Folding and Base Pairing of a Fibrinogen Specific DNA Aptamer

Abstract Nucleic acid aptamers can be directed to bind to a variety of target molecules that range widely in molecular size. Their high specificity and selectivity for their targets, in addition to the relative ease in generating aptamers, have sparked their development as drugs and use in diagnostic applications. The 90-mer DNA aptamer (Ap90), specific for the glycoprotein fibrinogen was analyzed by a combination of gel electrophoresis, secondary structure prediction software and NMR spectroscopy to determine what structural motifs are formed prior to binding to its target. Native gel electrophoresis and structure prediction indicate that the aptamer is partially folded. This was further supported by the NMR studies focusing on base pairing. The NMR experiments revealed that the aptamer only forms a maximum of 4-5 AT and 6-8 GC base pairs. Using several model substrates, the base paired region was identified as a hairpin structure originating from the primer region. Changing the solvent conditions did not elicit additional base pairs or promote stable tertiary structures. These results demonstrate that the majority of the aptamer has no established structure prior to binding and guides the design of more efficient aptamers

Understanding Integrase-DNA Interactions in Retroviruses Through 3\u27-processing

Retroviral integrase is one of the key enzymes needed to integrate viral DNA into a host cell’s genome for many retroviruses including HIV. Integrase’s role is three-fold. It prepares the ends of the DNA so that they can successfully bind to the target genomic DNA via 3’-processing, it creates a complex with the viral DNA that is capable of transporting it into the nucleus, and it facilitates the insertion of the viral DNA into the host genome. The goal of this research is to help determine what sequence and structural characteristics of the viral DNA terminus are responsible for successful integrase binding and 3’-processing. Through the use of polyacrylamide gel electrophoresis (PAGE) and 32P end labeling, different substrates are introduced to integrase and the effectiveness of the enzyme in binding to the DNA and carrying out 3’-processing is observed. The importance of terminal structural characteristics as well as individual nucleotides are then determined through a combination of PAGE results, modeling, and NMR-based structural comparisons

Non-Invasive Imaging of Neuroanatomical Structures and Neural Activation with High-Resolution MRI

Several years ago, manganese-enhanced magnetic resonance imaging (MEMRI) was introduced as a new powerful tool to image active brain areas and to identify neural connections in living, non-human animals. Primarily restricted to studies in rodents and later adapted for bird species, MEMRI has recently been discovered as a useful technique for neuroimaging of invertebrate animals. Using crayfish as a model system, we highlight the advantages of MEMRI over conventional techniques for imaging of small nervous systems. MEMRI can be applied to image invertebrate nervous systems at relatively high spatial resolution, and permits identification of stimulus-evoked neural activation non-invasively. Since the selection of specific imaging parameters is critical for successful in vivo micro-imaging, we present an overview of different experimental conditions that are best suited for invertebrates. We also compare the effects of hardware and software specifications on image quality, and provide detailed descriptions of the steps necessary to prepare animals for successful imaging sessions. Careful consideration of hardware, software, experiments, and specimen preparation will promote a better understanding of this novel technique and facilitate future MEMRI studies in other laboratories

Insight into the Modulation of Shaw2 Kv Channels by General Anesthetics: Structural and Functional Studies of S4-S5 linker and S6 C-terminal peptides in micelles by NMR

The modulation of the Drosophila Shaw2 Kv channel by 1-alkanols and inhaled anesthetics is correlated with the involvement of the S4–S5 linker and C-terminus of S6, and consistent with stabilization of the channel\u27s closed state. Structural analysis of peptides from S4–S5 (L45) and S6 (S6c), by nuclear magnetic resonance and circular dichroism spectroscopy supports that an α-helical conformation was adopted by L45, while S6c was only in an unstable/dynamic partially folded α-helix in dodecylphosphocholine micelles. Solvent accessibility and paramagnetic probing of L45 revealed that L45 lies parallel to the surface of micelles with charged and polar residues pointing towards the solution while hydrophobic residues are buried inside the micelles. Chemical shift perturbation introduced by 1-butanol on residues Gln320, Thr321, Phe322 and Arg323 of L45, as well as Thr423 and Gln424 of S6c indicates possible anesthetic binding sites on these two important components in the channel activation apparatus. Diffusion measurements confirmed the association of L45, S6c and 1-butanol with micelles which suggests the capability of 1-butanol to influence a possible interaction of L45 and S6c in the micelle environment

Unusual DNA Structure and DNA Damage Recognition: Structure and Dynamic Markers

Nucleic acids play a central role in many biological processes, including information storage, gene expression, serving as messengers or structural components and even catalysis. Their diverse roles have made them targets of interest to diagnose and treat an array of human disorders such as infections, degenerative diseases and cancer. Nature has evolved proteins and ligands that recognize specific nucleic acid sequences or structures and control their function, demonstrating that this can be efficiently accomplished. This has led to the development of wide variety of synthetic molecules that selectively bind to nucleic acids. In turn, this has precipitated numerous studies which showed that nucleic acid structures and their dynamic properties must be understood in order to efficiently target specific sequences or structures

