@article { ISI:000229223600004, title = {Conformationally constrained PNA analogues: structural evolution toward DNA/RNA binding selectivity}, journal = {Accounts of Chemical Research}, volume = {38}, number = {5}, year = {2005}, month = {MAY}, pages = {404-412}, publisher = {AMER CHEMICAL SOC}, type = {Article}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Since its discovery 12 years ago, aminoethylglycyl peptide nucleic acid (aeg-PNA) has emerged as one of the successful DNA mimics for potential therapeutic and diagnostic applications. An important requisite for in vivo applications that has received inadequate attention is engineering PNA analogues for able discrimination between DNA and RNA as binding targets. Our approach toward this aim is based on structural preorganization of the backbone to hybridization-competent conformations to impart binding selectivity. This strategy has allowed us to design locked PNAs to achieve specific hybridization with DNA or RNA with aims to increase the binding strength without losing the binding specificity. This Account presents results of our rationale in design of different conformationally constrained PNA analogues, their synthesis, and evaluation of hybridization specificities.

}, issn = {0001-4842}, doi = {10.1021/ar030277e}, author = {Kumar, VA and Ganesh, Krishna N.} } @article { ISI:000226473300004, title = {DNA and PNA as templates for building nanoassemblies via electrostatic complexation with gold nanoparticles}, journal = {Current Applied Physics}, volume = {5}, number = {2}, year = {2005}, note = {Indo-Japan Workshop on Advanced Molecular Electronics and Bionics, Kyushu Inst Technol, Grad Sch Life Sci \& Syst Engn, Kitakyushu, JAPAN, DEC 11-13, 2003}, month = {FEB}, pages = {102-107}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Organisation of nanoparticles on structurally well-defined templates is a first step towards creating nanomachines. In this respect, nucleic acids are ideal structural templates and a variety of secondary structures realizable from DNA/RNA - e.g., duplexes, hairpins, triplexes, cruciforms, tetraplexes can be exploited to engineer nanoparticle organization at will. We have used oligonucleotides and their analogues such as phosphorothioates and peptide nucleic acids to electrostatically encapsulate cationic-capped gold nanoparticles. This article describes synthesis and characterization of DNA/PNA-gold nanoparticle composites using TEM and UV-T-m techniques. These types of assemblies may have potential for creating nanowires and lithographic circuits. (C) 2004 Elsevier B.V. All rights reserved.

}, keywords = {DNA, DNA-gold nanoparticle interactions, nanoassemblies, PNA}, issn = {1567-1739}, doi = {10.1016/j.cap.2004.06.020}, author = {Gourishankar, A and Shukla, S and Pasricha, R and Sastry, M and Ganesh, Krishna N.} } @article { ISI:000231365900024, title = {PNA C-C+ i-motif: superior stability of PNA TC8 tetraplexes compared to DNA TC8 tetraplexes at low pH}, journal = {Chemical Communications}, number = {34}, year = {2005}, month = {JUL}, pages = {4330-4332}, publisher = {ROYAL SOC CHEMISTRY}, type = {Article}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Study of self-assembly of PNA TC8 monitored by UV thermal transition at 295 nm indicates formation of a C-C+ tetraplex (i-motif) in acidic pH, with higher stability than the analogous dTC(8).

