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List of works by Jyoti Chattopadhyaya

15N NMR spectra of wyosine (Y-nucleoside) triacetate and its 7-methyl congener. Chemical shifts and15N,1H coupling constants

2'/3'-O-peptidyl adenosine as a general base catalyst of its own external peptidyl transfer: implications for the ribosome catalytic mechanism

scientific article published in June 2005

2-(4-Tolylsulfonyl)ethoxymethyl (TEM)—a new 2′-OH protecting group for solid-supported RNA synthesis

scientific article published on 28 November 2006

270 MHz 1H-MNR Studies of four “branched” tetraribonucleotides: A3'p5'A2'p5'G3'p5'U, A3'p5'A2'p5'G'3'p5'U, U3'p5'A2'p5'G3'p5'U & U3'p5'A2'p5'G3'p5'C which are formed as the lariat branch-point in the pre-mRNA processing reactions (splicing)

A 270 MHz 1H-NMR study of three “branched” ribonucleotides A2'p5'U3'p5'g, A2'p5'C3'p5'G and A2'p5'G3'p5'G the importance of being branched with a 2'→5' phosphodiester bond in the pre-mRNA processing reactions (splicing)

article published in 1987

A 270 mhz 1H-NMR study of two “branched” ribonucleotides A3'p5'u2'p5'g and A3'p5'u2'p5'g which are products of pre-mRNA processing (“splicing”) reactions

A Convergent Regiospecific Synthesis of the Lariat-Trinucleotides and A2′p 5′Gand A2′p 5′G3′p 5′Cfrom A O4-2-Nitrophenyl) -Uridine Building Block

A Minute Amount of S-Puckered Sugars Is Sufficient for (6-4) Photoproduct Formation at the Dinucleotide Level

scientific article published on 11 December 2014

A New stereospecific synthesis of [3.1.0]bicyclic cyclopropano analog of 2'3'-dideoxyuridine

A comparative conformational study of thymidylyl(3′ → 5′)-thymidine, thymidylyl(3′ → 5′)-5′-thio-5′-deoxythymidine and thymidinylacetomido-[3′(O) →′ (C)]-5′-deoxythymidine

scientific article published on 01 November 1990

A comparative high-field n.m.r. study on tri-, tetra-, penta-, and hepta-mer ribonucleotides modelling the branch site of Group II and nuclear messenger RNA spliced lariat introns

A critical survey of the structure-function of the antisense oligo/RNA heteroduplex as substrate for RNase H.

scientific article

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

scientific article published on 12 March 2009

A new Synthesis of 1-(2,3-Dideoxy-β-D-Glycero-Pent-2-Enofuranosyl)- Thymine. A Highly Potent and Selective Anti-Hiv Agent

article

A new regiospecific synthesis of “Branched” tetraribonucleotide and its three analogues to delineate the chemospecific role of the “Branch-point” adenine nucleotide in splicing

A regio and stereoselective synthesis of 2',2',3',4'-tetradeuterio-2'-deoxy nucleosides

A repertoire of pyridinium-phenyl-methyl cross-talk through a cascade of intramolecular electrostatic interactions.

scientific article published in February 2003

A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

scientific article

A uniform mechanism correlating dangling-end stabilization and stacking geometry.

scientific article

Acidic hydrolysis of 6-substituted 9-(2-deoxy-β--- pentofuranosyl) purines and their 9-(1-alkoxyethyl) counter-parts: kinetics and mechanism.1

Allele-selective inhibition of ataxin-3 (ATX3) expression by antisense oligomers and duplex RNAs

scientific article published on 07 February 2011

Allele-selective inhibition of mutant huntingtin expression with antisense oligonucleotides targeting the expanded CAG repeat

scientific article

An 15n-nmr study of isomeric n1 and n3 substituted 7-methyl-10-oxo-9,10-dihydro pyrimido[l,2-a]purines and 9-oxo-8,9-dihydro-5-alkyl-imidazo[1,2-a] purines in neutral and acidic medium

article published in 1987

An Assessment of Electronic Properties of Pyrimidine and Purine Nucleosides by15N-NMR Spectroscopy

An analysis of the inhibition of replication of HIV and MuLV by some 3'-blocked pyrimidine analogs

scientific article (publication date: 1989)

