Molecular structure of hydrazoic acid with hydrogen-bonded tetramers in nearly planar layers

Hydrazoic acid (HN(3))--potentially explosive, highly toxic, and very hygroscopic--is the simplest covalent azide and contains 97.7 wt % nitrogen. Although its molecular structure was established decades ago, its crystal structure has now been solved by X-ray diffraction for the first time. Molecules of HN(3) are connected to each other by hydrogen bonds in nearly planar layers parallel to (001) with stacking sequence A, B, ... The layer distance, at 2.950(1) Å, is shorter than that in 2H-graphite [3.355(2) Å]. The hydrogen bonds N-H···N are of great interest, since the azido group consists of three homonuclear atoms with identical electronegativity, but different formal charges. These hydrogen bonds are bifurcated into moderate ones with ≈2.0 Å and into weak ones with ≈2.6 Å. The moderate ones build up tetramers (HN(3))(4) in a nearly planar net of eight-membered rings. To the best of our knowledge, such a network of tetramers of a simple molecule is unique.

Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries

Target TAR by NMR: Tripeptides containing arginines as terminal residues and non-natural amino acids as central residues are good leads for drug design to target the HIV trans-activation response element (TAR). The structural characterization of the RNA-ligand complex by NMR spectroscopy reveals two specific binding sites that are located at bulge residue U23 and around the pyrimidine-stretch U40-C41-U42 directly adjacent to the bulge.

Detecting Specific Ligand Binding to Nucleic Acids: A Test for Ultrasoft Laser Mass Spectrometry

Results from a new laser based mass spectrometry method termed LILBID (laser induced liquid bead ion desorption) are presented, which demonstrate the potential for the soft mass analysis of nucleic acids and their specific complexes in solution. On-demand micro droplets, injected into vacuum, are irradiated by intense mid IR-laser pulses. A subsequent explosive phase transition leads to the emission of solvated biomolecular ions into vacuum, which are then mass analyzed by time of flight mass spectrometry. The method is very soft and allows the detection of specific noncovalent complexes. Furthermore it is very tolerant against various buffers and detergents and the charge states of the observed ions reflect qualitatively the charge state in solution. With a required volume of analyte solution in the micro litre range at micromolar concentration, the total consumption of analyte is in the picomolar region. Regarding a single droplet only it is even three orders of magnitude lower, underlining the very high sensitivity of this method. Here we present first examples of the LILBID mass analysis of single stranded DNA (up to a 77mer) and of specific DNA duplices, which show nearly no dissociation under ultrasoft desorption conditions. In case of model hairpin DNA, forming duplices, a sequence specific binding of Dervan-type polyamides into the minor groove of the DNA was observed, and in case of a Tat-TAR model complex strong indications for a specific binding of the Tat protein into the bulge of the wt-RNA was found. Mass spectra of the ribosome of thermos thermophilus give evidence of the applicability of LILBID-MS to analyze large RNA/protein complexes even in the MDa region.

Binding sites of the viral RNA element TAR and of TAR mutants for various peptide ligands, probed with LILBID: a new laser mass spectrometry

A new laser-based mass spectrometry method, called laser induced liquid bead ion desorption (LILBID), was applied to investigate RNA:ligand interactions. As model system the HIV Tat:TAR transactivation complex and its binding behavior were analyzed. TARwt of HIV Type 1 and Type 2 and different artificial mutants were compared regarding their binding to Tat and different peptide ligands. Specific and nonspecific association to TAR was deduced, with the bulge being the well known specific binding site of TAR. In the case of triple arginine (RRR) as a nonspecific ligand, multiple electrostatic binding to TAR was found at higher concentration of RRR. This contrasted with the formation of only ternary complexes in competitive binding studies with TAR, Tat, and potential inhibitors. The fact that the stoichiometries of the complexes can be determined is a major advantage of MS methods over the widely applied fluorimetric methods. A quantitative evaluation of the spectra by a numeric model for ternary complex formation allows conclusions about the role and strength of the binding sites of the RNAs, the specificity and affinity of different ligands, the determination of apparent IC50 and KD values, and a comparison of the binding efficiencies of potential inhibitors.

Fluorescence correlation spectroscopy at single molecule level on the Tat–TAR complex and its inhibitors

The TAR element of HIV and the viral protein Tat form a molecular switch regulating transcriptional efficiency in HIV. We show that fluorescence correlation spectroscopy at the single molecule level is a powerful method to study the association between a Tat-derived peptide and TAR fragments. We also investigated the inhibition of the peptide-RNA complex by different ligands. Utilizing cross correlation measurements, the dissociation constants (K(D)) were determined. To demonstrate the important role of the bulge for the binding of Tat, we compared wt-TAR with three RNA mutants, mainly differing in the bulge region. For the TAR mutants studied at equimolar concentration of RNA and peptide (25 nM), the K(D) values are 15-35 times larger than that of wt-TAR. This gives evidence that the bulge region is the most crucial part of the TAR RNA for specific Tat binding. The IC(50) values for different inhibitors of the Tat/TAR complex both with wt-TAR and mutants have been determined. Neamine conjugate proved to be the best inhibitor of the complex formation. Our results are in agreement with earlier published data on this system using alternative biophysical and biochemical methods, respectively.