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Kadekar, Sandeep
Publications (7 of 7) Show all publications
Nawale, G. N., Bahadorikhalili, S., Sengupta, P., Kadekar, S., Chatterjee, S. & Varghese, O. P. (2019). 4 '-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading. Chemical Communications, 55(62), 9112-9115
Open this publication in new window or tab >>4 '-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading
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2019 (English)In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 55, no 62, p. 9112-9115Article in journal (Refereed) Published
Abstract [en]

We designed novel 4 '-C-guanidinocarbohydrazidomethyl-5-methyl uridine (GMU) modified small interfering RNA (siRNA) and evaluated its biophysical and biochemical properties. Incorporation of GMU units significantly increased the thermodynamic stability as well as the enzymatic stability against nucleases in human serum. A gene silencing experiment indicated that GMU modfied siRNA (siRNA6) resulted in approximate to 4.9-fold more efficient knockdown than unmodified siRNA.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-392130 (URN)10.1039/c9cc04141a (DOI)000477960000008 ()31298670 (PubMedID)
Note

Correction in: CHEMICAL COMMUNICATIONS, Volume: 55, Issue: 67, Pages: 10028-10028, DOI: 10.1039/c9cc90352f

Available from: 2019-09-03 Created: 2019-09-03 Last updated: 2019-09-25Bibliographically approved
Paidikondala, M., Rangasami, V. K., Nawale, G. N., Casalini, T., Perale, G., Kadekar, S., . . . Varghese, O. P. (2019). An Unexpected Role of Hyaluronic Acid in Trafficking siRNA Across the Cellular Barrier: The First Biomimetic, Anionic, Non-Viral Transfection Method. Angewandte Chemie International Edition, 58(9), 2815-2819
Open this publication in new window or tab >>An Unexpected Role of Hyaluronic Acid in Trafficking siRNA Across the Cellular Barrier: The First Biomimetic, Anionic, Non-Viral Transfection Method
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2019 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 9, p. 2815-2819Article in journal (Refereed) Published
Abstract [en]

Circulating nucleic acids, such as short interfering RNA (siRNA), regulate many biological processes; however, the mechanism by which these molecules enter the cell is poorly understood. The role of extracellular-matrix-derived polymers in binding siRNAs and trafficking them across the plasma membrane is reported. Thermal melting, dynamic light scattering, scanning electron microscopy, and computational analysis indicate that hyaluronic acid can stabilize siRNA via hydrogen bonding and Van der Waals interactions. This stabilization facilitated HA size- and concentration-dependent gene silencing in a CD44-positive human osteosarcoma cell line (MG-63) and in human mesenchymal stromal cells (hMSCs). This native HA-based siRNA transfection represents the first report on an anionic, non-viral delivery method that resulted in approximately 60% gene knockdown in both cell types tested, which correlated with a reduction in translation levels.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2019
Keywords
nanoparticles, extracellular matrix, hyaluronic acid, RNAi, transfection
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-379591 (URN)10.1002/anie.201900099 (DOI)000459807200045 ()30644615 (PubMedID)
Funder
Swedish Foundation for Strategic Research , SBE13-0028
Available from: 2019-03-18 Created: 2019-03-18 Last updated: 2019-03-18Bibliographically approved
Paidikondala, M., Kadekar, S. & Varghese, O. P. (2019). Innovative strategy for 3D transfection of primary human stem cells with BMP-2 expressing plasmid DNA: A clinically translatable strategy for ex vivogene therapy. International Journal of Molecular Sciences, 20(1), Article ID 56.
Open this publication in new window or tab >>Innovative strategy for 3D transfection of primary human stem cells with BMP-2 expressing plasmid DNA: A clinically translatable strategy for ex vivogene therapy
2019 (English)In: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 20, no 1, article id 56Article in journal (Refereed) Published
Abstract [en]

