Sepsis is among the most prevalent diagnosed critical illnesses in the United States today. Although advances have reduced the overall morbidity and mortality associated with this illness, the enormous number of deaths associated with it shows a need for improved diagnostic and therapeutic optionsgent. Our laboratory has utilized RNA based technologies to aid in the treatment of histone induced multiple organ dysfunction syndrome seen in sepsis. Histones are proteins found in the nucleus of every cell in our body and have been shown to be released during sepsis. Such release induces damage to other cells, causing a feed forward cycle that results in organ failure and death. Several therapeutics have been utilized to neutralize histones but have shown considerable toxicity. This thesis describes the generation of single stranded RNA aptamers to bind and neutralize histone mediate damage without unwanted toxicity. We demonstrate that our aptamers selectively bind to histones but not serum proteins. In addition, we establish that our aptamers can neutralize all histone mediated cellular response in vitro and in vivo. Finally, we determined that our aptamers are able inhibit the histone feed forward cycle in a temporal fashion in our murine model of multiple organ dysfunction. This novel therapeutic demonstrates the selectivity and effectiveness needed to inhibit histones in several critical illnesses.

Thesis advisor: Michelle M. Meyer / Thesis advisor: Jeffery A. Byers / Riboswitches are a class of regulatory structures located in the 5’ untranslated region of many bacterial mRNAs. Validating riboswitch-ligand interactions has historically been costly and low-throughput. Recently, graphene field-effect transistors (G-FETs) have emerged as effective biosensors in detecting interactions of such regulators with charged, high molecular weight analytes. However, a bottleneck still exists in detecting relatively neutral small molecules. The Bacillus subtilis guanine riboswitch (Xpt) within the xpt-pbuX operon contains a purine-responsive aptamer region with affinity for guanine, hypoxanthine, and other purine analogs. The G-FET sensor revealed successful detection of Xpt-hypoxanthine interactions at saturating concentrations. The specificity of Xpt was also demonstrated by a lack of signal detection when incubated with adenine. Therefore, such G-FET devices are effective in detecting aptamer binding to small, electrically-neutral molecules, which will allow for rapid screening of potential therapeutic ligands. Further, different electrical observations of n-doping upon aptamer functionalization and p-doping upon ligand binding reveal unique interactions at the graphene surface. Molecular dynamics simulations were carried out to interpret experimental results and to determine if another well characterized aptamer (FMN) is a suitable candidate for G-FET studies. Trajectory data from the Xpt aptamer domain complexed with hypoxanthine (PDBID: 4FE5) and guanine (PDBID: 1Y27) showed significant differences in root mean square deviation (RMSD) and radius of gyration (Rg) from their respective non-binding mutants. These findings provide evidence that compaction of the RNA phosphodiester backbone is responsible for graphene detection. RMSD and Rg differences from FMN (PDBID: 3F4E) indicate that this aptamer may not show a significant change in G-FET signal. These findings suggest that G-FET biosensors can provide an avenue for the discovery of novel antibiotics for aptamer targets to combat burgeoning antibiotic resistance. / Thesis (BS) — Boston College, 2021. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Departmental Honors. / Discipline: Biochemistry.

No description available.

Yes / We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base−graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene−aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine−graphene interactions.

