@article { ISI:000288386600095, title = {Probing the furanose conformation in the 2 {\textquoteleft}-5 {\textquoteleft} strand of isoDNA:RNA duplexes by freezing the nucleoside conformations}, journal = {Chemical Communications}, volume = {47}, number = {13}, year = {2011}, month = {FEB}, pages = {4007-4009}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Sugar conformations in the isoDNA strand of isoDNA : RNA duplexes are preferred S-type locked/frozen in contrast to N-type locked conformations preferred in DNA: RNA duplexes.

}, issn = {1359-7345}, doi = {10.1039/c0cc05402j}, author = {Erande, Namrata D. and Gunjal, Anita D. and Fernandes, Moneesha and Kumar, Vaijayanti A.} } @article { ISI:000310005700032, title = {Comparing the interactions of DNA, polyamide (PNA) and polycarbamate nucleic acid (PCNA) oligomers with graphene oxide (GO)}, journal = {Physical Chemistry Chemical Physics}, volume = {14}, number = {43}, year = {2012}, month = {SEP}, pages = {15003-15006}, publisher = {ROYAL SOC CHEMISTRY}, type = {Article}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The fluorescently labelled short octameric oligothymine sequences of DNA, PNA and PCNA were used in fluorescence quenching studies in conjunction with dispersed graphene oxide. The measurable restoration of their fluorescence by complementary oligodeoxyadenylate was compared. This is the first study aimed at replacing the natural DNA probes with synthetic DNA mimics that show excellent properties in terms of formation of very strong duplexes with cDNA in addition to their stability towards proteases and nucleases.

}, issn = {1463-9076}, doi = {10.1039/c2cp42770b}, author = {Kotikam, Venubabu and Fernandes, Moneesha and Kumar, Vaijayanti Anil} } @article { ISI:000303362900001, title = {Highly efficient (R-X-R)-type carbamates as molecular transporters for cellular delivery}, journal = {Journal of the American Chemical Society}, volume = {134}, number = {17}, year = {2012}, month = {MAY}, pages = {7196-7199}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

The (R-X-R) motif-containing arginine-rich peptides are among the most effective cell-penetrating peptides. The replacement of amide linkages in the (R-X-R) motif by carbamate linkages as in (r-ahx-r)(4) or (r-ahx-r-r-apr-r)(2) increases the efficacy of such oligomers several-fold. Internalization of these oligomers in mammalian cell lines occurs by an energy-independent process. These oligomers show efficient delivery of biologically active plasmid DNA into CHO-K1 cells.

}, issn = {0002-7863}, doi = {10.1021/ja210026m}, author = {Patil, Kiran M. and Naik, Rangeetha J. and Rajpal and Fernandes, Moneesha and Ganguli, Munia and Kumar, Vaijayanti A.} } @article { ISI:000312946200007, title = {Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2 {\textquoteleft}-5 {\textquoteleft} linked oligonucleotides}, journal = {Organic \& Biomolecular Chemistry}, volume = {11}, number = {5}, year = {2013}, month = {NOV}, pages = {746-757}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

2{\textquoteright}-endo locked or frozen (S-type)/3{\textquoteright}-endo locked or frozen (N-type) nucleoside analogues were synthesized. Conformational analysis based on (3)J(HH) and NOE measurements is presented which is further confirmed by X-ray crystal structural studies. 2{\textquoteright}-5{\textquoteright} isoDNA oligonucleotides (ON) were synthesized using these modified nucleoside analogues and UV-T-m studies of the resultant 2{\textquoteright}-5{\textquoteright} isoDNA : RNA duplexes reflect the site-and sequence-dependent effects and confirm that the S-type sugar conformations were preferred over the N-type sugar geometry in such duplexes.

