If the circular DNA were nicked (had a single-stranded break) on one strand, what would be the effect on supercoiling?
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Consider a relaxed, covalently-closed circular DNA plasmid that has 1040 base pairs with Wr = 0. An intercalator is added, such that there is one intercalator per 104 base pairs. The effect of the intercalator is to cause the twist between the base pairs that flank it to be reduced to zero. What will be the resulting change in supercoiling for the intercalator-bound DNA?
Madhur L.
You have discovered an enzyme secreted by a particularly virulent bacterium that cleaves the C2'-C3' bond in the deoxyribose residues of duplex DNA. What is the effect of this enzyme on supercoiled DNA?
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(a) What is the $L k$ of a 5,000 bp circular duplex DNA molecule with a nick in one strand? (b) What is the $L k$ of the molecule in (a) when the nick is sealed (relaxed)? (c) How would the $L k$ of the molecule in (b) be affected by the action of a single molecule of $E .$ coli topoisomerase I? (d) What is the $L k$ of the molecule in $(b)$ after eight enzymatic turnovers by a single molecule of DNA gyrase in the presence of ATP? (e) What is the $L k$ of the molecule in (d) after four enzymatic turnovers by a single molecule of bacterial type I topoisomerase? (f) What is the $L k$ of the molecule in (d) after binding of one nucleosome?
Lainey R.
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