RNA Mango

In this page, structures, sequences, properties and applications of RNA Mango aptamers can be found.

Crystal structures of Mango aptamers

Mango I

Mango I

PDB: 5V3F
Mango II

Mango II

PDB: 6C63
Mango III

Mango III

PDB: 6E8S

Binding and fluorescent properties of Mango aptamers

The following table gives the sequences binding affinity and brightness along with reference to the original publications.
Aptamer Sequence (5' - 3') TO1-Biotin TO3-Biotin YO3-Biotin Reference
KD (nM) Brightness KD (nM) Brightness KD (nM) Brightness
Mango I G GCA CGU ACG AAG GGA CGG UGC GGA GAG GAG AGU ACG UGC 2.2 ± 0.3 10,900 5.1 ± 0.3 9,500 26 ND 1, 2, 3
Mango II G GCA CGU ACG AAG GAG AGG AGA GGA AGA GGA GAG UAC GUG C 0.7 ± 0.3 17,000 1.8 ± 0.1 16,900 ND ND 1, 2
Mango III G GCA CGU ACG AAG GAA GGA UUG GUA UGU GGU AUA UUC GUA CGU GCC 5.6 ± 0.2 43,000 15 ± 1 11,000 ND ND 1, 2
Mango III (A10U) G GCA CGU ACG AAG GAA GGU UUG GUA UGU GGU AUA UUC GUA CGU GC 1.7 ± 1.0 51,200 160 ± 20 8,000* 120 ± 10* 47,600* 2, 4
Mango IV G GCA CGU ACC GAG GGA GUG GUG AGG AUG AGG CGA GUA CGU GC 11 ± 1 32,000 10 ± 1 18,700* ND ND 1, 2
In bold is the Mango core sequence of the aptamer, which is inserted into a flanking RNA stem of nearly arbitrary sequence. *Not published.

Resistance properties of Mango Aptamers

Some Mango aptamers are highly resistant to formaldehyde and formamide making them very useful for imaging using established fixed cell methodologies.
Aptamer Formamide* Formaldehyde 1 Mg2+ Resistance 1 Cell Imaging Use RNA Pulldown Transcription Reporting
Mango I Upto 12% 4% Up to 8 mM NA 6 NA
Mango II Up to 34% 8% Up to 260 mM 1, 5 NA NA
Mango III Up to 8% 0% Up to 130 mM NA NA 7, 8, 9
Mango III (A10U) ND 0% Up to 130 mM NA NA NA
Mango IV Up to 12% 0% Up to 260 mM 1 NA 7

Applications

Pathogen detection Single Molecule Imaging Transcriptional reporter Cellular FRET sensors RNP pull down

References

1. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells

2. Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers

3. Development of a genetically encodable FRET system using fluorescent RNA aptamers

4. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer

5. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays

6. Ribonucleoprotein purification and characterization using RNA Mango

7. Nanomechanics and co-transcriptional folding of Spinach and Mango

8. Structural basis of Q-dependent transcription antitermination

9. CueR activates transcription through a DNA distortion mechanism