}, issn = {1477-0520}, doi = {10.1039/c2ob26762d}, author = {Erande, Namrata D. and Gunjal, Anita D. and Fernandes, Moneesha and Gonnade, Rajesh G. and Kumar, Vaijayanti A.} } @article { ISI:000328650000032, title = {Functional isoDNA aptamers: modified thrombin binding aptamers with a 2{\textquoteright}-5{\textquoteright}-linked sugarphosphate backbone (isoTBA)}, journal = {Chemical Communications}, volume = {50}, number = {5}, year = {2014}, month = {NOV}, pages = {605-607}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The regioisomeric 3{\textquoteright}-deoxy-2{\textquoteright}-5{\textquoteright}-linked thrombin binding DNA aptamers (isoTBAs) were chemically synthesized and their ability to form unimolecular anti-parallel G-quadruplexes in the presence of K+ ions was evaluated. These modified sequences retain the function of the native thrombin binding aptamer (TBA), exhibit better stability against exonuclease and are capable of slowing down the process of blood clotting.

}, issn = {1359-7345}, doi = {10.1039/c3cc47569g}, author = {Gunjal, Anita D. and Fernandes, Moneesha and Erande, Namrata D. and Rajamohanan, P. R. and Kumar, Vaijayanti A.} } @article { ISI:000341339300024, title = {Second generation, arginine-rich (R-X {\textquoteleft}-R)(4)-type cell-penetrating alpha-omega-alpha-peptides with constrained, chiral omega-amino acids (X {\textquoteleft}) for enhanced cargo delivery into cells}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {24}, number = {17}, year = {2014}, month = {SEP}, pages = {4198-4202}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

The syntheses of novel N-aminoalkyl proline-derived spacers (X{\textquoteright}) in polycationic (R-X{\textquoteright}-R)-motif cell-penetrating alpha-omega-alpha-peptides are described as improved molecular transporters and their structural features studied by CD. FACS analysis shows enhanced cellular uptake and confocal microscopy indicates predominantly cytoplasmic localization. The oligomers are efficient at transporting pDNA into cells. The chirality together with the hydrophobicity and flexibility derived from the spacer chain are found to have marked influence on the cell-penetrating and cargo delivery properties of the cell-penetrating peptides (CPPs). The peptides containing N-(3-aminopropyl)-D-proline spacers are found to be the best at cell penetration and cargo delivery in the present study. (C) 2014 Elsevier Ltd. All rights reserved.

}, keywords = {(R-X-R)-motif, alpha-omega-alpha-Peptide, Cell-penetrating peptide, Constrained chiral amino acid, Peptidomimetics}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2014.07.040}, author = {Patil, Kiran M. and Naik, Rangeetha J. and Vij, Manika and Yadav, Amit K. and Kumar, Vaijayanti A. and Ganguli, Munia and Fernandes, Moneesha} } @article { ISI:000361559700081, title = {N-(3-Aminoalkyl)proline derivatives with potent antigycation activity}, journal = {RSC Advances}, volume = {5}, number = {94}, year = {2015}, month = {SEP}, pages = {77332-77340}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The importance of amino acids in the therapy of conditions such as renal failure, neurological disorders and congenital defects has been documented. Some amino acids such as lysine and glycine have also been reported to have antiglycating activity. Herein we report the synthesis of a new series of N-(3-aminoalkyl)proline derivatives which are non-natural in nature. The compounds were unambiguously characterized by NMR, mass and IR spectroscopy. Their in vitro antiglycation activity was studied by circular dichroism and fluorescence spectrometry. The mechanism of action was also studied and found to take place by inhibition of Amadori product formation. The inhibition of AGE formation was further confirmed by western blot and LC-MS/MS analyses and the IC50 values of the potent compounds were determined. Compounds containing hydroxyl substituents at C4 were found to have superior antiglycation properties than those containing azide substituents at the same position. The compounds were additionally found to possess good anti-oxidant properties, which could lead to further reduction in AGE formation. Moreover, the title compounds were found to have low cytotoxicity in mammalian cells, another important attribute. Thus, the title compounds represent a novel promising class of antiglycating agents.

