Solid-state NMR spectroscopy for characterization of RNA and RNP complexes

Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA and protein–RNA complexes and provides relevant examples

Synthesis and Characterization of a Novel Verdazyl Spin Probe

The use of probe molecules has been integral to the understanding of protein structure and dynamics. Spin labels are commonly used as probes on molecules, such as phospholipids, peptides, proteins, or drugs in vivo. The probes enable the precise and quantitative measuring of the movements of these molecules which has led to the elucidation of function. Nitroxides are the most widely studied and employed spin probes, despite being reduced to hydroxylamines by ascorbic acid in vivo in a matter of minutes. Verdazyls provide comparable applications to nitroxide radicals, with the added benefits of having tunable conformation and hydrophobicity by altering the R1/R5 ligand groups. Verdazyls are defined by their 6-membered ring containing four nitrogen atoms, and are notable for their exceptional stability and high variability in substitution. The radicals are stable in solutions over a wide range of pH, resistant to reduction by ascorbic acid, and can quench the fluorescence of organic dyes. We have synthesized a chloromethyl verdazyl as a possible spin probe for biological molecules, as well as a fluorescence quenching agent. The precursor tetrazane species was definitively identified by NMR spectroscopy, and the novel verdazyl by EPR, UV, and IR spectroscopy. Replacement of chlorine with iodide in the chloromethyl verdazyl demonstrated its ability to undergo SN2 nucleophilic substitution. The chloromethyl verdazyl can be incorporated onto a peptide as a side chain attached label via an SN2 nucleophilic substitution reaction

A facile method for attaching nitroxide spin labels at the 5′ terminus of nucleic acids†

In site-directed spin labeling (SDSL), a nitroxide moiety containing a stable, unpaired electron is covalently attached to a specific site within a macromolecule, and structural and dynamic information at the labeling site is obtained via electron paramagnetic resonance (EPR) spectroscopy. Successful SDSL requires efficient site-specific incorporation of nitroxides. Work reported here presents a new method for facile nitroxide labeling at the 5′ terminus of nucleic acids of arbitrary sizes. T4-polynucleotide kinase was used to enzymatically substitute a phosphorothioate group at the 5′ terminus of a nucleic acid, and the resulting phosphorothioate was then reacted with an iodomethyl derivative of a nitroxide. The method was successfully demonstrated on both chemically synthesized and naturally occurring nucleic acids. The attached nitroxides reported duplex formation as well as tertiary folding of nucleic acids, indicating that they serve as a valid probe in nucleic acid studies

Fluorescence and NMR Studies of the Role of Metal Ions in HIV-1 Genomic RNA Dimerization and Maturation

The dimerization initiation site (DIS) is an essential RNA element responsible for dimerization of HIV-1 genomic RNA through a kissing loop interaction. The DIS loop contains six auto-complementary nucleotides stabilized by 5'- and 3'-flanking purines. NCp7 chaperone protein catalyzes conversion of an intermediate DIS kissing dimer to a more thermodynamically stable extended duplex dimer in the presence of Mg2+. Sequence constructs intended to model the extended duplex, (DIS 21), and the kissing dimer, DIS23(GA)*DIS23(HxUC), were designed to examine the structural information and biochemical behaviors during maturation. We introduced the fluorescent labeling, 2-aminopurine (2-AP) into these RNA constructs, to finely probe structural transition and local dynamics accompanied by the formation of the DIS dimer. The 2-AP nucleotides were inserted either in the DIS loop or junction to study loop-loop interaction or purine base stacking conformation at the junction responding to the metal ion effect. High resolution NMR methods were then used to probe structural changes associated with mono versus divalent cation binding to the DIS dimers and also determine the Mg2+ binding sites. Significant chemical shift perturbations (CSP) were found upon Mg2+ binding and used to map structural changes. Further Mn2+ paramagnetic relaxation enhancement (PRE) experiments provided evidence for specific Mg2+ ion binding are localized around the 5' purine bases in both the extended duplex and kissing dimers with profound line broadening effects. Mapping the CSP and PRE data onto the available X-ray crystal and NMR solution structures allowed localization of specific Mg2+ ions at binding sites on the DIS dimers created by the unpaired flanking DIS loop purine nucleotides. Our data indicates that the conformations that are metal cation dependent. These findings are consistent with previous results that suggested a role for divalent metal cations in stabilizing the DIS kissing dimer structure and influencing its maturation to an extended duplex form through interactions with the DIS loop