}, issn = {1359-7345}, doi = {10.1039/b506870c}, author = {Sharma, NK and Ganesh, Krishna N.} } @article { ISI:000232886800001, title = {Proceedings of the National Conference on Nanoscience and Technology Part I - National Chemical Laboratory - Pune - 7-8 March 2005 - Foreword}, journal = {Pramana-Journal of Physics}, volume = {65}, number = {4, SI}, year = {2005}, month = {OCT}, pages = {547-548}, publisher = {INDIAN ACAD SCIENCES}, type = {Editorial Material}, address = {C V RAMAN AVENUE, SADASHIVANAGAR, P B \#8005, BANGALORE 560 080, INDIA}, issn = {0304-4289}, author = {Sood, AK and Ganesh, Krishna N. and Sundar, CS and Raychaudhuri, AK} } @article { ISI:000233616100001, title = {Proceedings of the National Conference on Nanoscience and Technology - Part II - Foreword}, journal = {Pramana-Journal of Physics}, volume = {65}, number = {5, SI}, year = {2005}, month = {NOV}, publisher = {INDIAN ACAD SCIENCES}, type = {Editorial Material}, address = {C V RAMAN AVENUE, SADASHIVANAGAR, P B \#8005, BANGALORE 560 080, INDIA}, issn = {0304-4289}, author = {Sood, AK and Ganesh, Krishna N. and Sundar, CS and Raychaudhuri, AK} } @article { ISI:000230522300022, title = {Quantitative method for normalization of transfection efficiency using enhanced green fluorescent protein}, journal = {Analytical Biochemistry}, volume = {342}, number = {2}, year = {2005}, month = {JUL}, pages = {341-344}, publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE}, type = {Article}, address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}, issn = {0003-2697}, doi = {10.1016/j.ab.2005.02.006}, author = {Dandekar, D. H. and Kumar, M. and Ladha, J. S. and Ganesh, Krishna N. and Mitra, Debashis} } @article { ISI:000227895500014, title = {(SR/RS)-cyclohexanyl PNAs: conformationally preorganized PNA analogues with unprecedented preference for duplex formation with RNA}, journal = {Journal of the American Chemical Society}, volume = {127}, number = {12}, year = {2005}, month = {MAR}, pages = {4144-4145}, publisher = {AMER CHEMICAL SOC}, type = {Article}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, issn = {0002-7863}, doi = {10.1021/ja044142v}, author = {Govindaraju, T and Kumar, VA and Ganesh, Krishna N.} } @article { ISI:000247546800008, title = {Structure-editing of nucleic acids for selective targeting of RNA}, journal = {Current Topics in Medicinal Chemistry}, volume = {7}, number = {7}, year = {2007}, month = {JAN}, pages = {715-726}, publisher = {BENTHAM SCIENCE PUBL LTD}, type = {Article}, address = {EXECUTIVE STE Y26, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

The synthesis of backbone-modified nucleic acids has been an area of very intense research over the last two decades. The main reason for this research activity is the instability of nucleic acid based drugs in the intracellular conditions. Changes in the sugar-phosphate backbone invariably bring about the changes in the complementation properties of the nucleic acids. The naturally occurring deoxyribose- (DNA) and ribose (RNA) sugar-phosphate backbones are endowed with considerable differences in their binding affinities towards themselves. This occurs because of the different sugar conformations prevalent in DNA and RNA and the subtle structural changes accruing from these in hydrogen bonding, base-stacking interactions and hydration of major/minor grooves. The six-atom phosphodiester linkages and pentose-sugars give immense opportunities for chemical modifications that lead to several backbone-modified nucleic acid structures. This article is focused on such modifications that impart RNA-selective binding properties to the modified nucleic acid mimics and the rationale behind the said selectivity. It is found that the six-atom sugar-phosphate backbone could be replaced by either one-atom extended or one-atom edited repeating units, leading to the folded or extended geometries to maintain the internucleoside distance-complementarity. Other important contributions come from electronegativity of the substituent groups, hydration in the major/minor groove, base stacking etc.

}, issn = {1568-0266}, doi = {10.2174/156802607780487722}, author = {Kumar, Vaijayanti A. and Ganesh, Krishna N.} } @article { ISI:000253646700006, title = {Cyanuryl peptide nucleic acid: synthesis and DNA complexation properties}, journal = {Tetrahedron Letters}, volume = {49}, number = {8}, year = {2008}, month = {FEB}, pages = {1314-1318}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

The synthesis of cyanuryl PNA monomer (CyaPNA) 6 was achieved by direct N-monoalkylation of cyanuric acid with N-(2-Boc-aminoethyl)-N{\textquoteright}-(bromoacetyl)glycyl ethyl ester 4. Compound 6 was incorporated as a T-mimic into PNA oligomers and biophysical studies on their triplexes/duplex complexes with complementary DNA oligomers indicated unusual stabilization of PNA:DNA hybrids when the cyanuryl unit was located in the middle of the PNA oligomer. (c) 2008 Elsevier Ltd. All rights reserved.

}, keywords = {cyanuryl PNA, PNA}, issn = {0040-4039}, doi = {10.1016/j.tetlet.2007.12.095}, author = {Vysabhattar, Raman and Ganesh, Krishna N.} } @article { ISI:000253152700039, title = {Ferrocene-linked thymine/uracil conjugates: base pairing directed self-assembly and supramolecular packing}, journal = {Journal of Organic Chemistry}, volume = {73}, number = {4}, year = {2008}, month = {FEB}, pages = {1508-1515}, publisher = {AMER CHEMICAL SOC}, type = {Article}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Ferrocene-linked bis(nucleobase) (la-c) and chimeric nucleobase (1d) conjugates have been synthesized from mono- and bis(hydroxybutyl)ferrocene 6 via Mitsunobu reaction as the key step. X-ray crystallographic studies of ferrocene bis(nucleobase) conjugates reveal two-dimensional supramolecular organizations of backbones through self-assembled Watson-Crick and reverse Watson-Crick type pairs. Ferrocene-bis(thymine) conjugate self-assembles by reverse Watson-Crick pairing, while the corresponding bis(uracil) conjugate self-assembles by alternating WC and reverse WC type pairing. Such continuous assemblies are not seen in monosubstituted ferrocene nucleobase conjugates which form only planar sheets. The results are interesting from the point of understanding and engineering supramolecular assemblies through rational design of base pairing patterns.

