Difference between revisions of "Part:BBa K3380151"

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DIR2s-Apt is a fluorescent RNA aptamer comprising a short ribonucleotide sequence that exhibits fluorescence upon binding to a specific fluorophore.  
 
DIR2s-Apt is a fluorescent RNA aptamer comprising a short ribonucleotide sequence that exhibits fluorescence upon binding to a specific fluorophore.  
 
===Characterization===
 
===Characterization===
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The DIR2s-Apt fluorescent RNA aptamer was described by [https://pubs.acs.org/doi/full/10.1021/jacs.7b04211 Tan ''et al.'' (2017)].
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The DIR2s-Apt fluorescent RNA aptamer was described by [https://pubs.acs.org/doi/full/10.1021/jacs.7b04211 Tan ''et al.'' (2017)]. '''Figure 1''' shows the DIR2s-Apt folding prediction as simulated by [http://www.nupack.org// NUPACK].  
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The DIR2s-Apt folding prediction as simulated by [http://www.nupack.org// NUPACK] is shown below.  
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{| style="color:black" cellpadding="6" cellspacing="2" border="2" align="right"
 
{| style="color:black" cellpadding="6" cellspacing="2" border="2" align="right"
 
! colspan="3" style="background:#C0C0C0"|'''DIR2s-Apt Characteristics'''
 
! colspan="3" style="background:#C0C0C0"|'''DIR2s-Apt Characteristics'''
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|style="background:#FF0000" align="center"|Red|| style="background:#0000ff" align="center"|Blue
 
|style="background:#FF0000" align="center"|Red|| style="background:#0000ff" align="center"|Blue
 
|-
 
|-
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|'''Excitation wavelength'''
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|'''Excitation wavelength (nm)'''
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|600 (nm)|| 380
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|600 || 380
 
|-
 
|-
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|'''Emission wavelength '''
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|'''Emission wavelength (nm)'''
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|658 (nm)||
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|658 || 421
 
|-
 
|-
 
|'''Quantum Yield'''
 
|'''Quantum Yield'''
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|0.33
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|0.33 || 0.51
 
|-
 
|-
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|'''Extinction coefficient'''
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|'''Extinction coefficient (M^-1 cm^-1)'''
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|164000 (M^-1 cm^-1)
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|164000 || 73000
 
|-
 
|-
 
|'''Source'''
 
|'''Source'''
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|[https://pubs.acs.org/doi/full/10.1021/jacs.7b04211]
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|colspan="3" align="center"|[https://pubs.acs.org/doi/full/10.1021/jacs.7b04211]
  
 
|}
 
|}
  
 
[[File:Part BBa K3380151.png|400px|DIR2s-Apt folding]]
 
[[File:Part BBa K3380151.png|400px|DIR2s-Apt folding]]
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'''Figure 1: DIR2s-Apt secondary structure prediction.''' The adenine (A), cytosine (C), guanine (G) and uracil (U) nucleobases are shown in green, blue, black and red respectively.
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===Usage and Biology===
 
===Usage and Biology===
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It is usually used in live-cell imaging, however it can also be used in vitro. DIR2-Apt can be used for visualisation by gene fusion to the target of interest. Its fluorescent colour depends on the fluorophore it binds to. It can bind to DIR ( dimethylindole red) derivatives to give a red colour and OTB (oxazole thiazole blue) derivatives to give a blue colour. The emission spectra also depends on the bound fluorophore. The [https://pubs.acs.org/doi/full/10.1021/jacs.7b04211/ DIR-Pro]fluorophore has an excitation wavelength of 600 (nm) and an emission wavelength of 658 (nm). The  [https://pubs.acs.org/doi/full/10.1021/jacs.7b04211 OTB-SO3]fluorophore has an excitation wavelength of 380 (nm) and an emission wavelength of 421 (nm).
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It is usually used in live-cell imaging, however it can also be used in vitro. DIR2-Apt can be used for visualisation by gene fusion to the target of interest. Its fluorescent colour depends on the fluorophore it binds to. It can bind to DIR ( dimethylindole red) derivatives to give a red colour and OTB (oxazole thiazole blue) derivatives to give a blue colour. The emission spectra also depends on the bound fluorophore.  
  
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DIR2s-Apt promiscuity for multiple fluorophores (DIR and OTB) allows its colour change just by addition of different fluorophores. Its short length also allows it to be synthesized rather than being cloned using a plasmid.  
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DIR2s-Apt promiscuity for multiple derivatives of fluorophores (DIR and OTB) allows its colour change just by addition of different fluorophores. Its short length also allows it to be synthesized rather than being cloned using a plasmid.  
  
 
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Latest revision as of 16:28, 23 October 2020


DIR2s-Apt fluorescent RNA aptamer

DIR2s-Apt is a fluorescent RNA aptamer comprising a short ribonucleotide sequence that exhibits fluorescence upon binding to a specific fluorophore.

Characterization

The DIR2s-Apt fluorescent RNA aptamer was described by Tan et al. (2017). Figure 1 shows the DIR2s-Apt folding prediction as simulated by [http://www.nupack.org// NUPACK].

DIR2s-Apt Characteristics
Fluorophore DIR-PRO OTB-SO3
Fluorescence colour Red Blue
Excitation wavelength (nm) 600 380
Emission wavelength (nm) 658 421
Quantum Yield 0.33 0.51
Extinction coefficient (M^-1 cm^-1) 164000 73000
Source [1]

DIR2s-Apt folding

Figure 1: DIR2s-Apt secondary structure prediction. The adenine (A), cytosine (C), guanine (G) and uracil (U) nucleobases are shown in green, blue, black and red respectively.


Usage and Biology

It is usually used in live-cell imaging, however it can also be used in vitro. DIR2-Apt can be used for visualisation by gene fusion to the target of interest. Its fluorescent colour depends on the fluorophore it binds to. It can bind to DIR ( dimethylindole red) derivatives to give a red colour and OTB (oxazole thiazole blue) derivatives to give a blue colour. The emission spectra also depends on the bound fluorophore.

DIR2s-Apt promiscuity for multiple derivatives of fluorophores (DIR and OTB) allows its colour change just by addition of different fluorophores. Its short length also allows it to be synthesized rather than being cloned using a plasmid.

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]