Prabodhika Mallikaratchy

Prabodhika Mallikaratchy
City University of New York City - Lehman College | CUNY

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42
Publications
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3,306
Citations

Publications

Publications (42)
Article
Full-text available
The current detection methods of malignant cells are mainly based on the high expression levels of certain surface proteins on these cells. However, many of the same surface marker proteins are also expressed in normal cells. Growing evidence suggests that the molecular signatures of the tumor microenvironment (TME) are related to the biological st...
Preprint
The current detection methods of malignant cells are mainly based on the high expression levels of certain surface proteins on these cells. However, many of the same surface marker proteins are also expressed in normal cells. Growing evidence suggests that the molecular signatures of the tumor microenvironment (TME) are related to the biological st...
Article
Full-text available
DNA nanotechnology is undergoing rapid progress in the assembly of functional devices with biological relevance. In particular, currently, the research attention is more focused on the application of nanodevices at the interface of chemistry and biology, on the cell membrane where protein receptors communicate with the extracellular environment. Th...
Article
Full-text available
Recently, immunotherapeutic modalities with engineered cells and monoclonal antibodies have been effective in treating several malignancies. Nucleic acid aptamers can serve as alternative molecules to design immunotherapeutics with high functional diversity. Here, we report a synthetic prototype consisting of DNA aptamers, which can activate T-cell...
Preprint
Full-text available
Recently, immunotherapeutic modalities with engineered cells and monoclonal antibodies have been effective in treating several malignancies. However, growing evidence suggests that immune-related adverse events (irAE) lead to severe and long-term side effects. Most iRAEs involve prolonged circulation of antibodies. To address this problem, nucleic...
Article
Here we are reporting, for the first time, a Ligand Guided Selection (LIGS) experiment using artificially expanded genetic information system (AEGIS) to successfully identify an AEGIS-DNA aptamer against T-cell receptor-CD3ε expressed on Jurkat.E6 cells. Thus, we have effectively combined the enhanced diversity of an AEGIS DNA library with LIGS to...
Article
Full-text available
With the success of RNA based therapeutic drugs, the demand has increased for sophisticated nucleic acid-based targeting agents. Nucleic acid aptamers (NAAs), in this regard, represent a suitable class of molecules with synthetic versatility. Aptamers are composed of single-stranded RNA/DNA/XNA molecules, which can be identified using a method call...
Article
Full-text available
To discover DNA ligands against a predetermined receptor protein complex, we introduce a comprehensive version of ligand-guided selection (LIGS). LIGS is, itself, a variant of systematic evolution of ligands by exponential enrichment (SELEX). Herein, we have optimized LIGS to identify higher affinity aptamers with high specificity. In addition, we...
Article
Exploiting a variant of SELEX called “Ligand-Guided Selection” (LI-GS), we recently identified two novel truncated G-rich aptamers, called R1.2 and R1.3, specific for membrane-bound IgM (mIgM), the hallmark of B cells. Herein, the conformational behaviour of these aptamers has been analysed by multiple biophysical methods. In order to investigate t...
Article
Nucleic Acid Aptamers (NAAs) are a class of synthetic DNA or RNA molecules that bind specifically to their target. We recently introduced an aptamer termed R1.2 against membrane Immunoglobulin M (mIgM) expressing B-cell neoplasms using Ligand Guided Selection (LIGS). While LIGS-generated aptamers are highly specific, their lower affinity prevents a...
Article
Full-text available
Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be cou...
Article
Aptamers are synthetic, short nucleic acid molecules capable of specific target recognition. Aptamers are selected using a screening method termed Systematic Evolution of Ligands by Exponential enrichment (SELEX). We recently have introduced a variant of SELEX called "Ligand-Guided-Selection" (LIGS) that allows the identification of specific aptame...
Article
Full-text available
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed o...
Article
We recently introduced a screening technology termed ligand-guided selection, (LIGS), to selectively identify target-specific aptamers from an evolved cell-SELEX library. Cell-SELEX utilizes a large combinatorial single-stranded oligonucleotide library and progressively selects DNA ligands against whole cells with variable DNA-binding affinities an...
Article
We report on a new strategy for identifying highly specific aptamers against a predetermined epitope of a target. Termed “ligand-guided selection” (LIGS), this method uniquely exploits the selection step, the core of SELEX (Systematic Evolution Exponential enrichment). LIGS uses a naturally occurring stronger and highly specific bivalent binder, an...
Chapter
The knowledge of biomarkers relevant to diseases has a significant impact on the diagnosis, the prognosis, and the fundamental understanding of the disease. In the context of biomarker discovery in cell-SELEX, the definition of a biomarker referred to a molecular entity overly expressed in an immortalized cell line in which the origin of this cell...
Article
Monoclonal antibodies (mAbs) have naturally evolved as suitable, high affinity and specificity targeting molecules. However, the large size of full-length mAbs yields poor pharmacokinetic properties. A solution to this issue is the use of a multistep administration approach, in which the slower clearing mAb is administered first and allowed to reac...
Article
Full-text available
Long-term survival still eludes most patients with leukemia and non-Hodgkin’s lymphoma. No approved therapies target the hallmark of the B cell, its mIgM, also known as the B-cell receptor (BCR). Aptamers are small oligonucleotides that can specifically bind to a wide range of target molecules and offer some advantages over antibodies as therapeuti...