An assessment of the reactivity of guanosine and some of its derivatives to electrophiles by 15N-NMR spectroscopy

An efficient synthesis of y-nucleoside (wyosine) by regiospecific methylation of n4-desmethylwyosine using organozinc reagent

article published in 1987

An electrochemical probe of DNA stacking in an antisense oligonucleotide containing a C3'-endo-locked sugar

scientific article published in September 2002

An energetic correlation of ab initio and NMR studies of the 3'-gauche effect in 3'-substituted thymidines

scientific article published in April 2001

Antisense oligonuclotides with oxetane-constrained cytidine enhance heteroduplex stability, and elicit satisfactory RNase H response as well as showing improved resistance to both exo and endonucleases

scientific article

Arenesulfonylethoxycarbonyl- a Set of Amino Protecting Groups for DNA and RNA Synthesis

Assessment of competing 2′«5′ versus 3′«5′ stackings in solution structure of branched-RNA by 1H- & 31 P-NMR spectroscopy

Base-pair exchange kinetics of the imino and amino protons of the 3'-phenazinium tethered DNA-RNA duplex, r(5'GAUUGAA3'):d(5'TCAATC3'-Pzn), and their comparison with those of B-DNA duplex

scientific article published on June 1995

Bausteine für Oligonucleotid-Synthesen mit einheitlich fragmentierbaren β-halogenierten Schutzgruppen /Building Blocks for Oligonucleotide Syntheses with Uniformly Fragmentable β-Halogenated Protecting Groups

scientific article published in 1987

Building blocks for oligonucleotide syntheses with uniformly fragmentable beta-halogenated protective groups

scientific article published on April 1987

Carba-LNA modified siRNAs targeting HIV-1 TAR region downregulate HIV-1 replication successfully with enhanced potency

article

Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3'-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry.

scientific article published on 4 May 2011

Challenges in the Chemistry of Small Interfering RNA as Potential Therapeutics to Inhibit Cellular mRNA Expression

Chemical and Structural Implications of 1‘,2‘- versus 2‘,4‘- Conformational Constraints in the Sugar Moiety of Modified Thymine Nucleosides

scientific article published on 25 May 2007

Chemical synthesis and molecular cloning of a STOP oligonucleotide encoding an UGA translation terminator in all three reading frames

scientific article published in September 1983

Comparative assessment of structure and reactivity of wyosine by chemistry, spectroscopy and ab initio calculations

Comparison of the RNase H cleavage kinetics and blood serum stability of the north-conformationally constrained and 2'-alkoxy modified oligonucleotides

scientific article published on 06 April 2007

Computational and NMR study of quaternary ammonium ion conformations in solution

Conformation of Lariat Structures Formed in the Splicing of Pre-mRNA by NMR Spectroscopy

Conformation-specific cleavage of antisense oligonucleotide-RNA duplexes by RNase H

Conformational studies of thymidine dimers containing sulfonate and sulfonamide linkages by NMR spectroscopy

Conformational studies on some C1′-branched β-d-nucleosides by 1H-NMR spectroscopy and molecular mechanics calculations

scientific article published on 01 July 1993

Conformational studies op 3'--methyl and 2'--methyl analogues of cordycepin

Conformationally constrained 2'-N,4'-C-ethylene-bridged thymidine (aza-ENA-T): synthesis, structure, physical, and biochemical studies of aza-ENA-T-modified oligonucleotides.

scientific article

Conformationally-2',4'-locked Aza-ENA and carbocyclic ribo-thymidine

scientific article published in January 2007

Conformationally-constrained indeno[2,1-c]quinolines--a new class of anti-mycobacterial agents

scientific article published on 15 March 2010

Cross-modulation of physicochemical character of aglycones in dinucleoside (3'-->5') monophosphates by the nearest neighbor interaction in the stacked state

scientific article

Cross-modulation of the pKa of nucleobases in a single-stranded hexameric-RNA due to tandem electrostatic nearest-neighbor interactions

scientific article published in August 2003

Design and Divergent Synthesis of Aza Nucleosides from a Chiral Imino Sugar

scientific article published on 02 May 2012

Design, synthesis and biological evaluation of novel triazole, urea and thiourea derivatives of quinoline against Mycobacterium tuberculosis.

