Abstract
Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and their topology. Due to their chirality, double helices are tightly packed into stable right-handed crossovers. Simple packing rules that are imposed by DNA geometry and sequence dictate the overall architecture of higher order DNA structures. Close DNA-DNA interactions also provide the missing link between local interactions and DNA topology, thus explaining how type II DNA topoisomerases may sense locally the global topology. Finally this paper proposes that through its influence on DNA self-assembled structures, DNA chirality played a critical role during the early steps of evolution.
Highlights
Transient or long-term DNA self-assembly participates in essential genetic functions
B-DNA double helix dictates the geometry of inter-helical assembly, cytosines play a key role in controlling the interaction through specific interaction of their N4 amino groups with phosphate groups [22,23,24]
This study showed that right-handed DNA crossovers (Figure 1a) are thermodynamically stable in solution in the presence of divalent cations
Summary
Transient or long-term DNA self-assembly participates in essential genetic functions. Short-range contacts between double helices have been considered to be strongly repulsive, DNA is condensed under various conditions of condensing agents, cations or polyamines and may form organized phases or DNA liquid crystals [4,5]. Sci. 2013, 14 do not form direct intermolecular interactions [6,7] In these conditions, the parallel packing of helices is only moderately influenced by the helical nature of DNA and its sequence [8,9,10]. Recent theoretical and experimental studies have indicated that close DNA-DNA interactions can occur in solution, in the presence of divalent cations [14,15,16,17,18] Largely overlooked, these interactions have been found to play important biological roles for both controlling the architecture of higher-order DNA structure and DNA topology [19,20,21]. It is proposed here that the structural simplification of the genetic material in passing from the RNA to the DNA world has contributed to store and pack larger genomes, in favouring inter-helical interactions governed by simple rules that are compatible with the codified hierarchical assembly of double helices at multiple levels
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