Isolation of DNA-free RNA from human bone marrow mononuclear cells: comparison of laboratory methods.

RNA quality (purity and integrity) and quantity are of critical importance to ensure reliable gene expression analysis, reproducibility of RNA sequencing and microarray data and validation by RT-PCR. Currently available methods for isolating RNA either are labor intensive (requiring the use of toxic organic solvents and separate DNase treatment) or require automation (with extensive setup and startup costs). To optimize both the quality and quantity of RNA from bone marrow, we recommend stabilization and storage of bone marrow mononuclear cells in RNAprotect® Cell Reagent, followed by extraction using the RNeasy® Protect Cell Mini Kit (Qiagen, Hilden, Germany). This method achieves optimal quantity and high-quality RNA for sequencing and RT-PCR while remaining efficient and cost effective.

HIV-1 Matrix Protein Interactions with tRNA: Implications for Membrane Targeting.

The N-terminally myristoylated matrix (MA) domain of the HIV-1 Gag polyprotein promotes virus assembly by targeting Gag to the inner leaflet of the plasma membrane. Recent studies indicate that, prior to membrane binding, MA associates with cytoplasmic tRNAs (including tRNALys3), and in vitro studies of tRNA-dependent MA interactions with model membranes have led to proposals that competitive tRNA interactions contribute to membrane discrimination. We have characterized interactions between native, mutant, and unmyristylated (myr-) MA proteins and recombinant tRNALys3 by NMR spectroscopy and isothermal titration calorimetry. NMR experiments confirm that tRNALys3 interacts with a patch of basic residues that are also important for binding to the plasma membrane marker, phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. Unexpectedly, the affinity of MA for tRNALys3 (Kd = 0.63 ± 0.03 µM) is approximately 1 order of magnitude greater than its affinity for PI(4,5)P2-enriched liposomes (Kd(apparent) = 10.2 ± 2.1 µM), and NMR studies indicate that tRNALys3 binding blocks MA association with liposomes, including those enriched with PI(4,5)P2, phosphatidylserine, and cholesterol. However, the affinity of MA for tRNALys3 is diminished by mutations or sample conditions that promote myristate exposure. Since Gag-Gag interactions are known to promote myristate exposure, our findings support virus assembly models in which membrane targeting and genome binding are mechanistically coupled.