Nanoparticles produced with surfaces functionalised by highly specific molecular tags are able to target aberrant cells and detect or eliminate them without causing damage to surrounding healthy tissues. Single-stranded DNA (ssDNA) and RNA which fold to form secondary or tertiary structures, termed aptamers, represent a new class of such molecular tags. The nanoparticles, in turn, may carry therapeutic payload or luminescent entities which enable elimination or visualisation of targeted cells respectively. This project presents fabrication and isolation of a surface-functionalised nanoparticle construct, namely aptamer-tagged silica nanoparticles. DNA aptamers were chosen with the intention to make them useful for clinical or diagnostic applications of targeting neoplastic cells. Indeed, the ssDNA applied here is known to bind mucin-1 which in turn is a biomarker found on the surface of metastatic breast cancer cells. The separation of the construct was made possible by the inclusion of oligonucleotide-bound superparamagnetic particles in the construct; these enabled separation by magnetic capture. This project investigates two approaches to fabrication of the construct. In the first approach, aptamers, oligonucleotides and magnetic particles are mixed in solution. In the second, silica nanoparticles are functionalised with aptamers, oligonucleotides are bound to magnetic particles and the resulting two parts are hybridised together. The first approach gives higher yields. This may suggest that binding of silica nanoparticles to aptamers may hinder aptamer hybridisation to oligonucleotide fragments, thus resulting in lower construct synthesis yields. However, it is not known yet how the yield changes upon addition of silica nanoparticles into the solution. Therefore, the second experimental approach provides a starting point for fabrication and purification of an anti-cancer drug targeting platform in a simple bench-top setting. In addition, this thesis discusses the fabrication of silica nanoparticles which were intended to constitute an element of the construct. The work on nanoparticle fabrication aimed to develop a quick and repeatable synthesis method which would result in monodisperse entities. Despite trying various experimental approaches, suitable particles could not be reproducibly obtained. Agglomeration was identified as a major obstacle in the silica nanoparticle production process. Finally, this project assesses whether the chosen aptamers bind to the metastatic breast cancer cells, which would be necessary if they were to be used for diagnosis or therapy. FACS analysis indeed indicate that ssDNA aptamers attach to the MCF7 cell line, but the optimum conditions for that attachment remain to be determined.

DNA-functionalized gold nanoparticles (DNA-NPs) have enormous potential as building blocks for materials due to their ability to specifically recognize and respond to target molecules and surfaces. The ability of DNA aptamers to adopt different conformations and bind either complementary DNA sequences or analyte molecules allows them to mediate nanoparticle assembly or disassembly, generating selective colorimetric responses. Aptamer-mediated nanoparticle assembly and disassembly is sensitive to the nanoparticle ligand shell composition and structure, yet these topics have not been extensively explored. In this dissertation, a method for determining the ligand shell composition of DNA-NPs is described and a framework for understanding the impact of the DNA assembly arrangement and recognition strand density upon aptamer-mediated nanoparticle assembly and disassembly is developed. Design rules for creating sensors with desired properties are elucidated, leading to creation of sensors with improved detection limits and quantification ranges. A technique was needed to determine the number of DNA strands of any base composition attached to gold nanoparticles (AuNPs) of any core size. A rapid, convenient and inexpensive method to quantify the number of label-free DNA strands attached to AuNPs was therefore developed. This technique was extended to determine two different DNA sequences bound to AuNPs using UV-visible and fluorescence spectroscopy. Based on the results of quantifying the ligand shells of DNA-NPs functionalized with two sequences, disulfide-terminated DNA non-specifically adsorbs and then rearranges to specifically bind the gold surface. The position of the AuNPs and DNA strands within DNA-NP assemblies had a profound influence on their ability to assemble and sense adenosine. Assemblies designed for large inter-AuNP spacing were stable but unable to sense adenosine. Assemblies designed for short inter-AuNP spacing were unstable until the DNA ligand shell was diluted. AuNPs functionalized with the fewest number of aptamers produced assemblies with the lowest detection limit and apparent disassociation constant and the largest analyte quantification range. Increasing the number of aptamer strands per AuNP increased the cooperativity of the AuNP disassembly response to adenosine. This dissertation includes previously unpublished co-authored material.

Polychlorinated biphenyls (PCBs) are persistent environmental chemicals. Mono-hydroxylated polychlorinated biphenyls (OH-PCBs) are PCB metabolites found commonly in human blood, environmental water and sediment samples. Detection of small amounts of PCBs and their OH-PCB metabolites in biological matrices from epidemiological and laboratory studies remains a challenge. The application of aptamers is studied as a means to identify and quantify PCBs and OH-PCBs. Aptamers are single stranded short oligonucleotides that arrange into unique shape of three-dimensional structures when binding to their target. Like antibodies they have high affinity and specificity for their specific target. The hypothesis is that aptamers can identify PCBs and PCB metabolites in environmental and biological samples. To test this hypothesis, three different OH-PCBs, 4’-OH-PCB3, 4-OH-PCB72 and 2-OH-PCB106 along with 4-OH-biphenyl as a control, were covalently attached to beads with carboxylic acid groups on their surface. Several methods were explored to characterize covalent binding of OH-PCBs to the beads: FTIR-spectroscopy, Dynamic Light Scattering (DLS) and Zeta-Potential (ZP) measurements. The beads were then used in in vitro assays to test binding of two different aptamers specific to OH-PCBs. In this study, these aptamers were tested for the ability to distinguish structurally different OH-PCB congeners and other environmental pollutants. In future studies, aptamers can be selected for a PCB metabolite of interest, 4’-OH-PCB3, via a modified form of Systemic Evolution of Ligands by Exponential Enrichment (SELEX). Single stranded DNA (ssDNA) aptamers generated will be applied as a biosensor for the detection and quantification of traces of 4’-OH-PCB3.

