ISSN:
0006-3525
Keywords:
Chemistry
;
Polymer and Materials Science
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
The interaction of propidium with three self-complementary oligodeoxyribonucleotides has been investigated by 1H- (base-pair imino proton assigned by 1D NOE and saturation transfer methods) and 31P-nmr as a function of ratio of propidium to oligomer (from zero to saturation) and temperature. The three oligomers are dTATATGCGCATATA (1), dTATATGTGCATATA (2), which has the same sequence as 1 except for the mismatched base pair at position 7, and dTATGTGCATA (3), which is a shortened version of 2. The imino proton chemical-shift changes of 1 on titration with propidium can be explained by the effects of the ring-current anisotropy of propidium at intercalation (3.4 Å) and next-neighbor sites (6.8 Å). The results indicate that propidium binds with neighbor exclusion but with no significant specificity for any intercalation site in the sequence of 1. The addition of propidium to 1 results in general downfield shifts of all 31P signals, as expected for a nonspecific intercalator. Imino and 31P-nmr spectra for 2 indicate that this oligomer forms a hydrogen-bonded G · T base pair at position 7 with little change in base pairing and stacking of base pairs 1-6 compared to 1. The results for addition of propidium to 2 and 3 are quite different than with 1. At low ratio only secondary shifts (6.8 Å) are seen for the G and T imino protons of base-pair 7 on addition of propidium. At higher ratios of propidium, the signals for these G and T protons are lost in 2 and severely broadened in 3, even at low temperature. The other potential intercalation sites in 2 and 3 appear to bind propidium strongly and without significant specificity as with 1. 31P spectra of 2 in the presence of propidium show the expected downfield shifts and broadening. Thus, the minor differences in local helix geometry in 1, and in 2 and 3, away from the G · T base pair do not significantly affect propidium intercalation specificity. Having one or two G · T base pairs at a site, however, makes intercalation in the standard manner significantly less favorable.
Additional Material:
9 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/bip.360251013
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