}, issn = {0022-3263}, doi = {10.1021/jo7023416}, author = {Patwa, Amit N. and Gupta, Susmita and Gonnade, Rajesh G. and Kumar, Vaijayanti A. and Bhadbhade, Mohan M. and Ganesh, Krishna N.} } @article { ISI:000256530800003, title = {SbCl(3) as a highly efficient catalyst for the acetylation of alcohols, phenols, and amines under solvent-free conditions}, journal = {Synthetic Communications}, volume = {38}, number = {10}, year = {2008}, month = {APR}, pages = {1518-1526}, publisher = {TAYLOR \& FRANCIS INC}, address = {325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA}, abstract = {

Antimony trichloride has been found to be an efficient and expedient catalyst for the acylation of alcohols, phenols, amines, and sugars with acetic anhydride in high yields and in a short reaction time under solvent-free conditions at room temperature. Also, racemization of chiral alcohols and epimerization of sugars were not observed in any of the substrates.

}, keywords = {acetic anhydride, acetylation, antimony trichloride, solvent-free conditions}, issn = {0039-7911}, doi = {10.1080/00397910801928640}, author = {Bhattacharya, Asish K. and Diallo, Mamadou A. and Ganesh, Krishna N.} } @article { ISI:000284499400011, title = {Base dependent pyrrolidine ring pucker in aep-PNA monomers NMR and PSEUROT analysis}, journal = {Tetrahedron}, volume = {66}, number = {47}, year = {2010}, month = {NOV}, pages = {9165-9170}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

The aep-PNA is a chiral and cyclic PNA analogue which has a stronger and base dependent binding affinity with complementary DNA To understand the base dependent properties at monomer level the structural studies of aep-PNA-(T/C/A) monomers have been carried out focussing on the conformational analysis of pyrrolidine ring pucker in aep-PNA by H-1 NMR and the coupling constant data fitted into PSEUROT software The results indicate that the type of pyrrolidine pucker depends on the electronic nature of substituent implying the effect of pyrimidine or purine substituents in determining the ring pucker in monomers This may consequently influence the aep-PNA oligomer conformation Since pyrrolidine nucleic acids have emerged as an important class of PNA analogues present results may have importance for their future development (C) 2010 Elsevier Ltd All rights reserved

}, keywords = {A T G and C, aep PNA, Conformational analysis, DNA RNA and PNA, Pyrrolidine ring}, issn = {0040-4020}, doi = {10.1016/j.tet.2010.09.082}, author = {Sharma, Nagendra K. and Ganesh, Krishna N.} } @article { ISI:000285081100050, title = {Ferrocene-Bis(thymine/uracil) conjugates: base pairing directed, spacer dependent self-assembly and supramolecular packing}, journal = {Journal of Organic Chemistry}, volume = {75}, number = {24}, year = {2010}, month = {DEC}, pages = {8705-8708}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

X-ray crystallographic studies of methylene linked Ferrocene-bis(thymine/uracil) conjugates Fc(T:T)m and Fc(U:U)(M) reveal base dependent 2-D supramolecular assemblies generated via wobble self-pairing for bis-thymine and reverse wobble self-pairing for bis-uracil conjugates, differing in architecture from the corresponding butylene spacer linked conjugates

}, issn = {0022-3263}, doi = {10.1021/jo101813z}, author = {Patwa, Amit N. and Gonnade, Rajesh G. and Kumar, Vaijayanti A. and Bhadbhade, Mohan M. and Ganesh, Krishna N.} } @article { ISI:000285370100021, title = {In situ, on-resin synthesis of 8-Br/NH2 adeninyl peptide nucleic acid (PNA) oligomers and complementation studies with DNA}, journal = {Tetrahedron Letters}, volume = {51}, number = {50}, year = {2010}, month = {DEC}, pages = {6560-6564}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

A new, novel and efficient in situ synthesis of 8-aminoadeninyl PNA oligomers from corresponding 8-bromoadeninyl PNA oligomers is reported. The study of hybridisation properties of (8-Br/8-NH2) PNA oligomers with cDNA reveals substitution-site dependent stabilization of derived triplexes and duplexes. (C) 2010 Elsevier Ltd. All rights reserved.

