Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment.
The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.
Gidden
Jennifer
J
Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, USA.
Ferzoco
Alessandra
A
Baker
Erin Shammel
ES
Bowers
Michael T
MT
D002942:Circular Dichroism; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D011066:Poly C / Q000138:chemical synthesis / Q000737:chemistry*; D011068:Poly G / Q000138:chemical synthesis / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization; D013329:Structure-Activity Relationship
D009841:Oligonucleotides; D011068:Poly G; C023826:poly(dC); C026628:poly(dG); D011066:Poly C; D006147:Guanine; D003596:Cytosine; D004247:DNA