scientific article

Design, synthesis, biological evaluation and molecular modelling studies of novel quinoline derivatives against Mycobacterium tuberculosis

scientific article published on 21 February 2009

Determination of the Tautomeric Populations of the Y-Base

Deuteriation of sugar protons simplify NMR assignments and structure determination of large oligonucleotide by the 1H-NMR window approach

scientific article published on November 1993

Diastereospecific chemical synthesis of ribonucleosides-3′,4′,5′,5″ -d4

Diastereospecific synthesis of 2′- or 3′-c-branched nucleosides through intramolecular free-radical capture by silicon-tethered acetylene

Diels-alder reaction of 2′,3′-unsaturated-3′-nitro-thymidine. First chemical evidence of nitroxide radical formation in the radical-promoted denitration reaction

article

Different patterns of inhibition of avian myeloblastosis virus reverse transcriptase activity by 3'-azido-3'-deoxythymidine 5'-triphosphate and its threo isomer

scientific article

Direct estimation of base-pair exchange kinetics in oligo-DNA by a combination of NOESY and ROESY experiments

scientific article published on September 1993

Distal Two-Bond versus Three-Bond Electronegative Oxo-Substituent Effect Controls the Kinetics and Thermodynamics of the Conversion of a C-Nitroso Function to the Corresponding Oxime in the Conformationally Locked Pentofuranose (Bicyclo[2.2.1]heptane

scientific article published on 04 August 2014

Double sugar and phosphate backbone-constrained nucleotides: synthesis, structure, stability, and their incorporation into oligodeoxynucleotides

scientific article

Electrostatic cross-modulation of the pseudoaromatic character in single-stranded RNA by nearest-neighbor interactions

Enhancement of molecular ion intensity of nucleic acids in negative ion fast-atom bombardment mass spectroscopy

Facile preparation of the oxetane-nucleosides

scientific article published on 7 November 2005

Fine tuning of electrostatics around the internucleotidic phosphate through incorporation of modified 2',4'-carbocyclic-LNAs and -ENAs leads to significant modulation of antisense properties.

scientific article published in January 2009

Five- and Six-Membered Conformationally Locked 2‘,4‘-Carbocyclicribo-Thymidines: Synthesis, Structure, and Biochemical Studies

scientific article published on 07 June 2007

Fluorescence Properties of Y-Nucleoside Derivatives

Free-radical ring closure to conformationally locked α-L-carba-LNAs and synthesis of their oligos: nuclease stability, target RNA specificity, and elicitation of RNase H.

scientific article published on September 2010

Functional analysis of influenza RNA polymerase activity by the use of caps, oligonucleotides and polynucleotides

scientific article

High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions

article

How Does the 2'-Hydroxy Group Drive the Pseudorotational Equilibrium in Nucleoside and Nucleotide by the Tuning of the 3'-Gauche Effect?

scientific article published in 1994

How RNase HI (Escherichia coli) promoted site-selective hydrolysis works on RNA in duplex with carba-LNA and LNA substituted antisense strands in an antisense strategy context?

scientific article published on 29 March 2017

How do the aglycones drive the pseudorotational equilibrium of the pentofuranose moiety in C-nucleosides?

How does the 3′-phosphate drive the sugar conformation in DNA?

article by J. Plavec et al published 1994 in Journal of the Chemical Society. Chemical communications

How does the steric effect drive the sugar conformation in the 3′-C-branched nucleosides?

article by Janez Plavec et al published 1993 in Journal of the Chemical Society. Chemical communications

How kinetically accessible is an RNA target for hybridization with an antisense oligo? A lesson from an RNA target which is as small as a 20mer

How much hydration is necessary for the stabilisation of DNA-duplex?

scientific article published on September 1993

In vivo efficacy and off-target effects of locked nucleic acid (LNA) and unlocked nucleic acid (UNA) modified siRNA and small internally segmented interfering RNA (sisiRNA) in mice bearing human tumor xenografts

scientific article

Inhibition of hepatitis B virus DNA polymerase by 3'-azido-3'-deoxythymidine triphosphate but not by its threo analog

scientific article

Inhibition of the reverse transcriptase from HIV by 3'-azido-3'-deoxythymidine triphosphate and its threo analogue

scientific article (publication date: March 1987)