}, issn = {0040-4039}, doi = {10.1016/j.tetlet.2010.10.040}, author = {Vysabhattar, Raman and Ganesh, Krishna N.} } @article { ISI:000275756700010, title = {Synthesis of the antibacterial benzoquinone primin and its water-soluble analogue, primin acid}, journal = {Synthesis-Stuttgart}, number = {7}, year = {2010}, month = {APR}, pages = {1141-1144}, publisher = {GEORG THIEME VERLAG KG}, address = {RUDIGERSTR 14, D-70469 STUTTGART, GERMANY}, abstract = {

The biologically active natural product, primin and its water-soluble acid analogue, primin acid are prepared in 34\% and 25\% overall yields, respectively, from a common intermediate using a Grignard reaction and a Johnson-Claisen rearrangement as the key steps.

}, keywords = {1, 4-benzoquinones, Antibacterial, Johnson-Claisen rearrangement, primin, primin acid}, issn = {0039-7881}, doi = {10.1055/s-0029-1218666}, author = {Bhattacharya, Asish K. and Kaur, Tanpreet and Ganesh, Krishna N.} } @article { ISI:000284555600009, title = {Water-induced switching of beta-structure to polyproline II conformation in the 4s-aminoproline polypeptide via H-bond rearrangement}, journal = {Organic Letters}, volume = {12}, number = {23}, year = {2010}, month = {DEC}, pages = {5390-5393}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

4S-Aminoproline polypeptide 2 forms unusual beta-structure in trifluoroethanol that switches to the polyproline II (PPII) form in aqueous medium. while 4R-aminoproline peptide 1 retains PPII form in both solvents. This first instance of a polyproline derivative showing a beta-structure is attributed to competitive pH-dependent (4-NH3+/NH2) stereoelectronic effect (4R vs 4S) and the overriding importance of stercospecific intra/intermolecular H-bonding in (2,4)-cis-4S-aminoproline in contrast to (2,4)-trans-4R-aminoproline oligomers.

}, issn = {1523-7060}, doi = {10.1021/ol1021993}, author = {Sonar, Mahesh V. and Ganesh, Krishna N.} } @article { ISI:000286431500017, title = {Enhanced stability of G-quadruplexes from conformationally constrained aep-PNA backbone}, journal = {Organic \& Biomolecular Chemistry}, volume = {9}, number = {3}, year = {2011}, month = {NOV}, pages = {725-729}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Nucleic (DNA) acids having contiguous stretch of G sequence form quadruplex structure, which is very critical to control cell division. Recently the existence of G-quadruplex in RNA is also reported in presence of monovalent metal ion. PNA is a promising DNA analogue which binds strongly to DNA to form PNA: DNA duplex or PNA(2) : DNA triplex. PNA also forms quadruplexes such G-quadruplex and i-motif in G and C-rich sequences respectively. aep-PNA containing a prolyl ring is one of several PNA analogues that provide rigidity and chirality in backbone and has binding affinity to natural DNA which is higher than that of PNA. Here we examine the ability of aep-PNA-G to form a quadruplex by UV, CD and mass spectroscopic techniques.

}, issn = {1477-0520}, doi = {10.1039/c0ob00528b}, author = {Sharma, Nagendra K. and Ganesh, Krishna N.} } @article { ISI:000286055700020, title = {PNAs grafted with (alpha/gamma, R/S)-aminomethylene pendants: Regio and stereo specific effects on DNA binding and improved cell uptake}, journal = {Chemical Communications}, volume = {47}, number = {4}, year = {2011}, month = {JAN}, pages = {1198-1200}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

PNAs grafted with cationic aminomethylene (am) pendants on the backbone at the glycyl (alpha) or ethylenediamine (gamma) segments show regio (alpha/gamma) and stereochemistry (R/S) dependent binding with complementary DNA. These are efficiently taken up by cells, with gamma(S-am) aeg-PNA being the best in all properties.