Ex vivo gene therapy offers enormous potential for cell-based therapies, however, cumbersome in vitro cell culture conditions have limited its use in clinical practice. We have optimized an innovative strategy for the transient transfection of bone morphogenetic protein-2 (BMP-2) expressing plasmids in suspended human stem cells within 5-min that enables efficient loading of the transfected cells into a 3D hydrogel system. Such a short incubation time for lipid-based DNA nanoparticles (lipoplexes) reduces cytotoxicity and at the same time reduces the processing time for cells to be transplanted. The encapsulated human mesenchymal stromal/stem cells (hMSCs) transfected with BMP-2 plasmid demonstrated high expression of an osteogenic transcription factor, namely RUNX2, but not the chondrogenic factor (SOX9), within the first three days. This activation was also reflected in the 7-day and 21-day experiment, which clearly indicated the induction of osteogenesis but not chondrogenesis. We believe our transient transfection method demonstrated in primary MSCs can be adapted for other therapeutic genes for different cell-based therapeutic applications.

Place, publisher, year, edition, pages
Basel, Switzerland: MDPI, 2019
Keywords
hydrogel; DNA; transfection; ex vivo; hyaluronic acid
National Category
Biomaterials Science
Identifiers
urn:nbn:se:uu:diva-369655 (URN)10.3390/ijms20010056 (DOI)000459747700056 ()30583610 (PubMedID)
Funder
EU, FP7, Seventh Framework Programme, FP7/2007-2013/607868Swedish Foundation for Strategic Research , SBE13-0028
Available from: 2018-12-14 Created: 2018-12-14 Last updated: 2019-03-18Bibliographically approved
Kadekar, S., Nawale, G. N., Karlsson, K., Ålander, C., Podiyan, O. & Varghese, O. P. (2019). Synthetic design of asymmetric miRNA with engineered 3′-overhang to improve strand selection. Molecular Therapy - Nucleic Acids, 16, 597-604
Open this publication in new window or tab >>Synthetic design of asymmetric miRNA with engineered 3′-overhang to improve strand selection
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2019 (English)In: Molecular Therapy - Nucleic Acids, ISSN 2162-2531, E-ISSN 2162-2531, Vol. 16, p. 597-604Article in journal (Refereed) Published
Abstract [en]

We have developed a novel miRNA design that significantly improves strand selection within the RISC complex by engineering the 3′-end by adding extra nucleotides. Addition of seven nucleotides at the 3′-ends of the miR or miR* strand resulted in a thermodynamic asymmetry at either of the two-ends, which resulted in selective RISC recruitment as demonstrated by the stem-loop quantitative PCR experiment. Such selective recruitment was also corroborated at the protein level by Western blot analysis. In order to investigate the functional effect due to selective recruitment, we performed apoptosis and metastasis studies using human colon carcinoma cells (HCT116) and human osteosarcoma cells (MG63). These experiments indicated that the recruitment of miR strand is responsible for inducing apoptosis as well as to inhibit invasiveness of cancer cells. Recruitment of miR* strand, on the other hand, showed opposite effect. To the best of our knowledge, our strand engineering strategy is the first report of improved strand selection of desired miRNA strand by RISC without using any chemical modifications or mismatches. We believe such structural modifications of miR34a could mitigate some of the off-target effects of miRNA therapy and would also allow a better understanding of sequence-specific gene regulation. Such a design could also be adapted to other miRNA to enhance their therapeutic potential.

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
RNA interference, miRNA, miR34a, strand selection, anticancer therapy
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-382299 (URN)10.1016/j.omtn.2019.04.012 (DOI)000470250900053 ()31085353 (PubMedID)
Funder
Swedish Foundation for Strategic Research , SBE13-0028National initiative on Stem Cells for Regenerative Therapy, 2009-1035
Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-06-26Bibliographically approved
Wang, S., Nawale, G. N., Kadekar, S., Oommen, O. P., Jena, N. K., Chakraborty, S., . . . Varghese, O. P. (2018). Saline Accelerates Oxime Reaction with Aldehyde and Keto Substrates at Physiological pH. Scientific Reports, 8, Article ID 2193.
Open this publication in new window or tab >>Saline Accelerates Oxime Reaction with Aldehyde and Keto Substrates at Physiological pH
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 2193Article in journal (Refereed) Published
Abstract [en]

