Cruciforms

One local alternative DNA structures stabilized by negative DNA supercoiling is a cruciform in which an inverted repeat nucleotide sequence rearranges from a fully double-stranded structure into two base-paired hairpins. Although DNA cruciforms are often drawn as having a cross-like shape, in collaboration with Dr. Yuri L. Lyubchenko we have shown by atomic force microscopy (AFM) that cruciforms exist in either an extended (low salt, low supercoiling) or a folded X-type (high salt, high supercoiling) conformations [1,2]. The X-type conformation induces a sharp kink in DNA molecule that, similar to permanently curved sequences, is localized at the apex of a plectonemic superhelix. The apical cruciform positioning limits the intersegmental mobility in the supercoiled DNA molecule. The transition of the cruciform from the X-type into the extended conformation is accompanied by straightening of the double helix around the cruciform which eliminates the limitations imposed by the X-type cruciform on the topographical dynamics within a superhelical domain [2]. The conformational rearrangement of the cruciform was hypothesized to play a role as a molecular switch for global DNA dynamics and be involved in regulation of various processes that require the interaction of distant DNA sites [2]. Thus, similar to other alternative DNA structures that form and/or rearrange in response to the changes in environmental conditions and DNA supercoiling induced by enzymes, the cruciform may dynamically affect global DNA conformation. This is in contrast to permanently existing DNA distortion such as inherently curved sequences. Interestingly, global DNA structures may affect the formation of local structures [3]. The localization of an inverted repeat to an apical position (which was provided by a diametrically positioned permanently bent region) increases the cruciform formation rate and reduces the superhelical energy required to drive the transition. Other mutual localizations of a cruciform and a permanent bend in a plasmid as a model of a topological domain show that their positioning at 6 o’clock increases the plasmid propensity to form an unbranched interwound superhelix, whereas positioning at 9 o’clock increases the yield of branched molecules. Thus, localization of alternative conformation-forming sequences to specific positions within a domain provides a potential regulatory mechanism for the utilization of DNA structural transition in biological processes.

Publications

1. Shlyakhtenko LS, Potaman VN, Sinden RR, Lyubchenko YL (1998) Structure and dynamics of supercoil-stabilized DNA cruciforms. J Mol Biol 280: 61-72 (request a copy).
2. Shlyakhtenko LS, Hsieh P, Grigoriev M, Potaman VN, Sinden RR, Lyubchenko YL (2000) A cruciform structural transition provides a molecular switch for chromosome structure and dynamics. J Mol Biol 296: 1169-1173 (request a copy).
3. Oussatcheva EA, Pavlicek J, Sankey OF, Sinden RR, Lyubchenko YL, Potaman VN (2004) Influence of global DNA topology on cruciform formation in supercoiled DNA. J Mol Biol 338: 735-743 (request a copy).

AFM images of the cruciform formed in the 106 bp inverted repeat at (i) low salt concentration and low plasmid superhelicity and (ii) higher salt concentration and higher superhelicity [1].