}, issn = {2046-2069}, doi = {10.1039/c5ra12148e}, author = {Chilukuri, Harsha and Kolekar, Yogesh M. and Bhosle, Govind S. and Godbole, Rashmi K. and Kazi, Rubina S. and Kulkarni, Mahesh J. and Fernandes, Moneesha} } @article { ISI:000359951700161, title = {RXR-carbamate - a novel molecular transporter for skin}, journal = {Molecular Therapy}, volume = {23}, number = {1}, year = {2015}, note = {18th Annual Meeting of the American-Society-of-Gene-and-Cell-Therapy (ASGCT), New Orleans, LA, MAY 13-16, 2015}, month = {MAY}, pages = {S64-S64}, publisher = {Amer Soc Gene \& Cell Therapy}, address = {75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}, issn = {1525-0016}, author = {Natarajan, Poornemaa and Patil, Kiran M. and Vij, Manika and Yadav, Amit K. and Kumar, Vaijayanti A. and Ganguli, Munia and Fernandes, Moneesha} } @article {42435, title = {Unimolecular antiparallel G-quadruplex folding topology of 2{\textquoteright}-5{\textquoteright}-isoTBA sequences remains unaltered by loop composition}, journal = {Organic \& Biomolecular Chemistry}, volume = {13}, year = {2015}, month = {OCT}, pages = {11696-11703}, type = {Journal Article}, abstract = {

A 2{\textquoteright}-5{\textquoteright}-linked isoTBA 15 mer sequence with (232) loop composition formed stable antiparallel quadruplex structures similar to the SELEX derived 15 mer TBA sequence with (232) loop composition. A parallel versus antiparallel topology of 3{\textquoteright}-5{\textquoteright}-G-quadruplexes is largely dictated by the loop length, and it is known that the truncated loops favour parallel quadruplexes. In contrast to TBA, systematic reduction of the loop length in isoTBA from (232) to (222), (131) or even (111) did not alter the antiparallel topology of the resulting 14 mer, 13 mer and 11 mer G-rich modified isoTBA-like sequences.

}, doi = {10.1039/c5ob01923k}, author = {Aher, Manisha N.}, editor = {Erande, Namrata D.} } @article {45819, title = {4 {\textquoteleft}-Epi-DNA: A DNA Mimic Containing 4 {\textquoteleft}-hydroxymethyl-alpha-l-Xylo-thymidine with compact backbone like RNA}, journal = {Nucleosides Nucleotides \& Nucleic Acids}, volume = {35}, year = {2016}, month = {APR}, pages = {445-458}, type = {Article}, abstract = {

Synthesis of C4-epi-DNA containing 3 5 linkages is reported for the first time. Crystal structure study of the monomer indicated that though the dihedral angle O3-C3-C4-C5 in this case would be like in RNA, the sugar conformation would remain like that in DNA. The study of the effect of this backbone configuration in DNA with respect to its binding to cDNA and RNA is reported in this note.

