Removal of a single minor-groove functional group eliminates A-tract curvature.
Much of the work in studying the phenomenon of A-tract curvature has involved the insertion of modified residues into the A-tract sequence and then cross-correlation of the structural differences with the resulting curvature effects. In the A-tract sequence d(A-T)5, removal of a single functional group (the O2-carbonyl of the central dT residue) by its replacement with hydrogen completely eliminates the curvature properties. This atom-specific change was accomplished by using the C-nucleoside dm32P in which the O2-carbonyl is replaced with -H but normal Watson-Crick hydrogen bonding is maintained. Similar derivatives with -F (dF62P) or -CH3 (dm62P) when present for the central dT residue also eliminate curvature. Finally, we have shown that the extent of curvature for sequences containing this carbonyl are sensitive to the [Mg2+], while those lacking the carbonyl show little to no Mg2+ dependence, strongly suggesting, we believe, a role for Na+/Mg2+ cooperative interactions in the minor groove to explain the curvature phenomenon.
Meena
Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3801, USA.
Sun
Zhenhua
Z
Mulligan
Christine
C
McLaughlin
Larry W
LW
D002413:Cations, Divalent; D004247:DNA / Q000737:chemistry*; D011088:DNA Ligases / Q000737:chemistry; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009943:Organophosphorus Compounds / Q000737:chemistry; D011067:Poly dA-dT / Q000737:chemistry*; D013329:Structure-Activity Relationship
D002413:Cations, Divalent; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D011067:Poly dA-dT; D004247:DNA; D011088:DNA Ligases; D008274:Magnesium