Generation of Transgenic Mice to Evaluate Promoter Activity and Specificity of Two Human Endogenous Retrovirus Long Terminal Repeats = Untersuchungen zur Promotor-Aktivität und -Spezifität von zwei Long Terminal Repeats humaner endogener Retroviren in transgenen Mäusen

Generation of Transgenic Mice to Evaluate Promoter Activity and Specificity of two Human Endogenous Retrovirus Long Terminal Repeats Human Endogenous Retrovirus Long Terminal Repeats (HERV-LTRs) comprise 1.8% of the human genome (52.7 Mb). These sequences contain all the signal structures necessary for the regulation of gene transcription, such as promoters, enhancers and transcription factor binding sites. There is evidence that HERV-LTRs regulate gene expression in tissue-specific manner. This potential could be used to drive the expression of therapeutic genes, delivered by retroviral vector systems, in a safe and efficient manner. The HERV-H-H6 LTR and the HERV-L LTR were chosen for the generation of transgenic mice. Their promoter activity and specificity had prior been tested in a luciferase expression vector in vitro (Schoen et al., 2001). HERV-L was cloned into a luciferase expression vector and HERV-H-H6 was inserted into a enhanced green fluorescent protein (EGFP) expression vector. Transgenic mice were generated by DNAmicroinjection into pronuclei of zygotes. One pBL-HERV-L transgenic line and four pEGFP-HERV-H-H6 transgenic lines were established and analyzed. While the HERV-L promoter was not active in transgenic animals, pEGFP-HERV-H-H6 was expressed in gonads of mice of two transgenic lines. As only a single, non-expressing transgenic line was available, HERV-L promoter activity and specificity could not be evaluated. Additional transgenic lines have to be established. Expression level and pattern of the HERV-H-H6 promoter indicate specificity for gonad tissue. Whether the HERV-H-H6 promoter activity is linked to steroid production in cells remains to be clarified. Evaluating promoter activity in transgenic mice in two different expression vectors is not exclusively about the promoters, but also involves knowledge about the reporter genes. Advantages and limits of current applications of both luciferase and EGFP (with focus on the EGFP gene) are described in REVIEW OF THE LITERATURE. The conjunction of EGFP with the HERV-H-H6 promoter is to be seen critically, as all published methods for detection of EGFP in mice are described with EGFP linked to strong promoters. Problems like autofluorescence in fluorescence microscopy might be encountered when weaker promoters, such as HERV-LTRs, drive EGFP expression.Untersuchungen zur Promotor-Aktivität und –Spezifität von zwei Long Terminal Repeats humaner endogener Retroviren in transgenen Mäusen 1.8% des humanen Genoms bestehen aus Long Terminal Repeats Humaner Endogener Retroviren (HERV-LTRs). Solche Sequenzen enthalten alle Strukturen, die für die Regulierung von Transkription benötigt werden: Promotoren, Enhancer and Bindungsstellen für Transkriptionsfaktoren. Es gibt Hinweise, daß HERV-LTRs die Expression von Genen gewebespezifisch regulieren können. Eingebaut in retrovirale Genfähren, könnten HERV-LTRs therapeutische Gene sicher und effizient aktivieren. Zur Generierung transgener Mäuse wurden der HERV-H-H6 LTR und der HERV-L LTR ausgewählt. Deren Promoter Eigenschaften, wie Aktivität und Gewebespezifität, waren bereits in vitro untersucht worden (Schoen et al., 2001). Der HERV-L LTR wurde in einen Luciferase Expressionsvektor und der HERV-H-H6 LTR in einen Enhanced Green Fluorescent Protein (EGFP) Expressionsvektor kloniert. Transgene Mäuse enstanden durch DNA-Mikroinjektion in den Vorkern von Zygoten. Eine pBL-HERV-L transgene Linie und vier pEGFP-HERV-H-H6 transgene Linien wurden gezüchtet und auf Integration sowie Expression der Genkonstrukte untersucht. Während der HERV-L Promoter keine Aktivität zeigte, war Expression von pEGFP-HERV-H-H6 in Keimdrüsen von Mäusen aus zwei transgenen Linien nachweisbar. Da für das Genkonstrukt pBL-HERV-L nur eine einzige, nicht-exprimierende transgene Linie aufgebaut werden konnte, können keine Aussagen über die Aktivität und Gewebespezifität des HERV-L Promoters getroffen werden. Zu diesem Zwecke müssten weitere pBL-HERV-L transgene Linien untersucht werden. Das Expressionsmuster des pEGFP-HERV-H-H6 Genkonstruktes, weißt auf eine mögliche Gewebespezifität für Keimdrüsen hin. Eine eventuelle Verknüpfung der Aktivität des HERV-H-H6 LTRs mit der Produktion von Steroidhormonen müsste weitergehend geklärt werden.Da in dieser Arbeit zwei unterschiedliche Reportergen Systeme in der Maus angewandt wurden, sind im Literaturteil Vorteile und Einschränkungen von aktuellen Nachweisverfahren beider Reportergene, mit Schwerpunkt EGFP, in Mausgewebe zusammengefasst. Die Verbindung von EGFP mit dem HERV-H-H6 Promoter ist als kritisch zu beurteilen: Alle beschriebenen Nachweisverfahren für EGFP in der Maus gründen auf Mausmodellen, in denen das EGFP von einem starken Promoter kontrolliert wurde. Bei potenziell schwächeren Promotoren, wie HERV-LTRs, können Probleme auftreten, wie z.B. Autofluoreszenz bei der Fluoreszenzmikroskopie

