Rotational Correlation Times of Internuclear Vectors in a DNA Duplex with G–A Mismatch Determined in Aqueous Solution by Complete Relaxation Matrix Analysis of Off-Resonance ROESY (O-ROESY) Spectra
✍ Scribed by Kazuo Kuwata; He Liu; Thomas Schleich; Thomas L. James
- Publisher
- Elsevier Science
- Year
- 1997
- Tongue
- English
- Weight
- 298 KB
- Volume
- 128
- Category
- Article
- ISSN
- 1090-7807
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✦ Synopsis
Complete relaxation matrix analysis of the off-resonance multispin effects, often termed ''spin-diffusion,'' but these ROESY (O-ROESY) spectra is presented and demonstrated for a can be accommodated using a complete relaxation matrix synthetic DNA duplex with two G-A mismatches, d(GCTGTCanalysis of cross-peak intensities (1, 2). A correlation time GAAAGC) 2 , in solution. The internuclear distance and the rota-characterizing molecular motions is generally estimated intional correlation time of the internuclear vector could be garnered dependently of the NOESY or ROESY spectra using one of simultaneously using complete relaxation matrix analysis of Oseveral methods and may be utilized when analyzing the ROESY, by which spin diffusion effects could be accommodated.
intensities to obtain distances.
Correlation times in the terminal and the mismatched regions
Recently, it has been reported that the information on were significantly reduced compared to those in other regions, internuclear distances and on correlation times can be sepaindicating the conformational flexibility of the mismatched pair. rated using the off-resonance ROESY pulse sequence by The average structure obtained by restrained molecular dynamics simulation with inclusion of variations of the rotational correlation eliminating the zero quantum transition effect due to Harttimes also indicated a general tendency of the mismatched and mann-Hahn transfer (3-5). This report presents a novel contiguous bases to flip to the outside of the double strand. Offformulation of the off-resonance ROESY (O-ROESY) resonance ROESY combined with the complete relaxation matrix method (3, 4, 6) and its application to a DNA duplex with analysis method may offer an alternative way to investigate the complete relaxation matrix analysis to overcome several difstructures and dynamics of biological macromolecules. ᭧ 1997 ficulties associated with the original O-ROESY cross-peak Academic Press intensity analysis (6). Furthermore, we demonstrate that this approach can enable the garnering of both distance constraints and motional information from the O-ROESY spec-The three-dimensional structure of any molecule can be tra by encoding the spectrum along the off-resonance spindetermined with a sufficient number of experimental struclock frequency axis rather than the mixing time axis. tural constraints, e.g., internuclear distances and bond torsion angles, in conjunction with the holonomic constraints of COMPLETE RELAXATION MATRIX ANALYSIS bond lengths, bond angles, and atom connectivities. To date,