Nonproteolytic Roles of 19S ATPases in Transcription of CIITApIV Genes

Accumulating evidence shows the 26S proteasome is involved in the regulation of gene expression. We and others have demonstrated that proteasome components bind to sites of gene transcription, regulate covalent modifications to histones, and are involved in the assembly of activator complexes in mammalian cells. The mechanisms by which the proteasome influences transcription remain unclear, although prior observations suggest both proteolytic and non-proteolytic activities. Here, we define novel, non-proteolytic, roles for each of the three 19S heterodimers, represented by the 19S ATPases Sug1, S7, and S6a, in mammalian gene expression using the inflammatory gene CIITApIV. These 19S ATPases are recruited to induced CIITApIV promoters and also associate with CIITA coding regions. Additionally, these ATPases interact with elongation factor PTEFb complex members CDK9 and Hexim-1 and with Ser5 phosphorylated RNA Pol II. Both the generation of transcripts from CIITApIV and efficient recruitment of RNA Pol II to CIITApIV are negatively impacted by siRNA mediated knockdown of these 19S ATPases. Together, these results define novel roles for 19S ATPases in mammalian gene expression and indicate roles for these ATPases in promoting transcription processes

Microwave-assisted synthesis and antibacterial propensity of N0-s-benzylidene-2-propylquinoline- 4-carbohydrazide and N0-((s-1H-pyrrol- 2-yl)methylene)-2-propylquinoline- 4-carbohydrazide motifs

Microwave-assisted approach was utilized as green approach to access a series of 2-pro pylquinoline-4-carbohydrazide hydrazone derivatives 10a-j of aromatic and heteroaromatic aldehydes in highly encouraging yields. It involved four steps reaction which was initiated with ring opening reaction of isatin in a basified environment and subsequent cross-coupling with pentan-2-one to produce compound 7. Esterification of 7 in acid medium led to the formation of compound 8 which was reacted with hydrazine hydrate to access 9 which upon microwave-assisted condensed with aromatic and heteroaromatic aldehydes furnished the targeted compounds 10a-j. The structures of 10aj were confirmed by physico-chemical, elemental analyses and spectroscopic characterization which include UV, FT-IR, 1H and 13C NMR as well as DEPT-135. The targeted compounds 10a-j, alongside with gentamicin clinical standard, were investigated for their antibacterial efficacies using agar diffusion method. 2-Propyl-N0-(pyridine-3-ylmethylene) quinoline-4-carbohydrazide 10j emerged a

Selective G-Quadruplex DNA Recognition by a New Class of Designed Cyanines

A variety of cyanines provide versatile and sensitive agents acting as DNA stains and sensors and have been structurally modified to bind in the DNA minor groove in a sequence dependent manner. Similarly, we are developing a new set of cyanines that have been designed to achieve highly selective binding to DNA G-quadruplexes with much weaker binding to DNA duplexes. A systematic set of structurally analogous trimethine cyanines has been synthesized and evaluated for quadruplex targeting. The results reveal that elevated quadruplex binding and specificity are highly sensitive to the polymethine chain length, heterocyclic structure and intrinsic charge of the compound. Biophysical experiments show that the compounds display significant selectivity for quadruplex binding with a higher preference for parallel stranded quadruplexes, such as cMYC. NMR studies revealed the primary binding through an end-stacking mode and SPR studies showed the strongest compounds have primary KD values below 100 nM that are nearly 100-fold weaker for duplexes. The high selectivity of these newly designed trimethine cyanines for quadruplexes as well as their ability to discriminate between different quadruplexes are extremely promising features to develop them as novel probes for targeting quadruplexes in vivo

The CSF-1 receptor fashions the intestinal stem cell niche

AbstractGastrointestinal (GI) homeostasis requires the action of multiple pathways. There is some controversy regarding whether small intestine (SI) Paneth cells (PCs) play a central role in orchestrating crypt architecture and their relationship with Lgr5+ve stem cells. Nevertheless, we previously showed that germline CSF-1 receptor (Csf1r) knock out (KO) or Csf1 mutation is associated with an absence of mature PC, reduced crypt proliferation and lowered stem cell gene, Lgr5 expression. Here we show the additional loss of CD24, Bmi1 and Olfm4 expression in the KO crypts and a high resolution 3D localization of CSF-1R mainly to PC. The induction of GI-specific Csf1r deletion in young adult mice also led to PC loss over a period of weeks, in accord with the anticipated long life span of PC, changed distribution of proliferating cells and this was with a commensurate loss of Lgr5 and other stem cell marker gene expression. By culturing SI organoids, we further show that the Csf1r−/− defect in PC production is intrinsic to epithelial cells as well as definitively affecting stem cell activity. These results show that CSF-1R directly supports PC maturation and that in turn PCs fashion the intestinal stem cell niche

A Systems Biology Approach Reveals the Role of a Novel Methyltransferase in Response to Chemical Stress and Lipid Homeostasis

Using small molecule probes to understand gene function is an attractive approach that allows functional characterization of genes that are dispensable in standard laboratory conditions and provides insight into the mode of action of these compounds. Using chemogenomic assays we previously identified yeast Crg1, an uncharacterized SAM-dependent methyltransferase, as a novel interactor of the protein phosphatase inhibitor cantharidin. In this study we used a combinatorial approach that exploits contemporary high-throughput techniques available in Saccharomyces cerevisiae combined with rigorous biological follow-up to characterize the interaction of Crg1 with cantharidin. Biochemical analysis of this enzyme followed by a systematic analysis of the interactome and lipidome of CRG1 mutants revealed that Crg1, a stress-responsive SAM-dependent methyltransferase, methylates cantharidin in vitro. Chemogenomic assays uncovered that lipid-related processes are essential for cantharidin resistance in cells sensitized by deletion of the CRG1 gene. Lipidome-wide analysis of mutants further showed that cantharidin induces alterations in glycerophospholipid and sphingolipid abundance in a Crg1-dependent manner. We propose that Crg1 is a small molecule methyltransferase important for maintaining lipid homeostasis in response to drug perturbation. This approach demonstrates the value of combining chemical genomics with other systems-based methods for characterizing proteins and elucidating previously unknown mechanisms of action of small molecule inhibitors