Negative superhelicity

PNA targeting of duplex DNA is not limited to homopurine sequences. Under special circumstances (high negative superhelical stress) mixed purine-pyrimidine PNA-peptide conjugates can bind by duplex invasion (Fig. 4.7) [31], but such complexes are of limited stability. However, using a set of pseudo-complementary PNAs containing diaminopurine-thiouracil substitutions, very stable double duplex invasion complexes can be formed (Fig. 4.4) and the only sequence requirement is about 50% AT content. Very recently, it was also demonstrated that reasonably stable helix invasion complexes can be obtained with tail-clamp PNA comprising a short (>six bases) homopyrimidine bis-PNA clamp and a mixed sequence tail extension [32] (Fig. 4.7). 

If the torsional strain generated by DNA translocation is utilized for mobilizing nucleosomes [195] then the direction of translocation will play an important role in determining the direction in which DNA is passed over the nucleosome surface and the orientation in which torsion is altered. Provided that rotation of the remodeling complex is restricted, incremental translocation of the motor towards the nucleosome will apply positive superhelical torsion to the particle whereas translocation away the nucleosome will apply negative superhelical torsion [119] (Fig. 3). The problem then is how to translate the motion of the translocase into translational... 

Maintaining DNA Structure (a) Describe two structural features required for a DNA molecule to maintain a negatively supercoiled state, (b) List three structural changes that become more favorable when a DNA molecule is negatively supercoiled. (c) What enzyme, with the aid of ATP, can generate negative superhelicity in DNA (d) Describe the physical mechanism by which this enzyme acts. 

The structure of plasmid, viral, and bacterial DNA is often closed circular with negative superhelical turns. It is possible under various experimental... 

DNA Gyrase An enzyme that is able to introduce negative superhelical turns into a circular DNA helix. 

---