5102003](https://parts.igem.org/Part:BBa_K5102003)) as switching fluorescent proteins indicating the current tape state. Alternative proteins may be utilized if they comply with sequence requirements. The sequence of the current array was enabled by removing hidden stop codons and optimizing for various other parameters, including codon adaptation, minimization of repeats, and exclusion of splice and polyadenylation sites, among others, which is explained in detail on the [iGEM Munich 2024 model page](https://2024.igem.wiki/munich/model/#codon-optimization).
+<li><strong>Recording tape</strong> (700–751): recording tape, functioning as a deamination target and translation initiation site. In the current instance, a 3.0 tape design (<a href="https://parts.igem.org/Part:BBa_K5102041">BBa_K5102041</a>). This is a recording tape based on the REPAIR system using 30 nt long gRNAs. Alternative designs based on a co-optimal length of 50 nt, are also provided (<a href="https://parts.igem.org/Part:BBa_K5102106">BBa_K5102106</a> and <a href="https://parts.igem.org/Part:BBa_K5102107">BBa_K5102107</a>). Alternative 30 nt-based design comprises parts <a href="https://parts.igem.org/Part:BBa_K5102072">BBa_K5102072</a> to <a href="https://parts.igem.org/Part:BBa_K5102078">BBa_K5102078</a> The deamination site (writing site), also known as the central base triplet (CBT), was chosen for its high deamination efficacy and fidelity to be at the +22 position. A sequence of &#39;CAU&#39; was chosen for the CBT following the mammalian Kozak consensus sequence, which results in the deamination environment of moderate efficiency. The reading site was chosen for its high potency towards Cas13b binding disruption to be at the +12 position. The current instance of the tape features 3 intact START codons, corresponding to the initial 0th state, with each START codon having a +1 frame shift relative to its predecessor. The tape was constructed from these minimal sequence constraints, as highlighted on the <a href="https://2024.igem.wiki/munich/model/#tape-construction-algorithm">iGEM Munich 2024 model page</a>.</li>
-- **3'UTR** (4241–4284): 3' untranslated region. In the current instance, human beta-globin 3'UTR ([BBa_K5102053](https://parts.igem.org/Part:BBa_K5102053)).
+<li><strong>Coding region</strong> (753–4237): <em>in vivo</em> reporter system featuring a fluorescent proteins array. Each array element comprises T2A-XFP-P2A-eUnaG-STOP, with a +1 frame shift relative to its predecessor. The T2A (<a href="https://parts.igem.org/Part:BBa_K5102012">BBa_K5102012</a>, <a href="https://parts.igem.org/Part:BBa_K5102013">BBa_K5102013</a>, and <a href="https://parts.igem.org/Part:BBa_K5102014">BBa_K5102014</a>) site divides a near-native XFP from the upstream sequences, while the P2A (<a href="https://parts.igem.org/Part:BBa_K5102015">BBa_K5102015</a>, <a href="https://parts.igem.org/Part:BBa_K5102016">BBa_K5102016</a>, and <a href="https://parts.igem.org/Part:BBa_K5102017">BBa_K5102017</a>) site functions as a separator between the XFP and the eUnaG. This arrangement of 2A peptides was chosen to approach proportionality between expressed proteins. eUnaG (<a href="https://parts.igem.org/Part:BBa_K5102009">BBa_K5102009</a>, <a href="https://parts.igem.org/Part:BBa_K5102010">BBa_K5102010</a>, and <a href="https://parts.igem.org/Part:BBa_K5102011">BBa_K5102011</a>) is used as total protein expression control and is present in all 3 reading frames. The current instance features miRFP670nano3 (<a href="https://parts.igem.org/Part:BBa_K5102001">BBa_K5102001</a>),  mScarlet3 (<a href="https://parts.igem.org/Part:BBa_K5102002">BBa_K5102002</a>), and mTagBFP2 (<a href="https://parts.igem.org/Part:BBa_K5102003">BBa_K5102003</a>) as switching fluorescent proteins indicating the current tape state. Alternative proteins may be utilized if they comply with sequence requirements. The sequence of the current array was enabled by removing hidden stop codons and optimizing for various other parameters, including codon adaptation, minimization of repeats, and exclusion of splice and polyadenylation sites, among others, which is explained in detail on the <a href="https://2024.igem.wiki/munich/model/#codon-optimization">iGEM Munich 2024 model page</a>.</li>
-- **Aptamer** (4295-4317): an RNA aptamer acting as an anchor, enabling tape pulldown or localization. In the current instance, PP7 phage aptamer ([BBa_K5102054](https://parts.igem.org/Part:BBa_K5102054)).
+<li><strong>3&#39;UTR</strong> (4241–4284): 3&#39; untranslated region. In the current instance, human beta-globin 3&#39;UTR (<a href="https://parts.igem.org/Part:BBa_K5102053">BBa_K5102053</a>).</li>
-- **T7 terminator** (4334–4381): phage T7 transcriptional terminator ([BBa_K73172](https://parts.igem.org/Part:BBa_K73172)) for *in vitro* expression of the ProgRAM.
+<li><strong>Aptamer</strong> (4295-4317): an RNA aptamer acting as an anchor, enabling tape pulldown or localization. In the current instance, PP7 phage aptamer (<a href="https://parts.igem.org/Part:BBa_K5102054">BBa_K5102054</a>). </li>
-- **WPRE** (4382–4979): woodchuck hepatitis virus posttranscriptional regulatory element ([BBa_K5102069](https://parts.igem.org/Part:BBa_K5102069)) for increasing transgene expression by minimizing readthrough transcription and improving termination.
+<li><strong>T7 terminator</strong> (4334–4381): phage T7 transcriptional terminator (<a href="https://parts.igem.org/Part:BBa_K73172">BBa_K73172</a>) for <em>in vitro</em> expression of the ProgRAM.</li>
-- **polyA** (4984–5105): a polyadenylation site for mammalian transcription termination and RNA polyadenylation. In the current instance, SV40 polyA ([BBa_K2217005](https://parts.igem.org/Part:BBa_K2217005)). Alternative polyA sites could be used.
+<li><strong>WPRE</strong> (4382–4979): woodchuck hepatitis virus posttranscriptional regulatory element (<a href="https://parts.igem.org/Part:BBa_K5102069">BBa_K5102069</a>) for increasing transgene expression by minimizing readthrough transcription and improving termination.</li>
+<li><strong>polyA</strong> (4984–5105): a polyadenylation site for mammalian transcription termination and RNA polyadenylation. In the current instance, SV40 polyA (<a href="https://parts.igem.org/Part:BBa_K2217005">BBa_K2217005</a>). Alternative polyA sites could be used.</li>
+</ul>