}, keywords = {4 {\textquoteleft}-hydroxymethyl nucleosides C4 {\textquoteleft}-epi-DNA, Antisense Oligonucleotide}, issn = {1525-7770}, doi = {10.1080/15257770.2016.1202963}, author = {Bagmare, Seema and Puranik, Vedavati G. and Fernandes, Moneesha and Kumar, Vaijayanti A.} } @article { ISI:000377424600004, title = {Efficient cellular entry of (r-x-r)-type carbamate-plasmid DNA complexes and its implication for noninvasive topical DNA delivery to skin}, journal = {Molecular Pharmaceutics}, volume = {13}, number = {6}, year = {2016}, month = {JUN}, pages = {1779-1790}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Arginine-rich cell penetrating peptides are powerful tools for in vitro as well as in vivo delivery of a wide plethora of biomolecules. However, presence of consecutive arginine residues leads to enhanced amenability for proteolytic degradation as well as steric hindrances for membrane interactions which compromise its bioavailability. In order to overcome these limitations we previously reported a safe and stable octaarginine based oligomer, i.e., (r-x-r)4-carbamate, where the backbone amide linkages were replaced by carbamate linkages and 6-aminohexanoic acid based spacer moieties were incorporated for better flexibility, hydrophobicity, optimal spacing of guanidinium groups, and protection against proteolytic cleavage; resulting in improved transfection efficiency over its amide counterpart. In the present work we have investigated the mechanism behind this enhanced transfection efficiency and, based on our observations, demonstrate how the synergistic effect of rationalized oligomer designing, complex characteristics, and cell type contributes to overall effective intracellular delivery. Our results indicate that the (r-x-r)4-carbamate plasmid DNA complexes primarily utilize lipid raft dependent pathway of cellular entry more than other pathways, and this possibly facilitates their increased entry in the lipid raft rich milieu of skin cells. We also emphasize the utility of oligomer (r-x-r)4-carbamate as an efficient carrier for topical delivery of nucleic acids in skin tissue. This carrier can be utilized for safe, efficient, and noninvasive delivery of therapeutically relevant macromolecular hydrophilic cargo like nucleic acids to skin.

}, keywords = {Cell penetrating peptides, endocytosis, nucleic acid delivery, skin penetration, transfection}, issn = {1543-8384}, doi = {10.1021/acs.molpharmaceut.5b00915}, author = {Vij, Manika and Natarajan, Poornemaa and Yadav, Amit K. and Patil, Kiran M. and Pandey, Tanuja and Gupta, Nidhi and Santhiya, Deenan and Kumar, Vaijayanti A. and Fernandes, Moneesha and Ganguli, Munia} } @article {44088, title = {Dendrimeric amide- and carbamate-linked lysine-based efficient molecular transporters}, journal = {Organic \& Biomolecular Chemistry}, volume = {15}, year = {2017}, month = {DEC}, pages = {9579-9584}, type = {Article}, abstract = {

Amide- and carbamate-linked dendrimeric oligomers are reported as molecular transporters. They effectively complex with pDNA and transport it into cells at an efficiency superior to Lipofectamine, when complexation is carried out by incubation overnight. The carbamate-linked K2C is superior to amide-linked K2A; their pDNA complexes have very low associated cytotoxicity.

}, doi = {10.1039/c7ob02552a}, author = {Yadav, Amit Kumar and Dey, Namit and Chattopadhyay, Sabyasachi and Ganguli, Munia and Fernandes, Moneesha} } @article {45708, title = {(R-X-R)(4)-Motif peptides containing conformationally constrained cyclohexane-derived spacers: effect on cellular uptake}, journal = {ChemMedChem}, volume = {12}, year = {2017}, month = {NOV }, pages = {1743-1747}, type = {Article}, abstract = {

Arginine-rich peptides having the (R-X-R) n motif are among the most effective cell-penetrating peptides (CPPs). Herein we report a several-fold increase in the efficacy of such CPPs if the linear flexible spacer (-X-) in the (R-X-R) motif is replaced by constrained cyclic 1,4-substituted-cyclohexane-derived spacers. Internalization of these oligomers in mammalian cell lines was found to be an energy-dependent process. Incorporation of these constrained, non-proteinogenic amino acid spacers in the CPPs is shown to enhance their proteolytic stability.

