I've read that the following formula: (G3+)(N1-7)(G3+)(N1-7)(G3+)(N1-7)(G3+) is used to algorithmically search for potential g-quadruplex motifs in various genomes. I'm wondering whether certain combinations are far more likely to form these structures than others (ex: G3-N2-G3-N2-G3-N2-G3 seems like it would be more conducive for this structure whereas a more random example like G7-N7-G3-N7-G7-N7-G3 seems like it may have the propensity to form other tertiary structures).
I found a tentative answer in case anyone else was wondering the same thing. There are three motifs I found that have the minimum number of nucleotides and the highest G-scores (with four or less guanines per tract):
Where X is 1 of any nucleotide (A/T/G/C)
3'-GGGG-X-GGGG-X-GGGG-X-GGGG-5' G-Score: 63
3'-GGG-X-GGG-X-GGG-X-GGG-5' G-Score: 43
3'-GG-X-GG-X-GG-X-GG G-Score: 21
These appear to by the 'idealized' sequences, or as near as I can find, that I was inquiring about. Increasing the number of guanine nucleobases in the polyG tracts and reducing the number of nucleobases between these tracts increases the probability of forming the tetrameric structure. The paper gives a specific example of 3'-GGGGGGTGGGGGGTGGGGGGTGGGGGG-5' as having the largest G-score but none of my sequences have polyG runs longer than 4. I wanted to mention that in case anyone is looking for the absolute highest probability. I parsed the information from the QGRS-Mapper manuscript (attached).
Hello!
I just took a number of articles and order the known oligonucleotides with G-quadruplex. I also bought a mesoporphyrin and check in vitro the formation of the quadruplex using this intercalaiting agent.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA