The conformation about the exocyclic C4'-C5'bond in the DNA backbone plays a crucial rule in the bending of DNA. The conformers about this bond can be represented as a rapid equilibrium mixture of the three classical rotamers, gauche' (g' ), gauche- (g- ) and trans (t). For example, transition from the gauche+ conformer to the trans will increase the interphosphate distance between residues. This will cause local unstacking, thereby making the base pair roll into the major groove, creating a kink or hinge. In crystals, the overwhelmingly preferred conformation is g+ with a few instances of t, and g- is seldom observed. Examination of the P-P distances vis-a vis the C5'-C4' torsion in seventeen B-DNA, thirty two A-DNA and eleven RNA crystal structures with resolutions better than 2.5A reveal the following: 652 occurrences of g', and 54 of trans conformations about the C5'-C4' bond. The P-P distance in the trans conformer was always found to be larger than what was in the g'conformer. However, attempts to determine the sequence dependence of DNA bending, by high resolution crystallography of DNA duplexes in the absence of proteins, are often thwarted by artifacts associated with crystal packing. The ECOSY technique was developed to directly extract small passive couplings in the presence of large active couplings. Because H5'/H5" is a geminal system, it should be possible to employ the ECOSY technique to extract the values for 'JH'-H5. and'JHI'-H5". However, there could be three problems associated with this approach. First, many of the ECOSY cross peaks between 114' and H5'/H5" are expected to remain very close to the diagonal. Second, the chemical shifts of H2' and H2" of the deoxyribose ring are in general significantly different from each other and situated far away from the corresponding Hl'; the magnitudes of JHI'-H2' and JHI'-H2" are large, in the range of 6 to 9 Hz. On the other hand, the H4'-H5'/H5" is a tightly coupled AB system with small couplings between H4'and H5'/H5". Thus, the ECOSY spectra will have to simulated in order'JH'.H5' and 3 JH4'-H5". Third, the chemical shift anisotropy of "P may cause considerable line broadening, making it difficult to extract the se small coupling constants. With respect to the first problem, higher frequencies may provide a partial solution; however this will aggravate the third problem. With respect to the second problem, we have examined computer generated ECOSY spectra for typical values for H F, H2'& H2" as well as for H4', H5' & H5". It is seen that for H2'/H2", there are seven lobes of equal intensity in which the cc and P spin states are well-displaced in co2 and just overlap in (o 1. For H5'/H5 " there are eight lobes, and the displacements of the spin states are opposite to what is obsereved for H2'/H2". This difference in appearance has to do with the magnitude of the geminal coupling vis-a-vis that of J12'512" and J4'5'/4'5". In the H5'/H5" system, the intensities of the outer 8 lobes are significantly less than the inner 8 lobes because it is a typical AB system. To investigate the effect of chemical shift anisotropy we recorded ECOSY spectra of the 11 mer duplex AAA at 500, 600 and 750 MHz NMR systems at different temperatures in the presence and absence of "P decoupling. In the absence of "P decoupling, the proton line width increases with increasing magnetic field strength. "P decoupling, on the other hand, leads to a spectacular improvement in the ECOSY spectra, which contain multiplets with 8 lobes displaying a typical AB pattern. Thus, we have shown that "P decoupled ECOSY spectra can be employed to unambigously extract the JH4'-H5' and JH4'-H5" coupling constants in DNA oligonucleotides. However, the method will be useful only for those residues that display their H4'-H5'/H5" cross peaks off the diagonal. Unfortunately, these conclusions were based on "P decoupled ECOSY experiments at 600 MHz. Our attempts to perform "P decoupled ECOSY at 750 Mhz resulted in the loss of signals from 4',5' and 5" region.
NIH ExPorter
NIH ExPorter