}, keywords = {(R-X-R)-motif, cell-penetrating peptides, cellular uptake, protease stability}, issn = {1860-7179}, doi = {10.1002/cmdc.201700498}, author = {Bhosle, Govind S. and Fernandes, Moneesha} } @article {44424, title = {Antibacterial and anti-TB tat-peptidomimetics with improved efficacy and half-life}, journal = {European Journal of Medicinal Chemistry}, volume = {152}, year = {2018}, month = {MAY}, pages = {358-369}, abstract = {Non-natural antimicrobial peptides are ideal as next-generation antibiotics because of their ability to circumvent the problems of drug resistance and in vivo instability. We report novel all-alpha- and alpha,gamma-mixed Tat peptide analogues as potential antibacterial and anti-TB agents. These peptides have broad spectrum antibacterial activities against Gram-positive (MICs 0.61 +/- 0.03 to 1.35 +/- 0.21 mu M with the peptide gamma TatM4) and Gram-negative (MICs 0.71 +/- 0.005 to 1.26 +/- 0.02 M with gamma TatM4) bacteria and are also effective against active and dormant forms of Mycobacterium tuberculosis, including strains that are resistant to rifampicin and isoniazid. The introduction of the non-natural amino acids of the study in the Tat peptide analogues results in increased resistance to degradation by proteolysis, significantly increasing their half-life. The peptides appear to inhibit bacteria by a membrane disruption mechanism, and have only a low cytotoxic effect on mammalian cells. (C) 2018 Elsevier Masson SAS. All rights reserved.}, doi = {10.1016/j.ejmech.2018.04.039}, author = {Bhosle, Govind S. and Nawale, Laxman and Yeware, Amar M. and Sarkar, Dhiman and Fernandes, Moneesha} } @article {44357, title = {Favorable 2 {\textquoteright}-substitution in the loop region of a thrombin-binding DNA aptamer}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {28}, year = {2018}, month = {JUN}, pages = {1765-1768}, type = {Article}, abstract = {Simple 2{\textquoteright}-OMe-chemical modification in the loop region of the 15mer G-rich DNA sequence GGTTGGTGTGGTTGG is reported. The G-quadruplex structure of this thrombin-binding aptamer (TBA), is stabilized by single modifications (T -> 2{\textquoteright}-OMe-U), depending on the position of the modification. The structural stability also renders significantly increased inhibition of thrombin-induced fibrin polymerization, a process closely associated with blood-clotting. (C) 2018 Elsevier Ltd. All rights reserved.}, doi = {10.1016/j.bmcl.2018.04.027}, author = {Awachat, Ragini and Wagh, Atish A. and Aher, Manisha and Fernandes, Moneesha and Kumar, Vaijayanti A.} } @article {44188, title = {Superior HIV-1 TAR binders with conformationally constrained R52 arginine mimics in the Tat(48-57) peptide}, journal = {Chemmedchem}, volume = {13}, year = {2018}, month = {FEB }, pages = {220-226}, type = {Article}, abstract = {

We report a 100-fold increase in binding affinity of the Tat(48-57) peptide to HIV-1 transcriptional activator-responsive element (TAR) RNA by replacing Arg52, an essential and critical residue for Tat{\textquoteright}s specific binding, with (2S,4S)-4-guanidinoproline. The resulting Tat1M peptide is a far superior binder than Tat1M, a peptide containing another conformationally constrained arginine mimic, (2S,4S)-4-amino-N-(3-guanidinopropyl)proline, or even the control Tat peptide (CtrlTat) itself. Our observations are supported by circular dichroism (CD), isothermal titration calorimetry (ITC), gel electrophoresis and UV spectroscopy studies. Molecular dynamics simulations suggest increased interactions between the more compact Tat1M and TAR RNA, relative to CtrlTat. The CD signature of the RNA itself remains largely unchanged upon binding of the peptides. The Tat mimetics further have better cell uptake properties than the control Tat peptide, thus increasing their potential application as specific TAR-binding molecules.

