Protonation of deoxycytidine residues in dC4 tetraloops: UV spectrophotometric study of dC10 and d(A14C4T14)

It is shown that component analysis could be applied to study the UV difference spectra of cytidine oligomers and hairpin oligonucleotides with cytidines in the loop region in order to account for the melting and titration results in terms of cytidine stacking and protonation. Upon acid titration, t...

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Bibliographic Details
Published in:Biophysical chemistry 2003-06, Vol.104 (2), p.429-447
Main Authors: Raukas, E, Kooli, K
Format: Article
Language:English
Subjects:
Base Pairing
Deoxycytidine - chemistry
Hydrogen-Ion Concentration
Nucleic Acid Denaturation
Oligodeoxyribonucleotides - chemistry
Protons
Spectrophotometry, Ultraviolet
Thermodynamics
Titrimetry
Transition Temperature
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Summary:It is shown that component analysis could be applied to study the UV difference spectra of cytidine oligomers and hairpin oligonucleotides with cytidines in the loop region in order to account for the melting and titration results in terms of cytidine stacking and protonation. Upon acid titration, the dC(10) oligomer undergoes cooperative conformational transition at pH 6.3 accompanied by protonation and formation of the i-structure with half of the residues protonated. The stability of the hemiprotonated structure increases with decreasing pH, the i-structure persisting still in the region of pH
ISSN:0301-4622
DOI:10.1016/S0301-4622(03)00032-2