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  1. Article: Interface of G-quadruplex with both stabilizing and destabilizing ligands for targeting various diseases

    Chaudhary, Swati / Kumar, Mohan / Kaushik, Mahima

    International journal of biological macromolecules. 2022 Oct. 31, v. 219

    2022  

    Abstract: Guanine-rich DNA sequences may fold back into non-canonical four-stranded secondary structures termed as G-quadruplexes. The role of G-quadruplexes has already been well established in different diseases like cancer, neurological and viral disorders etc. ...

    Abstract Guanine-rich DNA sequences may fold back into non-canonical four-stranded secondary structures termed as G-quadruplexes. The role of G-quadruplexes has already been well established in different diseases like cancer, neurological and viral disorders etc. Also, several small molecules have been reported, which can influence the involvement of G-quadruplexes either through stabilization or destabilization in the cellular environment. Growing statistics have associated G-quadruplex assemblies to a discrete biological process in vivo, including DNA replication, transcription, genomic stability, and epigenetic regulation. DNA G-quadruplex existence in human telomere is well recognized attractive target for anticancer drugs. G-quadruplex-interactive ligands have been known to prevent telomerase access as well as telomere capping. To the best of our understanding, the role of G-quadruplexes in virology, neuropharmacology, cancer progression and its treatment has not been discussed on a single platform till date. This review aims to enhance our knowledge regarding these magical sticky quadruplex structures, which have been quite significantly proved to be the part of many cellular processes along with their established in vivo existence. Understanding regarding stabilizing or destabilizing ligands of these multistranded guanine quadruplex structures might be proved as the facilitator of drug discovery process for many incurable diseases in future.
    Keywords DNA ; DNA replication ; epigenetics ; genomics ; guanine ; humans ; ligands ; neoplasm progression ; nucleic acid conformation ; statistics ; telomerase ; telomeres ; virology
    Language English
    Dates of publication 2022-1031
    Size p. 414-427.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.07.248
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  2. Article: Exploring the interaction of guanidine ligands Amiloride, Rimeporide and Cariporide with DNA for understanding their role as inhibitors of Na+/H+ exchangers (NHEs): A spectroscopic and molecular docking investigation

    Chaudhary, Swati / Kumar, Pankaj / Kaushik, Mahima

    International journal of biological macromolecules. 2022 July 31, v. 213

    2022  

    Abstract: The inhibition of Na⁺/H⁺ Exchangers (NHEs) has shown efficacy in the pathology of several diseases like tumors, cardiovascular, and neurological disorders. The role of guanidine ligands such as amiloride, cariporide, and rimeporide as NHE inhibitors is ... ...

    Abstract The inhibition of Na⁺/H⁺ Exchangers (NHEs) has shown efficacy in the pathology of several diseases like tumors, cardiovascular, and neurological disorders. The role of guanidine ligands such as amiloride, cariporide, and rimeporide as NHE inhibitors is very well documented but their interaction studies with genomic DNA are still unexplored. In this study, a combination of various biophysical and molecular docking studies was employed to investigate their binding aspects.UV–Visible, fluorescence, and circular dichroism (CD) studies indicated that guanidine ligands bind to the grooves of Calf Thymus DNA (ctDNA). Fluorescence titration studies depict that amiloride binds to ctDNA with a binding constant in the order of 10² M⁻¹ and free energy change (ΔG⁰) of −14.05 KJ mol⁻¹. Competitive fluorescence studies indicated the minor groove binding property of amiloride, whereas major groove binding mode was deduced for rimeporide and cariporide. Molecular docking studies were also found to be in accordance with the experimental results, revealing the information about the binding energy of the guanidine ligand-ctDNA complex. The docked structures depicted binding energy of −6.4 kcal mol⁻¹ for amiloride and − 6.6 kcal mol⁻¹ for rimeporide and cariporide. Such physicochemical studies of DNA-ligand interactions may facilitate the understanding of the mechanisms of NHE inhibition.
    Keywords DNA ; Gibbs free energy ; calves ; circular dichroism spectroscopy ; energy ; fluorescence ; guanidines ; ligands ; titration
    Language English
    Dates of publication 2022-0731
    Size p. 834-844.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.06.009
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  3. Article ; Online: Recent Advances in Additive Manufacturing, Applications and Challenges for Dentistry: A Review.

    Chaudhary, Swati / Avinashi, Sarvesh Kumar / Rao, Jitendra / Gautam, Chandkiram

    ACS biomaterials science & engineering

    2023  Volume 9, Issue 7, Page(s) 3987–4019

    Abstract: Technological advancement in the field of dentistry has to be proven in new avenues for professionals as well as laboratory programmers. An advanced type of technology is emerging based on digitalization, as a computerized three-dimensional (3-D) model, ... ...

