Conformational junctions between left‐handed DNA in (dA‐dT)₁₆ and contiguous B‐DNA in a supercoiled plasmid contain chemically reactive bases

Abstract

Alternating adenine-thymine sequences in supercoiled DNA may undergo a transition to the left-handed Z-conformation in the presence of Ni2+ ions and high Na' concentrations [(1989) FEBS Lett. 243, 313-3171. In this work we have studied the junctions between B-and Z-conformations in a supercoiled plasmid containing a (dAdT),, insert, by means of chemical probing. We observed enhanced reactivity of bases at both ends of the alternating tract to chloro-and bromoacetaldehyde. The degree of chemical reactivity was found to increase with the level of negative supercoiling. Only individual bases were observed to be reactive in the B-Z junctions, consistent with tightly localized interfacial regions.

Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity

“…Characterizing changes in supercoiling is therefore essential for understanding these processes in detail. Moreover, modulation of supercoiling accompanies conformational changes in duplex DNA such as cruciform extrusion [12, 24–28] and the formation of Z-DNA [12, 13, 27–30], and is thus an important topological method for analyzing alternative DNA conformations.…”

Effect of Flanking Sequences on the Right- to Left- Handed Transition of a (dA-dT)nTract in Supercoiled DNA

“…pXGAT15 is a 3.8 kb plasmid that contains an (dA-dT) 15 tract (14,16). The polarity of the tract is the same as that in pAT32, but the context of the alternating tract is more similar to that found in pTA16 (Figure 3).…”

“…Furthermore, we have previously found that (dA-dT) 16 block can become lefthanded in the presence of high NaCI concentrations and Ni2+ ions if the structure is stabilised by negative supercoiling (13). Recently we have probed putative B-Z junctions adjoining the (dA-dT) 16 block using chemical agents, and found reactive bases at both boundaries between B-DNA and the left-handed segment in the supercoiled plasmid (14).…”

Energetics of Coupled Twist and Writhe Changes in Closed Circular pSM1 DNA

“…The longest alternating PyPu sequence in pSM1 DNA is 20 base-pairs long and is centered at nucleotide 2390. This sequence contains a stretch of alternating (dT-dA) 3 •(dT-dA) 3 base-pairs and is not surrounded by a region of high G + C content, hence is not likely to form a Z-DNA structure at any reasonably attainable level of supercoiling (McLean et al, 1986;Nejedly et al, 1993).…”