}, keywords = {antiviral agents, arginine mimics, RNA, Tat peptide analogues, Tat-TAR binding}, issn = {1860-7179}, doi = {10.1002/cmdc.201700653}, author = {Bhosle, Govind S. and Kharche, Shalmali and Kumar, Santosh and Sengupta, Durba and Maiti, Souvik and Fernandes, Moneesha} } @article {46346, title = {2 {\textquoteleft}-5 {\textquoteleft}-Isomerically linked thrombin-binding aptamer (isoTBA) forms a stable unimolecular parallel G-quadruplex in the presence of Sr2+ Ions}, journal = {ChemistrySelect}, volume = {4}, year = {2019}, month = {SEP }, pages = {10668-10673}, type = {Article}, abstract = {

The ability of the isomeri 2 {\textquoteleft}-5 {\textquoteleft}-phosphodiester-linked thrombin-binding DNA aptamer pentadecamer G(2)T(2)G(2)TGTG(2)T(2)G(2) (isoTBA), to fold into G-quadruplex structures in the presence of different mono- and divalent cations is reported. Strikingly, Sr2+ ions cause isoTBA to fold into a stable parallel unimolecular G-quadruplex, in contrast to the antiparallel unimolecular G-quadruplex fold observed in the presence of K+. IsoTBA being advantageously more stable than TBA to nuclease degradation, may thus be useful in the selective detection of Sr2+ ions, which it can sense with a detection limit of similar to 55 mu M.

}, keywords = {2 {\textquoteleft}-5 {\textquoteleft}-phosphodiester, parallel DNA G-quadruplex, strontium binding, thrombin-binding aptamer, unimolecular G-quadruplex}, issn = {2365-6549}, doi = {10.1002/slct.201902005}, author = {Wagh, Atish A. and Fernandes, Moneesha} } @article {46049, title = {Phyto-inspired cyclic peptides derived from plant Pin-II type protease inhibitor reactive center loops for crop protection from insect pests}, journal = {Biochimica ET Biophysica Acta-General Subjects}, volume = {1863}, year = {2019}, month = {AUG}, pages = {1254-1262}, type = {Article}, abstract = {

Background: Natural defence of plants against insect pests involves protease inhibitors (PIs) that interfere with insect digestive proteases. Pin-II type plant PIs are wound inducible upon insect damage and possess multiple inhibitory repeat domains that can inhibit trypsin and chymotrypsin-like proteases in the insect midgut. Yet, their agricultural ex-vivo application is limited due to large molecular size and environmental instability, which could be overcome by small peptides. Methods: Bicyclic peptides were designed by grafting Pin-II PIs derived reactive center loop (RCL) on synthetic tris(bromomethyl)benzene scaffold. In vitro binding with trypsin-like proteases was evaluated by biochemical and biophysical assays, followed by molecular dynamics simulations. In vivo effects on two major lepidopteran insect pests, Helicoverpa armigera and Spodoptera litura were studied upon feeding with peptide treated leaves. Affinity based pull down assays were used to identify target proteins in insect gut. Results: Bicyclic RCLs showed ten-fold enhanced protease inhibition compared to their linear counterparts. They exhibited feeding deterrence and growth reduction of lepidopteran insects. Bicyclic peptides predominantly interact with midgut serine proteases. Possible binding modes involve simultaneous interaction with the active site and specificity-determining residues of insect gut trypsin. Conclusion: Bicyclic peptides are potent inhibitors of serine proteases in the insect midgut. They cause feeding aversion and larval growth retardation. Bi-domain cyclic peptides interact with two sites on trypsin, leading to enhanced efficacy over linear RCL peptides. General significance: Bicyclic peptides mimic natural PIs by inhibiting insect proteases leading to growth reduction, thus, could be used as pest control molecules in agriculture.

}, keywords = {Cyclic peptide, Lepidoptera, Pest control, protease inhibitor, Reactive loop}, issn = {0304-4165}, doi = {10.1016/j.bbagen.2019.05.003}, author = {Sailthedkar, Nidhi S. and Joshi, Rakesh S. and Yadav, Amit K. and Seal, Shubhendu and Fernandes, Moneesha and Giri, Ashok P.} } @article {46200, title = {p-Nitrophenylcarbonates: a new class of compounds for chemodosimetric colorimetric fluoride anion sensing detectable by the naked eye}, journal = {ChemistrySelect}, volume = {4}, year = {2019}, month = {FEB}, pages = {1830-1833}, type = {Article}, abstract = {

A new class of compounds containing the p-nitrophenylcarbonate motif is reported, that can selectively sense fluoride anions over other halide anions with a detection limit ranging from 0.29 to 0.48 mu M. The fluoride ion acts as nucleophile, leading to the liberation of p-nitrophenol, that is easily detectable and quantifiable colorimetrically.

