The structure of DNA within cationic lipid/DNA complexes.
The structure of DNA within CLDCs used for gene delivery is controversial. Previous studies using CD have been interpreted to indicate that the DNA is converted from normal B to C form in complexes. This investigation reexamines this interpretation using CD of model complexes, FTIR as well as Raman spectroscopy and molecular dynamics simulations to address this issue. CD spectra of supercoiled plasmid DNA undergo a significant loss of rotational strength in the signal near 275 nm upon interaction with either the cationic lipid dimethyldioctadecylammonium bromide or 1,2-dioleoyltrimethylammonium propane. This loss of rotational strength is shown, however, by both FTIR and Raman spectroscopy to occur within the parameters of the B-type conformation. Contributions of absorption flattening and differential scattering to the CD spectra of complexes are unable to account for the observed spectra. Model studies of the CD of complexes prepared from synthetic oligonucleotides of varying length suggest that significant reductions in rotational strength can occur within short stretches of DNA. Furthermore, some alteration in the hydrogen bonding of bases within CLDCs is indicated in the FTIR and Raman spectroscopy results. In addition, alterations in base stacking interactions as well as hydrogen bonding are suggested by molecular dynamics simulations. A global interpretation of all of the data suggests the DNA component of CLDCs remains in a variant B form in which base/base interactions are perturbed.
Braun
Chad S
CS
Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA.
Jas
Gouri S
GS
Choosakoonkriang
Sirirat
S
Koe
Gary S
GS
Smith
Janet G
JG
Middaugh
C Russell
CR
D002412:Cations; D002942:Circular Dichroism / Q000379:methods; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D005229:Fatty Acids, Monounsaturated / Q000737:chemistry; D005782:Gels / Q000737:chemistry; D008055:Lipids / Q000737:chemistry*; D008081:Liposomes / Q000737:chemistry*; D046911:Macromolecular Substances; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D010316:Particle Size; D010957:Plasmids / Q000737:chemistry*; D000644:Quaternary Ammonium Compounds / Q000737:chemistry; D012399:Rotation; D012996:Solutions / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods; D013057:Spectrum Analysis / Q000379:methods*; D013059:Spectrum Analysis, Raman / Q000379:methods
D002412:Cations; D005229:Fatty Acids, Monounsaturated; D005782:Gels; D008055:Lipids; D008081:Liposomes; D046911:Macromolecular Substances; D000644:Quaternary Ammonium Compounds; D012996:Solutions; C046112:didodecyldimethylammonium; D004247:DNA; C070046:1,2-dioleoyloxy-3-(trimethylammonium)propane