Article
Molecular mediation of singlet oxygen generation is demonstrated based on a newly engineered aptamer probe. Both ATP and human α-thrombin aptamers were engineered to testify to this design, and both showed that the production of singlet oxygen can be triggered and quantitatively mediated by the presence of target molecules. Moreover, both photosens...
Chapter
Introduction Molecular Diagnosis of Cancers Aptamers for Tumor Marker Detection Fluorescence Energy Transfer for Aptamerbased PDGF Analysis Aptamers as Fluorescence Anisotrpy Probes for Protein Analysis Whole-Cell-Based Aptamer Selection for Multiple Tumor Markers Conclusion References
Article
2711 Poster Board II-687 Non-Hodgkins lymphomas affect 450,000 patients in the United States and even with recent advances in antibody-based therapies; more than 20,000 people will die of their disease annually. The goal of this work was to develop a high affinity, stable aptamer selective for B-cell leukemias and lymphomas. Aptamers are small DNA...
Article
We report a chemically modified construct of the Sgc8 aptamer, selected against CEM cells, conjugated to an activator platform for stimulated release of molecules at the tumor surface using DNA template assisted functional group transfer reactions (DTGTR).
Chapter
Aptamers are single-stranded nucleic acid probes that can be evolved to have high specificity and affinity for different targets. These targets include biomar-ker proteins, small molecules, and even whole live cells that express a variety of surface proteins of interest. Aptamers offer several advantages over protein-based molecular probes such as...
Article
A novel aptamer-based molecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three elements: an aptamer, a short, partially cDNA sequence, and a PEG linker conjugating the aptamer with the short DNA strand. We have termed this aptamer probe an "aptamer switch probe", or ASP. The ASP design util...
Article
Disease biomarkers play critical roles in the management of various pathological conditions of diseases. This involves diagnosing diseases, predicting disease progression and monitoring the efficacy of treatment modalities. While efforts to identify specific disease biomarkers using a variety of technologies has increased the number of biomarkers o...
Article
Photodynamic therapy for tumors. This paper describes the application of a molecular construct of a photosensitizer and an aptamer for phototherapeutically targeting tumor cells. Coupled with the advantages of the cell-SELEX in generating multiple effective aptamers for diseased cell recognition, we will be able to develop highly efficient photosen...
Article
Full-text available
The identification of tumor related cell membrane protein targets is important in understanding tumor progression, the development of new diagnostic tools, and potentially for identifying new therapeutic targets. Here we present a novel strategy for identifying proteins that are altered in their expression levels in a diseased cell using cell speci...
Article
In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. Molecular medicine will require a large number of probes for molecular recognition and characterization of a variety of diseased cells. Aptamers, single-stranded DNA/RNA probes, are poised to become a chemist's antibody and have the potential...
Article
(Figure Presented) To cut a long story short. Single-stranded DNA aptamers that can recognize cancer cells specifically were optimized and modified. The modifications gave rise to aptamers that were much smaller in size (see scheme) and more stable in fetal bovine serum. This stability makes it possible to apply aptamers to in vivo applications, su...
Article
Protein kinase Cs are a family of serine and threonine kinases that mediate a wide variety of cellular signalling processes such as cell growth, differentiation, apoptosis and tumor development. We have selected high-affinity DNA aptamers for PKCdelta by capillary electrophoresis based SELEX (systematic evolution of ligands by exponential enrichmen...
Article
Full-text available
Using cell-based aptamer selection, we have developed a strategy to use the differences at the molecular level between any two types of cells for the identification of molecular signatures on the surface of targeted cells. A group of aptamers have been generated for the specific recognition of leukemia cells. The selected aptamers can bind to targe...
Article
Efficient access to bis(nitrophenyl) ditellurides was developed and their utility for the preparation of novel nitrogen-containing organotellurium heterocycles demonstrated. The nitration of diphenyl ditellurides resulted in their oxidation to benzenetellurinic acids, followed by nitration in ortho or meta positions relative to tellurium. Nitration...
Article
Full-text available
The title compound, C28H26N2Te2, prepared by reduction of (3,5-dimethyl­phen­yl)(2-nitro­phen­yl)tellurium(II), is the first structurally characterized example of an azo group bridging two TeII centers. The compound is centrosymmetric and the Te—N distance [2.6916 (19) Å] is longer than in non-bridging azo compounds.
Article
Efficient access to bis(nitrophenyl) ditellurides was developed and their utility for the preparation of novel nitrogen-containing organotellurium heterocycles demonstrated. The nitration of diphenyl ditellurides resulted in their oxidation to benzenetellurinic acids, followed by nitration in ortho or meta positions relative to tellurium. Nitration...
Article
All three title compounds, prepared from bis(3,5-di­methyl-2-nitro­phenyl)­ditellurium, exhibit high degrees of intramol­ecular Te—O coordination. Their Te—O distances increase in the order C8H8BrNOTe < C8H8BrNO2Te < C8H8Br3NO2Te, with distances of 2.165 (3), 2.306 (1) and 2.423 (6) Å, respectively, indicating that C8H8BrNOTe may be more aptly desc...
Article
All three title compounds, prepared from bis(3,5-dimethyl-2-nitrophenyl)ditellurium, exhibit high degrees of intramolecular Te-O coordination. Their Te-O distances increase in the order C(8)H(8)BrNOTe < C(8)H(8)BrNO(2)Te < C(8)H(8)Br(3)NO(2)Te, with distances of 2.165 (3), 2.306 (1) and 2.423 (6) A, respectively, indicating that C(8)H(8)BrNOTe may...

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