}, issn = {1359-7345}, doi = {10.1039/c0cc03988h}, author = {Mitra, Roopa and Ganesh, Krishna N.} } @article { ISI:000313235300008, title = {4(R/S)-Amino/guanidino-substituted proline peptides: design, synthesis and DNA transfection properties}, journal = {Chimia}, volume = {66}, number = {12, 1}, year = {2012}, month = {DEC}, pages = {936-940}, publisher = {SWISS CHEMICAL SOC}, address = {SCHWARZTORSTRASSE 9, CH-3007 BERN, SWITZERLAND}, abstract = {

Collagen is a major structural protein found in the connective tissues of higher organisms and mammals and its biomechanical properties are related to the high thermal stability of its triple helical structure. The primary structure of collagen is composed of the repeating tripeptide motif of Pro-Hyp-Gly, where Hyp is 4R-hydroxy proline. Cationic collagen mimetics consisting of [Pro(X)-Pro(Y)-Gly](6) where Pro(X) and Pro(Y) are 4(R/S)-amino/guanidine proline have been synthesized and shown to form triplexes more stable than the unmodified collagen peptide [Pro-Hyp-Gly](6). The origin of hyperstability is due to conformational pre-organization of proline pucker arising from the electronegativity of the cationic group. These cationic collagen peptides are shown to be effective cell penetrating and plasmid DNA transfecting agents. The results have potential for design of new collagen mimetics for biomaterial applications and efficient cell penetrating agents for drug delivery applications.

}, keywords = {4-Aminoproline peptides, 4-Guanidino proline peptides, Cationic collagen mimetics, Cell penetrating peptides}, issn = {0009-4293}, doi = {10.2533/chimia.2012.936}, author = {Umashankara, M. and Nanda, Manaswini and Sonar, Mahesh and Ganesh, Krishna N.} } @article { ISI:000302982000044, title = {4(R/S)-Guanidinylprolyl collagen peptides: on-resin synthesis, complexation with plasmid DNA, and the role of peptides in enhancement of transfection}, journal = {Journal of Organic Chemistry}, volume = {77}, number = {8}, year = {2012}, month = {APR}, pages = {4131-4135}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Chimeric collagen peptides containing cationic 4(R/S)-guanidinylproline are synthesized by in situ amidinylation of 4(R/S)-aminoproline residues. These peptides uniquely enhance the transfection efficiency of GFP-encoded plasmid DNA (pRmHa3-GFP) into cells through efficient DNA condensation resulting from nonspecific electrostatic interactions of cationic guanidino groups and localize in subcytoplasmic organelles.

}, issn = {0022-3263}, doi = {10.1021/jo300070p}, author = {Nanda, Manaswini and Ganesh, Krishna N.} } @article { ISI:000306049900024, title = {Aminomethylene peptide nucleic acid (am-PNA): synthesis, regio-/stereospecific DNA binding, and differential cell uptake of (alpha/gamma,R/S)am-PNA analogues}, journal = {Journal of Organic Chemistry}, volume = {77}, number = {13}, year = {2012}, month = {JUL}, pages = {5696-5704}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Inherently chiral, cationic am-PNAs having pendant aminomethylene groups at alpha(R/S) or gamma(S) sites on PNA backbone have been synthesized. The modified PNAs are shown to stabilize duplexes with complementary cDNA in a regio- and stereo-preferred manner with gamma(S)-am PNA superior to alpha(R/S)-am PNAs and alpha(R)-am PNA better than the alpha(S) isomer. The enhanced stabilization of am-PNA:DNA duplexes is accompanied by a greater discrimination of mismatched bases. This seems to be a combined result of both electrostatic interactions and conformational preorganization of backbone favoring the cDNA binding. The am-PNAs are demonstrated to effectively traverse the cell membrane, localize in the nucleus of He La cells, and exhibit low toxicity to cells.

}, issn = {0022-3263}, doi = {10.1021/jo300860f}, author = {Mitra, Roopa and Ganesh, Krishna N.} } @article {49231, title = {Supramolecular polyplexes from Janus peptide nucleic acids (bm-PNA-G5): self-assembled bm-PNA G-quadruplex and its tetraduplex with DNA}, journal = {ORGANIC \& BIOMOLECULAR CHEMISTRY}, volume = {22}, year = {2024}, month = {AUG 22}, pages = {6810-6821}, type = {Journal Article}, keywords = {DOUBLE-HEADED NUCLEOTIDES, ENERGY-TRANSFER, Guanine, MAJOR GROOVE}, issn = {1477-0520}, doi = {10.1039/d4ob00968a}, author = {Todkari, Iranna Annappa and Chaudhary, Preeti and Kulkarni, Mahesh J. and Ganesh, Krishna N.} }