Brownian-dynamics simulations of metal-ion binding to four-way junctions

• Published in: Nucleic acids research Vol. 30; no. 2; pp. 507 - 514
• Main Authors: van Buuren, Bernd N M, Hermann, Thomas, Wijmenga, Sybren S, Westhof, Eric
• Format: Journal Article
• Language: English
• Published: England Oxford Publishing Limited (England) 15.01.2002; Oxford University Press
• Subjects: Base Pair Mismatch; Base Sequence; Binding Sites; Cations - metabolism; Computer Simulation; Diffusion; DNA - chemistry; DNA - genetics; DNA - metabolism; four-way junctions; Metals - metabolism; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Nucleic Acid Hybridization; Recombination, Genetic - genetics; RNA - chemistry; RNA - genetics; RNA - metabolism; Static Electricity
• ISSN: 1362-4962; 0305-1048; 1362-4962
• DOI: 10.1093/nar/30.2.507

Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55 degrees or around -70 to -80 degrees. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.