We have discovered a simple and versatile reaction condition for oxime mediated bioconjugation reaction that could be adapted for both aldehyde and keto substrates. We found that saline accelerated the oxime kinetics in a concentration-dependent manner under physiological conditions. The reaction mechanism is validated by computational studies, and the versatility of the reaction is demonstrated by cell-surface labeling experiments. Saline offers an efficient and non-toxic catalytic option for performing the bioorthogonal-coupling reaction of biomolecules at the physiological pH. This saline mediated bioconjugation reaction represents the most biofriendly, mild and versatile approach for conjugating sensitive biomolecules and does not require any extensive purification step.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-347090 (URN)10.1038/s41598-018-20735-0 (DOI)000423787500168 ()29391582 (PubMedID)
Funder
Swedish Foundation for Strategic Research
Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2018-03-26Bibliographically approved
Bermejo, D., Kadekar, S., Tavares da Costa, M. V., Podiyan, O., Gamstedt, E. K., Hilborn, J. & Varghese, O. P. First Aldol-Crosslinked Hyaluronic Acid Hydrogel: Fast and Hydrolytically Stable Gel with Tissue Adhesive Properties. Chemical Sciences Journal
Open this publication in new window or tab >>First Aldol-Crosslinked Hyaluronic Acid Hydrogel: Fast and Hydrolytically Stable Gel with Tissue Adhesive Properties
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(English)In: Chemical Sciences Journal, ISSN 2150-3494Article in journal (Refereed) Submitted
Abstract [en]

Currently, there are limited approaches to tailor 3D scaffolds crosslinked with a stable covalent C-C bond that does not require any catalysts or initiators. We present here the first hydrogels employing aldol condensation chemistry that exhibit exceptional physicochemical properties. We investigated the aldol-crosslinking chemistry using two types of aldehyde-modified hyaluronic acid (HA) derivatives, namely; an enolizable HA-aldehyde (HA-Eal) and a non-enolizable HA-aldehyde (HA-Nal). Hydrogels formed using HA-Eal demonstrate inferior crosslinking efficiency (due to intramolecular loop formation), when compared with hydrogels formed by mixing HA-Eal and HA-NaI leading to a cross-aldol product. The change in mechanical properties as a result of crosslinking at different pH is determined using rheological measurements and is interpreted in terms of molecular weight between cross-links (Mc). The novel HA cross-aldol hydrogels demonstrate excellent hydrolytic stability and favorable mechanical properties but allow hyaluronidase mediated enzymatic degradation. Interestingly, residual aldehyde functionality within the aldol product leads to adhesion to tissue as demonstrated by bonding two bone tissues. The aldehyde functionality also permits facile post-synthetic modifications with nucleophilic reagents such as Alexa FluorTM 488. Finally, we demonstrate that the novel hydrogel is biocompatible with encapsulated stem cells that show a linear rate of expansion in our 3–6 days of study.

Keywords
hyaluronic acid, aldol chemisty, stable hydrogels, tissue adhesive
National Category
Materials Chemistry
Research subject
Chemistry with specialization in Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-374999 (URN)
Available from: 2019-01-24 Created: 2019-01-24 Last updated: 2019-01-24
Wang, S., Nawale, G. N., Kadekar, S., Oommen, O. P., Jena, N. K., Chakraborty, S., . . . Varghese, O. P. Saline catalyse oxime reaction at physiological pH: overcoming a major limitation of bioorthogonal reaction.
Open this publication in new window or tab >>Saline catalyse oxime reaction at physiological pH: overcoming a major limitation of bioorthogonal reaction
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(English)In: Article in journal (Refereed) Submitted
Abstract [en]

We have discovered a simple and versatile reaction condition for oxime mediated bioconjugation reaction that could be adapted for both aldehyde and keto substrates. We found that saline accelerated the oxime kinetics in a concentration dependent manner under physiological conditions. The reaction mechanism is validated by computational studies, and the versatility of the reaction is demonstrated by cell-surface labeling experiments. Saline offers an efficient and non-toxic catalytic option for performing the bioorthogonal-coupling reaction of biomolecules at the physiological pH. This saline mediated bioconjugation reaction represents the most bio-friendly, mild and versatile approach for conjugating sensitive biomolecules and does not require any extensive purification step.

Keywords
Oxime reaction, catalysis, kinetics, labeling
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-328905 (URN)
Available from: 2017-09-04 Created: 2017-09-04 Last updated: 2017-09-07Bibliographically approved
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