}, keywords = {colorimetric sensing, p-nitrophenyl carbonate, selective fluoride detection}, issn = {2365-6549}, doi = {10.1002/slct.201803103}, author = {Yadav, Amit Kumar and Chilukuri, Harsha and Kumari, Linthoinganbi Raj and Karthikeyan, Muthukumarasamy and Fernandes, Moneesha} } @article {46909, title = {Influence of fluorine substitution on the molecular conformation of 3 {\textquoteleft}-deoxy-3 {\textquoteleft}-fluoro-5-methyluriaine}, journal = {Acta Crystallographica Section C-Structural Chemistry}, volume = {76}, year = {2020}, month = {APR}, pages = {346+}, type = {Article}, abstract = {

{Fluorine substitutions on the furanose ring of nucleosides are known to strongly influence the conformational properties of oligonucleotides. In order to assess the effect of fluorine on the conformation of 3{\textquoteright}-deoxy-3{\textquoteright}-fluoro-5-methyluridine (T-R(F)), C-10 H13FN2O5, we studied its stereochemistry in the crystalline state using X-ray crystallography. The compound crystallizes in the chiral orthorhombic space group P2(1)2(1)2(1) and contains two symmetry-independent molecules (A and B) in the asymmetric unit. The furanose ring in molecules A and B adopts conformations between envelope (E-2, 2{\textquoteright}-endo

}, keywords = {crystal structure, fluoro nucleoside, pseudorotation parameter, sugar puckering, uridine}, issn = {2053-2296}, doi = {10.1107/S2053229620003083}, author = {Aher, Manisha N. and Erande, Namrata D. and Kumar, Vaijayanti A. and Fernandes, Moneesha and Gonnade, Rajesh G.} } @article {46999, title = {Methoxymethyl threofuranosyl thymidine (4 {\textquoteleft}-MOM-TNA-T) at the T7 position of the thrombin-binding aptamer boosts anticoagulation activity, thermal stability, and nuclease resistance}, journal = {ACS Omega}, volume = {5}, year = {2020}, month = {JAN }, pages = {498-506}, type = {Article}, abstract = {

The synthesis of 4{\textquoteright}-methoxymethyl threofuranosyl (4{\textquoteright}-MOM-TNA) thymidine and derived oligomers of the G-rich thrombin-binding aptameric (TBA) sequence is reported. The G-quadruplex stability, anticoagulation activity, and the enzymatic stability of these oligomers bearing the 2{\textquoteright}-3{\textquoteright}-phosphodiester backbone as single substitutions in the loop regions are studied. Amongst all the oligomers, TBA-7T bearing the 4{\textquoteright}-MOM-TNA unit at the T7 position formed a quadruplex with the highest thermal stability. It also resulted in enhanced anticlotting activity that allowed a one-third reduction in the dose, relative to TBA. Further, TBA-7T exhibited enhanced nuclease resistance properties to both endo- and exonucleases.

}, issn = {2470-1343}, doi = {10.1021/acsomega.9b03042}, author = {Varada, Manojkumar and Aher, Manisha and Erande, Namrata and Kumar, Vaijayanti A. and Fernandes, Moneesha} } @article {47088, title = {PNA-mediated efflux inhibition as a therapeutic strategy towards overcoming drug resistance in Mycobacterium smegmatis}, journal = {Microbial Pathogenesis}, volume = {151}, year = {2021}, month = {FEB}, pages = {104737}, type = {Article}, abstract = {