    Abstract Technological advancement in the field of dentistry has to be proven in new avenues for professionals as well as laboratory programmers. An advanced type of technology is emerging based on digitalization, as a computerized three-dimensional (3-D) model, additive manufacturing also called 3-D printing, allows formation of block pieces by adding material layer-by-layer. The additive manufacturing (AM) approach has offered extreme progress in the broad choice of distinct zones, permitting the production of fragments of all possible varieties of substances such as metal, polymer, ceramic, and composites. The significant goal of current the article is to recapitulate the recent scenarios including the imminent perspective of AM techniques and challenges in dentistry. Moreover, this article reviews the recent developments of 3-D printing advancements along with the advantages and disadvantages. Herein, various AM technologies comprising vat photopolymerization (VPP), material jetting, material extrusion, selective laser sintering (SLS), selective laser melting (SLM), and direct metal laser sintering (DMLS) technologies based powder bed fusion technologies/direct energy deposition/sheet lamination centered on binder jetting technologies were discussed in detail. This paper attempts to provide a balanced view by emphasizing the economic, scientific, and technical challenges and presenting an overview of methods to discuss the similarities based on the authors' continuing research and development.
    MeSH term(s) Printing, Three-Dimensional ; Ceramics ; Polymers ; Dentistry
    Chemical Substances Polymers
    Language English
    Publishing date 2023-06-11
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 2373-9878
    ISSN (online) 2373-9878
    DOI 10.1021/acsbiomaterials.2c01561
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  4. Article ; Online: Exploring the interaction of guanidine ligands Amiloride, Rimeporide and Cariporide with DNA for understanding their role as inhibitors of Na

    Chaudhary, Swati / Kumar, Pankaj / Kaushik, Mahima

    International journal of biological macromolecules

    2022  Volume 213, Page(s) 834–844

    Abstract: The inhibition of ... ...

    Abstract The inhibition of Na
    MeSH term(s) Amiloride/pharmacology ; Circular Dichroism ; DNA/chemistry ; Guanidine/pharmacology ; Guanidines/pharmacology ; Ligands ; Molecular Docking Simulation ; Sodium-Hydrogen Exchangers ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; Sulfones ; Thermodynamics
    Chemical Substances Guanidines ; Ligands ; Sodium-Hydrogen Exchangers ; Sulfones ; Amiloride (7DZO8EB0Z3) ; cariporide (7E3392891K) ; DNA (9007-49-2) ; Guanidine (JU58VJ6Y3B)
    Language English
    Publishing date 2022-06-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.06.009
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  5. Article ; Online: Interface of G-quadruplex with both stabilizing and destabilizing ligands for targeting various diseases.

    Chaudhary, Swati / Kumar, Mohan / Kaushik, Mahima

    International journal of biological macromolecules

    2022  Volume 219, Page(s) 414–427

    Abstract: Guanine-rich DNA sequences may fold back into non-canonical four-stranded secondary structures termed as G-quadruplexes. The role of G-quadruplexes has already been well established in different diseases like cancer, neurological and viral disorders etc. ...

    Abstract Guanine-rich DNA sequences may fold back into non-canonical four-stranded secondary structures termed as G-quadruplexes. The role of G-quadruplexes has already been well established in different diseases like cancer, neurological and viral disorders etc. Also, several small molecules have been reported, which can influence the involvement of G-quadruplexes either through stabilization or destabilization in the cellular environment. Growing statistics have associated G-quadruplex assemblies to a discrete biological process in vivo, including DNA replication, transcription, genomic stability, and epigenetic regulation. DNA G-quadruplex existence in human telomere is well recognized attractive target for anticancer drugs. G-quadruplex-interactive ligands have been known to prevent telomerase access as well as telomere capping. To the best of our understanding, the role of G-quadruplexes in virology, neuropharmacology, cancer progression and its treatment has not been discussed on a single platform till date. This review aims to enhance our knowledge regarding these magical sticky quadruplex structures, which have been quite significantly proved to be the part of many cellular processes along with their established in vivo existence. Understanding regarding stabilizing or destabilizing ligands of these multistranded guanine quadruplex structures might be proved as the facilitator of drug discovery process for many incurable diseases in future.
    MeSH term(s) Antineoplastic Agents/pharmacology ; DNA/chemistry ; Epigenesis, Genetic ; G-Quadruplexes ; Guanine/chemistry ; Humans ; Ligands ; Telomerase/chemistry ; Telomere/genetics ; Telomere/metabolism
    Chemical Substances Antineoplastic Agents ; Ligands ; Guanine (5Z93L87A1R) ; DNA (9007-49-2) ; Telomerase (EC 2.7.7.49)
    Language English
    Publishing date 2022-08-05
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.07.248
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  6. Book ; Online: Photogalvanic response in multi-Weyl semimetals

    Raj, Arpit / Chaudhary, Swati / Fiete, Gregory A.

