Proton-detected hetero-TOCSY experiments with application to nucleic acids

Phosphatidylcholines from Pieris brassicae eggs activate an immune response in Arabidopsis

Recognition of conserved microbial molecules activates immune responses in plants, a process termed pattern-triggered immunity (PTI). Similarly, insect eggs trigger defenses that impede egg development or attract predators, but information on the nature of egg-associated elicitors is scarce. We performed an unbiased bioactivity-guided fractionation of eggs of the butterfly Pieris brassicae. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry of active fractions led to the identification of phosphatidylcholines (PCs). PCs are released from insect eggs, and they induce salicylic acid and H₂O₂ accumulation, defense gene expression and cell death in Arabidopsis, all of which constitute a hallmark of PTI. Active PCs contain primarily C16 to C18-fatty acyl chains with various levels of desaturation, suggesting a relatively broad ligand specificity of cell-surface receptor(s). The finding of PCs as egg-associated molecular patterns (EAMPs) illustrates the acute ability of plants to detect conserved immunogenic patterns from their enemies, even from seemingly passive structures such as eggs.

Recent advances in RNA structure determination by NMR

Despite recent advances in the solution of NMR structures of RNA and RNA-ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J-coupling data with the measurement of dipolar couplings and cross-correlated relaxation rates in high-resolution NMR spectroscopy.

Improved methods for 1H-3H heteronuclear shift correlation

A better understanding of the structure of complex 3H-labeled molecules can be obtained by complete assignment of their 1H and 3H solution-state NMR spectra. The assignment process is aided by the detection of heteronuclear chemical shift correlations between 1H and 3H nuclei. Heteronuclear correlation (HETCOR) experiments previously applied to this task exhibit several drawbacks caused by the nature of both the pulse sequences and 1H-3H spin systems. The range of J-couplings involved in 1H-3H coupling networks make it challenging to perform correlation experiments using methods that rely on coherences created during free precession periods and interrupted by transfer pulses. Two alternative HETCOR experiments are demonstrated for 1H-3H systems in the present work and are shown to have advantages over earlier methods. The first experiment is known as hetero-TOCSY and correlates heteronuclear chemical shifts using J-cross polarization. This experiment achieves both homonuclear and heteronuclear mixing and connects the chemical shifts of all 1H and 3H nuclei in a coupling network. A second HETCOR experiment uses the heteronuclear Overhauser effect to obtain through-space correlations between nearby nuclei. The 1H-3H HETCOR experiments are phase sensitive and typically contain more correlations than other methods, which is beneficial for assignment purposes, while being sensitive enough to be applicable to routine analytical samples. The experiments were used to analyze 3H incorporation in sub-milligram quantities of 3H-labeled pharmaceutical derivatives with complex labeling schemes.

Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by a 1H, 13C, 31P triple resonance experiment: HCP-CCH-TOCSY

A three-dimensional 1H, 13C, 31P triple resonance experiment, HCP-CCH-TOCSY, is presented which provides unambiguous through-bond correlation of all 1H ribose protons on the 5' and 3' sides of the intervening phosphorus along the backbone bonding network in 13C-labeled RNA oligonucleotides. The correlation of the complete ribose spin system to the intervening phosphorus is obtained by adding a C,C-TOCSY coherence transfer step to the triple resonance HCP experiment. The C,C-TOCSY transfer step, which utilizes the large and relatively uniform 1J(C,C) coupling constant (approximately 40 Hz for ribose carbons), efficiently correlates the phosphorus-coupled carbons observed in the HCP correlation experiment (i.e., C4' and C5' in the 5' direction and C4' and C3' in the 3' direction) to all other carbons in the ribose spin system. Of the additional correlations observed in the HCP-CCH-TOCSY, that to the relatively well-resolved anomeric H1',C1' resonance pairs provides the greatest gain in terms of facilitating assignment. The gain in spectral resolution afforded by chemical shift labeling with the anomeric resonances should provide a more robust pathway for sequential assignment over the intervening phosphorus in larger RNA oligonucleotides. The HCP-CCH-TOCSY experiment is demonstrated on a uniformly 13C, 15N-labeled 19-nucleotide RNA stem-loop, derived from the antisense RNA I molecule found in the ColE1 plasmid replication control system.