New affinity molecules such as nucleic acid aptamers are in demand in the science and medical fields. Current aptamer selection technologies can generate unique aptamers with desired properties to targets of interest. My thesis describes a series of investigations on the protection of an oncolytic virus, the isolation of target cells from biological fluids, and aptamer-facilitated biomarker discovery. We tested individual aptamers and constructed a tetramer aptamer structure (quadramer) to increase virus infectivity. The quadramer protects vesicular stomatitis virus (VSV) during freeze–thaw cycles, shields the virus from neutralizing antibodies and increases viral active units. In addition to aptamers, we screened carbohydrate-based ice recrystallization inhibitors for the possible elimination of the cold chain of Vaccinia virus, VSV, and Herpes virus-1. N-octyl-gluconamide provides the longest shelf life for Vaccinia virus and Herpes virus-1 as tested according to the World Health Organization’s requirements for viral vaccines efficiency during transportation and distribution. We generated switchable aptamers capable of isolating cells expressing LIFR, NRP1, DLL4, uPAR, or PTCH1. These aptamers bind to the receptor positive cells in the presence of Mg2+ and Ca2+, and release the pure cells upon addition of EDTA. The aptamers were applied for a sequential positive immunomagnetic isolation of cells from mice bone marrow. We also utilized fluorescence-activated cell sorting (FACS) in our aptamer selections to develop switchable aptamers to positive isolation of monocytes from human blood. Moreover, we have selected non-switchable aptamers as an affinity probe to the cells expressing Axl receptor for immunofluorescent analysis and cell sorting. We determined aptamers to CD107a and applied them for biomarker discovery with mass spectrometry and found that CD107a was co-expressing with PD-1. Furthermore, we identified CD91 as binding partners to our aptamers in human monocytes using FACS and orbitrap mass spectrometry.

xvii, 203 p. / Gold nanoparticles have garnered recent attention due to their intriguing size- and shape-dependent properties. Routine access to well-defined gold nanoparticle samples in terms of core diameter, shape, peripheral functionality and purity is required in order to carry out fundamental studies of their properties and to utilize these properties in future applications. For this reason, the development of methods for preparing well-defined gold nanoparticle samples remains an area of active research in materials science. In this dissertation, two methods, diafiltration and aptamer mediated synthesis, are explored as possible routes towards well-defined gold nanoparticle samples. It is shown that diafiltration has considerable potential for the efficient and convenient purification and size separation of water-soluble nanoparticles. The suitability of diafiltration for (i) the purification of water-soluble gold nanoparticles, (ii) the separation of a bimodal distribution of nanoparticles into fractions, (iii) the fractionation of a polydisperse sample and (iv) the isolation of [rimers from monomers and aggregates is studied. NMR, thermogravimetric analysis (TGA), and X-ray photoelectron spectroscopy (XPS) measurements demonstrate that diafiltration produces highly pure nanoparticles. UV-visible spectroscopic and transmission electron microscopic analyses show that diafiltration offers the ability to separate nanoparticles of disparate core size, including linked nanoparticles. These results demonstrate the applicability of diafiltration for the rapid and green preparation of high-purity gold nanoparticle samples and the size separation of heterogeneous nanoparticle samples. In the second half of the dissertation, the identification of materials specific aptamers and their use to synthesize shaped gold nanoparticles is explored. The use of in vitro selection for identifying materials specific peptide and oligonucleotide aptamers is reviewed, outlining the specific requirements of in vitro selection for materials and the ways in which the field can be advanced. A promising new technique, in vitro selection on surfaces (ISOS), is developed and the discovery using ISOS of RNA aptamers that bind to evaporated gold is discussed. Analysis of the isolated gold binding RNA aptamers indicates that they are highly structured with single-stranded polyadenosine binding motifs. These aptamers, and similarly isolated peptide aptamers, are briefly explored for their ability to synthesize gold nanoparticles. This dissertation contains both previously published and unpublished co-authored material. / Adviser: James E. Hutchison

Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-10-31T16:54:52Z No. of bitstreams: 2 Dissertação - Elismar de Jesus Nunes Cnossen - 2014.pdf: 4126749 bytes, checksum: eacd4dd92411aa26514ec275da57a07e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-10-31T16:58:44Z (GMT) No. of bitstreams: 2 Dissertação - Elismar de Jesus Nunes Cnossen - 2014.pdf: 4126749 bytes, checksum: eacd4dd92411aa26514ec275da57a07e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-10-31T16:58:44Z (GMT). No. of bitstreams: 2 Dissertação - Elismar de Jesus Nunes Cnossen - 2014.pdf: 4126749 bytes, checksum: eacd4dd92411aa26514ec275da57a07e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-01-21 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / The increasing number of notifications of dengue infections is becoming a very important concern for global healthcare programs. Combinatorial technologies aiming the selection of specific short conformational nucleic acid ligands against viral targets, also called aptamers, can be achieved by large-scale selections using the genomic SELEX technology. Our hypothesis is that aptamers can be directly selected against dengue RNA conformational structures that present functional elements in the 5'-UTR sequence, which form RNA-RNA and protein- RNA interactions, and play significant roles in the infection process. Our aim was to select and characterize aptamers that bind to the 5’-UTR using the matrix-free SELEX method. Products from the eighth selection cycle were isolated, cloned and sequenced, and 14 ligands were chosen for in silico characterization. Aptamers were grouped into three families according to their sequence homology, and conserved ribonucleotides generated specific linear motifs. Sequences motifs were detected in random nucleotides regions ranging from 31 to 40 nt, which showed higher affinity to DENV1 and 3 virus. The novel molecules and processes described in this study open new insights for dengue research and applications, and the selected aptamers can be used either as diagnostic or therapeutic tools. In silico analyses revealed that aptamer binding to its RNA target may lead to alterations of viral RNA secondary structures, and is probably leading to the loss of its original conformational and preventing its replication and/or the transcription process. The analyses also demonstrated that aptamers presented a broad hybridization spectrum to DENV1 and 3 even in the presence of mutations in different subtypes, which suggest its possible use in the other two serotypes, DENV2 and 4. This is the first description of aptamers against the RNA structure of Dengue Virus with important implications in the disease control. / O aumento do número de notificações de infecções causadas pela dengue está se tornando uma grande preocupação para os programas globais de saúde. Tecnologias combinatórias destinadas à seleção de ligantes específicos de ácidos nucléicos curtos conformacionais contra alvos virais, também chamados aptâmeros, podem ser conseguidos pelas seleções em larga escala, utilizando a tecnologia do SELEX genômico. Nossa hipótese é que os aptâmeros podem ser selecionados diretamente contra as estruturas conformacionais de RNA da dengue, as quais apresentam elementos funcionais na sequência 5'-UTR, que formam interações RNA-RNA e RNA-proteína, e desempenham papéis importantes no processo de infecção. O nosso objetivo foi selecionar e caracterizar aptâmeros que se ligam a região 5'-UTR utilizando o método matrix-free SELEX . Produtos do oitavo ciclo de seleção foram isolados, clonados e sequenciados, e 14 ligantes foram escolhidos para a caracterização in silico. Os aptâmeros foram agrupados em três famílias de acordo com a homologia das sequências, e ribonucleotídeos conservados geraram motivos lineares específicos. Sequências motivos foram detectadas em regiões aleatórias de nucleotídeos variando de 31-40 nt que apresentaram a maior afinidade para DENV1 e 3. As novas moléculas e processos descritos neste estudo abrem novas perspectivas para a pesquisa e aplicações na dengue, e os aptâmeros selecionados podem ser usados tanto como ferramentas diagnósticas ou terapêuticas. As análises in silico revelaram que a ligação do aptâmeros ao seu alvo de RNA pode levar a alterações na estrutura secundária do RNA viral, e provavelmente levando à perda da sua conformação original e impedindo a sua replicação e/ou o processo de transcrição. As análises também demonstraram que os aptâmeros apresentaram um largo espectro de hibridação ao DENV1 e 3, mesmo na presença de mutações em diferentes subtipos, o que sugere a sua possível utilização nos outros dois sorotipos, DENV2 e 4. Esta é a primeira descrição de aptâmeros contra a estrutura de RNA do Vírus da Dengue com implicações importantes no controle da doença.