    2023  

    Abstract: We investigate the dependence of the photogalvanic response of a multi-Weyl semimetal on its topological charge, tilt, and chemical potential. We derive analytical expressions for the shift and injection conductivities for tilted charge-$n$ Weyl points $( ...

    Abstract We investigate the dependence of the photogalvanic response of a multi-Weyl semimetal on its topological charge, tilt, and chemical potential. We derive analytical expressions for the shift and injection conductivities for tilted charge-$n$ Weyl points $(n=1,2,3)$ using a low energy two-band effective Hamiltonian. For double-Weyl semimetals, we also compute the response from two-band and four-band tight-binding models with broken time-reversal symmetry to study the effect of band bending and the contributions from higher bands. We find a significant deviation in the responses obtained from the effective low-energy continuum model and more realistic four-band continuum and tight-binding models. We analyze several different limits of these models. We describe the nature of the deviations and provide estimates of their dependence on the frequency and other model parameters. Our analysis provides a simple explanation for the first-principle calculation based frequency dependence of the injection current in SrSi$_2$. Additionally, we find interesting parameter regimes where the frequency dependence of the non-linear optical response can be directly used to probe the type-I/type-II nature of the Weyl cone. We obtain analytical results for the charge-4 Weyl semimetal by reducing the original problem involving a triple $k$-space integral to one with only a double integral. This simplification allows us to extract all relevant information about the nature of its second-order dc response and the precise condition for observing circular photogalvanic effect quantization. The semi-analytical approach presented here can also be extended to a systematic study of second harmonic generation and first-order optical conductivity in charge-4 Weyl semimetals.

    Comment: 16 pages, 7 figures, references added, typos corrected
    Keywords Condensed Matter - Mesoscale and Nanoscale Physics
    Subject code 621 ; 539
    Publishing date 2023-03-22
    Publishing country us
    Document type Book ; Online
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  7. Article ; Online: Strategic targeting of non-small-cell lung cancer utilizing genetic material-based delivery platforms of nanotechnology.

    Chaudhary, Swati / Singh, Amit / Kumar, Pankaj / Kaushik, Mahima

    Journal of biochemical and molecular toxicology

    2021  Volume 35, Issue 7, Page(s) e22784

    Abstract: Several limitations of conventional cancer treatment such as non-specific targeting, solubility problems, and ineffective entry of chemotherapeutics into cancer cells can be overcome by using nanotechnology targeted drug delivery systems. Some ... ...

    Abstract Several limitations of conventional cancer treatment such as non-specific targeting, solubility problems, and ineffective entry of chemotherapeutics into cancer cells can be overcome by using nanotechnology targeted drug delivery systems. Some combinations of biomolecules and nanoparticles have proven to be excellent therapeutics for Non-small cell lung cancer (NSCLC) in the last decades. Targeted gene delivery has shown in vivo as well as in vitro promising results with therapeutic efficacy. Gene therapy has shown enhanced transfection efficiency and better targeting potential on several NSCLC cell lines. Still, there are several challenges in nanoparticle-mediated gene therapy, which include stability of biomolecules and nanoparticles during delivery, managing their biodistribution, and reducing the possible cytotoxic effects of the nanoparticles, which need to be solved before clinical trials. Evaluation of therapeutic efficacy of biomolecules and nanoparticle combination in gene therapy must be established to expand the application of nano-gene therapy in cancer treatment.
    MeSH term(s) Animals ; Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/metabolism ; Carcinoma, Non-Small-Cell Lung/therapy ; Cell Line, Tumor ; Gene Transfer Techniques ; Genetic Therapy ; Humans ; Lung Neoplasms/genetics ; Lung Neoplasms/metabolism ; Lung Neoplasms/therapy ; Nanoparticles/therapeutic use ; Nanotechnology
    Language English
    Publishing date 2021-04-07
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1410020-4
    ISSN 1099-0461 ; 1095-6670
    ISSN (online) 1099-0461
    ISSN 1095-6670
    DOI 10.1002/jbt.22784
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  8. Article ; Online: Spin-orbit exciton-induced phonon chirality in a quantum magnet.

    Lujan, David / Choe, Jeongheon / Chaudhary, Swati / Ye, Gaihua / Nnokwe, Cynthia / Rodriguez-Vega, Martin / He, Jiaming / Gao, Frank Y / Nunley, T Nathan / Baldini, Edoardo / Zhou, Jianshi / Fiete, Gregory A / He, Rui / Li, Xiaoqin

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 11, Page(s) e2304360121

    Abstract: The interplay of charge, spin, lattice, and orbital degrees of freedom in correlated materials often leads to rich and exotic properties. Recent studies have brought new perspectives to bosonic collective excitations in correlated materials. For example, ...

