Underwound

Every cell actively underwinds its DNA with the aid of enzymatic processes (described below), and the resulting strained state represents a form of stored energy. Cells maintain DNA in an underwound state to facilitate its compaction by coiling. The underwinding of DNA is also important to enzymes of DNA metabolism that must bring about strand separation as part of their function. 

The underwound state can be maintained only if the DNA is a closed circle or if it is bound and stabilized by proteins so that the strands are not free to rotate about each other. If there is a break in one strand of an isolated, protein-free circular DNA, free rotation at that point will cause the underwound DNA to revert spontaneously to the relaxed state. In a closed-circular DNA molecule, however, the number of helical turns cannot be changed without at least transiently breaking one of the DNA strands. The number of helical turns in a DNA molecule therefore provides a precise description of supercoiling. 

FIGURE 24-16 Linking number applied to closed-circular DNA molecules. A 2,100 bp circular DNA is shown in three forms (a) relaxed, Lk = 200 (b) relaxed with a nick (break) in one strand, Lk undefined and (c) underwound by two turns, Lk = 198. The underwound molecule generally exists as a supercoiled molecule, but underwinding also facilitates the separation of DNA strands. 

Plectonemic supercoiling, the form observed in isolated DNAs in the laboratory, does not produce sufficient compaction to package DNA in the cell. A second form of supercoiling, solenoidal (Fig. 24-24), can be adopted by an underwound DNA. Instead of the... 

Most cellular DNAs are supercoiled. Underwinding decreases the total number of helical turns in the DNA relative to the relaxed, B form. To maintain an underwound state, DNA must be either a closed circle or bound to protein. Underwinding is quantified by a topological parameter called linking number, Lk. 

In closed circular DNA the value of Wr is usually negative, the secondary structure being a fully formed Watson-Crick helix but with right-handed interwound superhelical turns or left-handed toroidal superhelical turns. The helix is said to be underwound (Lk < Tw). 

Most DNA in living organisms, whether bacteria or eukaryotes, is underwound. That is, the superhelix density (Chapter 5) is about -0.05 or one supercoil per 200 base pairs. In eukaryotes this negative supercoil-ing can be accounted for by the winding of DNA around the histones within the nucleosomes (Figs. 

Another important factor in determining the strength of a repressor-operator interaction is the twist of the DNA or any other distortion of its regular helical structure. For example, in the center of the cro 434-operator complex the DNA is wound, while at the ends it is underwound.92 Conformational changes in either the repressor or in the DNA or in both may be needed to provide optimal binding. As is seen in Fig. 28-3 the lac repressor causes a distinct bend in the DNA. 

Finally, the recent discovery of the unusual left-handed polydinucleotide helices for the alternating purine-pyrimidine polymers opens up a whole new field of nucleic acid secondary structures. The relevance and importance of these new structures in the visualization of overwound, as well as underwound, and supercoiled DNA molecules in biological.systems need hardly be emphasized. 

Normally, this DNA would have a linking number equal to 25, so it is underwound. The DNA double helical structures in the previous figure have the same value of Lk however, the DNA can be super-coiled, with the two underwindings taken up by the negative supercoils. This is equivalent to two turns -worth of single-stranded DNA and no supercoils. This interconversion of helical and superhelical turns is important in gene transcription and regulation. 

The writhing of DNA around the histone core in a left-handed helical manner also stores negative supercoils if the DNA in a nucleosome is straightened out, it will be underwound (Section 23.3.2). This underwinding is exactly what is needed to separate the two DNA strands during replication and transcription (Sections 27.5 and 28.1.5). 

All naturally occurring, superhelical DNA molecules are initially underwound and, hence, form negative... 

Different states of a covalent DNA circle, (a) A nonsupercoiled covalent DNA having 36 turns of the helix, (b) An underwound covalent circle having only 32 turns of the helix, (c) The molecule in (b), but with four superhelical turns to eliminate the underwinding. In solution, (b) and (c) would be in equilibrium the equilibrium would shift toward (b) with increasing temperature. 

Breakage and re-formation of phosphodiester linkages allow the conversion of a relaxed circular form (a) to the negatively supercoiled form (b). The strain relieved by the supercoiling process will be reintroduced when the underwound molecule is forced to lie in a plane (c). 

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