Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy.
Changes in bending of the DNA helix axis caused by the introduction of conformationally locked nucleotide analogs into the center region of the palindromic Dickerson dodecamer, d(CGCGAATTCGCG)(2), have been studied by NMR measurement of residual one-bond (13)C-(1)H dipolar couplings. Thymidine analogs, in which the deoxyribose was substituted by bicyclo[3.1.0]hexane, were incorporated in the T7, T8, and T7T8 positions. These nucleotide analogs restrict the ring pucker to the C2'-exo or "north" conformation, instead of C2'-endo or "south," which dominates in regular B-form DNA. For all three oligomers, bending toward the major groove is found relative to the native molecule. The effects are additive with bending of 5 +/- 1 degrees per locked nucleotide. Measurement of the change in bending is more accurate than measurement of the bending angle itself and requires far fewer experimental data.
Wu
Zhengrong
Z
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520.
Maderia
Melissa
M
Barchi
Joseph J
JJ
Marquez
Victor E
VE
Bax
Ad
A
D001643:Bridged Bicyclo Compounds / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*
D001643:Bridged Bicyclo Compounds; D009711:Nucleotides; C046059:bicyclo(3.1.0)hexane; D004247:DNA