Related Experiment Video
Updated: Sep 24, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR
Abstract:
A three-dimensional solution structure for the self-complementary dodecanucleotide [d-(GCCTGATCAGGC)]2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)]2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences.
Related Concept Videos
The DNA Helix
DNA as a Genetic Template
¹H NMR: Complex Splitting
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
Two-Dimensional (2D) NMR: Overview
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse.
The DNA Helix
2D NMR: Overview of Homonuclear Correlation Techniques
COSY90 is the standard two-dimensional (2D) COSY experiment that...

