Nucleic Acids Research Advance Access published online on October 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp730
Structural Biology |
Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A·A base pairing and a putative structure of the coralyne-induced homo-adenine duplex
1Department of Bioengineering, College of Engineering, University of Utah, Salt Lake City, UT 84112, 2School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, 3Department of Medicinal Chemistry and 4Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
*To whom correspondence should be addressed. Tel: +1 801 587 9652; Fax: +1 801 585 9119; Email: tec3{at}utah.edu
Correspondence may also be addressed to Nicholas V. Hud. Tel +1 404 385 1162; Fax: +1 404 894 7452; Email: hud{at}chemistry.gatech.edu
Received April 22, 2009. Revised August 17, 2009. Accepted August 19, 2009.
Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson–Crick DNA. Hud’s laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine–adenine hydrogen bonding between the two poly(dA) strands, we constructed 40 hypothetical homo-(dA) anti-parallel duplexes and docked coralyne into the six most favorable duplex structures. The two most stable structures had trans glycosidic bonds, but distinct pairing geometries, i.e. either Watson–Crick Hoogsteen (transWH) or Watson–Crick Watson–Crick (transWW) with stability of transWH > transWW. To narrow down the possibilities, 7-deaza adenine base substitutions (dA
7) were engineered into homo-(dA) sequences. These substitutions significantly reduced the thermal stability of the coralyne-induced homo-(dA) structure. These experiments strongly suggest the involvement of N7 in the coralyne-induced A·A base pairs. Moreover, due to the differential effect on melting as a function of the location of the dA7 mutations, these results are consistent with the N1–N7 base pairing of the transWH pairs. Together, the simulation and base substitution experiments predict that the coralyne-induced homo-(dA) duplex structure adopts the transWH geometry.
Present address: In Suk Joung, BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA.