Multivariate curve resolution: a powerful tool for the analysis of conformational transitions in nucleic acids.
A successful application is reported of the multivariate curve resolution alternating least-squares method (MCR-ALS) for the analysis of nucleic acid melting and salt-induced transitions. Under conditions where several structures co-exist in a conformational equilibrium, MCR-ALS analysis of the UV and circular dichroism (CD) spectra at different temperatures, ionic strength and oligonucleotide concentration allows for the resolution of concentration profiles and pure spectra of the different species. The methodology is illustrated by the case of the cyclic oligonucleotide d<pTGCTCGCT>. The melting transition of this molecule at different oligonucleotide concentrations was studied at 0, 2 and 10 mM MgCl2 by UV and CD spectroscopy. In addition, salt titration experiments were carried out at 21.0 and 54.0 degrees C. The MCR-ALS analysis indicates that three different conformations of this molecule co-exist in solution. In agreement with previous NMR studies, these conformations were assigned to a monomeric dumbbell-like structure, a dimeric four-stranded conformation and a disordered (random coil) structure. The MCR-ALS methodology allows for a detailed analysis of how this equilibrium is affected by temperature, salt and oligonucleotide concentration.
Jaumot
Joaquim
J
Departament de Química Analítica, Universitat de Barcelona, Diagonal 647, E-08028, Barcelona, Spain.
Escaja
Núria
N
Gargallo
Raimundo
R
González
Carlos
C
Pedroso
Enrique
E
Tauler
Romà
R
D000465:Algorithms; D001483:Base Sequence; D002942:Circular Dichroism; D016018:Least-Squares Analysis; D015636:Magnesium Chloride / Q000494:pharmacology; D015999:Multivariate Analysis; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009696:Nucleic Acids / Q000737:chemistry* / Q000187:drug effects; D012965:Sodium Chloride / Q000494:pharmacology; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature; D014867:Water / Q000494:pharmacology
D009696:Nucleic Acids; D015636:Magnesium Chloride; D014867:Water; D012965:Sodium Chloride