The emergence of antibiotic-resistant strains of Mycobacterium tuberculosis and the decelerating development of new and effective antibiotics has impaired the treatment of tuberculosis (TB). Efflux pump inhibitors (EPIs) have the potential to improve the efficacy of existing anti-TB drugs although with toxicity limitations. Peptide nucleic acids (PNAs), oligonucleotide mimics, by virtue of their high nucleic acid binding specificity have the capability to overcome this drawback. We, therefore, investigated the efflux pump inhibitory properties of a PNA designed against an efflux pump of Mycobacterium smegmatis. LfrA, an efflux pump found in M. smegmatis, is majorly involved in conferring innate drug resistance to this strain and, therefore, was selected as a target for gene silencing via PNA. qRT-PCR and EtBr assays confirmed the EPI activity of the anti-lfrA PNA. On testing the effect of the anti-lfrA PNA on the bactericidal activity of a fluoroquinolone, norfloxacin, we observed that 5 mu M of anti-lfrA PNA in combination with norfloxacin led to an enhanced killing of up to 2.5 log-fold against wild-type and a lab-generated multidrug resistant strain, exemplifying its potential in countering resistance. Improved efficacy was also observed against intra-macrophage mycobacteria, where the drug-PNA combination enhanced bacterial clearance by 1.3 log-fold. Further, no toxicity was observed with PNA concentrations up to 4 times higher than the efficacious anti-lfrA PNA concentration. Thus, PNA, as an adjuvant, presents a novel and viable approach to rejuvenate anti-TB therapeutics.

}, keywords = {Adjuvant, Antibiotic resistance, Antisense, Efflux pump, Gene silencing, Mycobacteria, Peptide nucleic acid (PNA)}, issn = {0882-4010}, doi = {10.1016/j.micpath.2021.104737}, author = {Ghosh, Saptarshi and Cotta, Karishma Berta and Hande, Aniket A. and Fernandes, Moneesha and Mehra, Sarika} } @article {47612, title = {Replacement of loop residues in TBA by an abasic ethylene glycol spacer: effect on stability, structure and function**}, journal = {ChemistrySelect}, volume = {6}, year = {2021}, month = {OCT }, pages = {10648-10650}, type = {Article}, abstract = {This article describes the synthesis of ethyleneglycol (E) phosphoramidite and its incorporation into the thrombin binding aptamer (TBA) sequence at loop positions. Circular dichroism (CD) study revealed no major disturbances in the secondary structure of TBA by the abasic E unit and the derived oligomers exhibited a typical antiparallel chair-like conformation similar to that of TBA. UV and CD spectroscopy, together with anti-coagulation and HPLC studies revealed that although nuclease stability was enhanced, and anti-coagulation reasonably good, the thermal stability of the quadruplexes was adversely affected.}, keywords = {aptamers, clotting time, ethylene glycol spacer, G-quadruplexes, nuclease stability}, issn = {2365-6549}, doi = {10.1002/slct.202102269}, author = {Wagh, Atish A. and Ghalawat, Monika and Fernandes, Moneesha} } @article {48269, title = {Unlike RNA-TBA (rTBA), iso-rTBA, the 2 {\textquoteleft}-5 {\textquoteleft}-linked RNA-thrombin-binding aptamer, is a functional equivalent of TBA}, journal = {Chemical Communications}, volume = {59}, year = {2023}, month = {FEB}, pages = {1461-1464}, type = {Article}, abstract = {

An antiparallel, functional RNA G-quadruplex of the 2 {\textquoteleft}-5 {\textquoteleft}-linked thrombin-binding aptamer (iso-rTBA) is reported for the first time. It can inhibit clotting and is remarkably stable to nuclease-degradation, besides having high thermal stability. It is thus, a superior candidate to TBA, rTBA or isoTBA, for further development as an anticoagulant.

}, issn = {1359-7345}, doi = {10.1039/d2cc05718b}, author = {Wagh, Atish A. A. and Kumar, Vaijayanti A. A. and Ravindranathan, Sapna and Fernandes, Moneesha} }