    Abstract The interplay of charge, spin, lattice, and orbital degrees of freedom in correlated materials often leads to rich and exotic properties. Recent studies have brought new perspectives to bosonic collective excitations in correlated materials. For example, inelastic neutron scattering experiments revealed non-trivial band topology for magnons and spin-orbit excitons (SOEs) in a quantum magnet CoTiO
    Language English
    Publishing date 2024-03-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2304360121
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    Zs.A 1148: Show issues Location:
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  9. Article ; Online: Formation of G-wires, bimolecular and tetramolecular quadruplex: Cation-induced structural polymorphs of G-rich DNA sequence of human SYTX gene.

    Ahmed, Saami / Kaushik, Mahima / Chaudhary, Swati / Kukreti, Shrikant

    Biopolymers

    2018  Volume 109, Issue 5, Page(s) e23115

    Abstract: An exceptional property of auto-folding into a range of intra- as well as intermolecular quadruplexes by guanine-rich oligomers (GROs) of promoters, telomeres and various other genomic locations is still one of the most attractive areas of research at ... ...

    Abstract An exceptional property of auto-folding into a range of intra- as well as intermolecular quadruplexes by guanine-rich oligomers (GROs) of promoters, telomeres and various other genomic locations is still one of the most attractive areas of research at present times. The main reason for this attention is due to their established in vivo existence and biological relevance. Herein, the structural status of a 20-nt long G-rich sequence with two G5 stretches (SG20) is investigated using various biophysical and biochemical techniques. Bioinformatics analysis suggested the presence of a 17-nt stretch of this SG20 sequence in the intronic region of human SYTX (Synaptotagmin 10) gene. The SYTX gene helps in sensing out the Ca
    MeSH term(s) Base Sequence ; Calcium/chemistry ; Cations, Divalent ; Cations, Monovalent ; Computational Biology ; G-Quadruplexes ; Gene Expression ; Guanine/chemistry ; Humans ; Oligonucleotides/chemistry ; Potassium/chemistry ; Sodium/chemistry ; Synaptotagmins/chemistry ; Synaptotagmins/genetics
    Chemical Substances Cations, Divalent ; Cations, Monovalent ; Oligonucleotides ; SYT10 protein, human ; Synaptotagmins (134193-27-4) ; Guanine (5Z93L87A1R) ; Sodium (9NEZ333N27) ; Potassium (RWP5GA015D) ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2018-04-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1123-x
    ISSN 1097-0282 ; 0006-3525
    ISSN (online) 1097-0282
    ISSN 0006-3525
    DOI 10.1002/bip.23115
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  10. Article ; Online: Structural polymorphism of a cytosine-rich DNA sequence forming i-motif structure: Exploring pH based biosensors.

    Ahmed, Saami / Kaushik, Mahima / Chaudhary, Swati / Kukreti, Shrikant

    International journal of biological macromolecules

    2018  Volume 111, Page(s) 455–461

    Abstract: Sequence recognition and conformational polymorphism enable DNA to emerge out as a substantial tool in fabricating the devices within nano-dimensions. These DNA associated nano devices work on the principle of conformational switches, which can be ... ...

    Abstract Sequence recognition and conformational polymorphism enable DNA to emerge out as a substantial tool in fabricating the devices within nano-dimensions. These DNA associated nano devices work on the principle of conformational switches, which can be facilitated by many factors like sequence of DNA/RNA strand, change in pH or temperature, enzyme or ligand interactions etc. Thus, controlling these DNA conformational changes to acquire the desired function is significant for evolving DNA hybridization biosensor, used in genetic screening and molecular diagnosis. For exploring this conformational switching ability of cytosine-rich DNA oligonucleotides as a function of pH for their potential usage as biosensors, this study has been designed. A C-rich stretch of DNA sequence (5'-TCCCCCAATTAATTCCCCCA-3'; SG20c) has been investigated using UV-Thermal denaturation, poly-acrylamide gel electrophoresis and CD spectroscopy. The SG20c sequence is shown to adopt various topologies of i-motif structure at low pH. This pH dependent transition of SG20c from unstructured single strand to unimolecular and bimolecular i-motif structures can further be exploited for its utilization as switching on/off pH-based biosensors.
    MeSH term(s) Biosensing Techniques ; Circular Dichroism ; Cytosine/chemistry ; Genetic Testing ; Humans ; Hydrogen-Ion Concentration ; Nucleic Acid Conformation ; Nucleotide Motifs ; Polymorphism, Single-Stranded Conformational/genetics ; RNA/chemistry ; RNA/genetics
    Chemical Substances RNA (63231-63-0) ; Cytosine (8J337D1HZY)
    Language English
    Publishing date 2018-01-10
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2018.01.053
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