Can anyone clearly explain: 1. What is end-stacking binding mode in Triplex DNA binding? 2. How...

Can anyone clearly explain:

1. What is end-stacking binding mode in Triplex DNA binding?

2. How are the effects of the end-stacking when a ligand binds with a triplex DNA?

3. How is binding affinity involved in this case?

Expert Solution

1. The triplex DNA structure represents the site-specific alteration of the genome. This can be either intermolecular in nature formed by the oligonucleotide to duplex sequence or it can be naturally occurring. End base stacking is required to stabilize antiparallel triplexes as they are not isomorphous with each other. There could be distortion within the oligonucleotide which signifies structural changes not as per the neighboring bases for which other than ligand–base stacking is required.

2. The end stacking causes ligand to adjust to its conformation in order to obtain the best position for stabilization when it binds with a triplex DNA

3. The affinity and specificity of binding ligand is critical to their success of a gene targeting molecules. In case of lack of optimal target site binding affinity and specificity , the stacking will not bind to the complementary RNA and DNA.

gladiator answered 2 years ago

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