Conformational dynamics in microRNAs : the example of miR-34a targeting Sirt1 mRNA

In biology, regulatory mechanisms are essential to achieve complex tasks, as virtually every process can be positively or negatively modulated in its outcome, upon different cues. In humans, microRNAs (miRNAs) constitute a fundamental layer of post-transcriptional gene expression regulation. This class of molecules finely tune protein expression, by downregulating messenger RNAs (mRNA) levels and their translation. The mechanism by which miRNAs find and act upon their targets primarily relies on their nucleotide sequence, relative to the corresponding binding site on the mRNA. The development of an exhaustive miRNA–mRNA interactome is particularly attractive because of the profound implication for basic biology as well as for diagnostics and therapeutics in human health. However, computational prediction of target sites and associated downregulation levels, using the limited sequence determinants available, is still an outstanding challenge in the field. In this thesis, we bring forward the hypothesis that modeling of miRNA–mRNA pairs might benefit from considering the inherent structural flexibility of these complexes, at the molecular level. In the introductory chapter, we present the structural features of RNAs with a focus on their conformational dynamics and NMR spectroscopy as a tool to investigate these motions. The molecular details of miRNA biogenesis and function are later introduced to contextualize the results of Paper I. Finally, the challenges associated with RNA sample preparation are discussed in light of the work presented in Paper II. In Paper I, we show that a miRNA–mRNA pair involved in a cancer-regulating pathway exploits its flexibility to toggle between lower and higher target repression states. This study shows that suboptimal structures of a given miRNA–mRNA pair, that are overlooked by computational prediction and that often elude experimental detection, can be functionally relevant and are essential to draw a mechanistic picture of miRNA function. The methods used in Paper I for RNA sample preparation and molecular simulation are described in Paper II and II, respectively. While these methods were essential to achieve the results of Paper I, they also find widespread application in the RNA field