Interactions of drugs and an oligonucleotide with charged membranes analyzed by immobilized liposome chromatography

scientific article published in January 2006

Intra- and intermolecular nucleophilic phosphorous - sulfur bond cleavage. The reaction of fluoride ion with O-aryl-O, S-dialkylphosphorothioates, & the degradation of phosphorothioate linkage in di-ribonucleotides by the vicinal 2′-hydroxyl group

article published in 1989

Intramolecular cyclization-trapping of carbon radicals by olefins as means to functionalize 2′- and 3′-carbons in β-D-nucleosides

Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics.

scientific article published on 24 April 2012

MOLECULAR MODELLING OF 2′-OH MEDIATED HYDROGEN BONDING IN RIBONUCLEOS(T)IDES BY NMR CONSTRAINED AM1 AND MMX CALCULATIONS

scientific article published on 01 April 2001

Measurement of Nucleobase pKaValues in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes

scientific article published on 01 March 2004

Michael addition reactions of α β-ene-3′-phenylselenone of uridine. New synthesis of 2′,3′-dideoxy-ribo-aziridino-, 2′,3′-dideoxy-2′, 3′-ribo-cyclopropyl- & 2,2′-O-anhydro-3′-deoxy-3′-amino uridine derivatives

article published in 1989

Modulation of pyrene fluorescence in DNA probes depends upon the nature of the conformationally restricted nucleotide

scientific article published on 11 March 2008

Molecular Structure of the Core-Modified siRNA Duplexes Containing Diastereomeric Pair of [C6′(R)-OH]- versus [C6′(S)-OH]-carba-LNAs Suggests a Model for RNAi Action

scientific article published on 01 November 2011

N23-ethenoguanosine and IA′-metamorphosine: 5N NMR Spectroscopy and elucidation of physico-chemical properties by kinetic and equilibrium measurements

NMR spectroscopic properties (1H at 500 MHz) of deuterated∗ ribonucleotide-dimers ApU∗, GpC∗, partially deuterated 2′-deoxyribonucleotide-dimers d(TpA∗, d(ApT∗, d(GpC∗ and their comparison with natural counterparts (1H-NMR window)

scientific article published on 01 February 1993

New antiprotozoal agents: their synthesis and biological evaluations

scientific article published on 22 February 2013

New diastereospecific synthesis of 2′,3′-dideoxy-2′- or 3′-C2-branched- or 2′,3′-α-fused-isoxazolidine nucleosides directly from the seconucleoside

New parasite inhibitors encompassing novel conformationally-locked 5'-acyl sulfamoyl adenosines

scientific article

New regiospecific synthesis of branched tetra-, nona- & deca-RNA modelling the lariat formed in RNA splicing reactions

article published in 1991

New regiospecific synthesis of the “branched” tri-, penta- & hepta-ribonucleic acids which are formed as the “lariat” in the pre-mRNA processing reactions[Splicing]

New stereocontrolled synthesis of isomeric C-branched-β-D-nucleosides by intramolecular free-radical cyclization- opening reactions based on temporary silicon connection

New syntheses of 2',3'-dideoxy-2',3'-di-substituted & -2'-mono-substituted uridines & adenosines by michael addition reactions

article

New synthesis of 2',3'-dideoxy-3'-C-cyano-2'-substituted thymidines by michael addition reactions

article

New synthesis of 2′, 3′-dideoxy-2′, 3′-didehydro-3′--substituted thymidines

New synthesis of 3′--substituted nucleosides

New synthesis of 3′--substituted-3′-nitromethyl-ribo-thymidines

Non-identical electronic characters of the internucleotidic phosphates in RNA modulate the chemical reactivity of the phosphodiester bonds

scientific article published on 2 February 2006

Novel quinoline and naphthalene derivatives as potent antimycobacterial agents.

scientific article published on 20 January 2010

Nucleic acid therapeutics for hematologic malignancies--theoretical considerations

scientific article published on October 2006

On the Structure and Reactivity of Y-Nucleoside [Wyosine]

Oxetane modified, conformationally constrained, antisense oligodeoxyribonucleotides function efficiently as gene silencing molecules

scientific article published on 28 October 2004

Partially-deuterated nucleotide residues in large DNA duplex simplify the spectral overlap and provide both the J-coupling and nOe informations by the “NMR-window” approach

Partially-deuterated oligo-DNA reduces overcrowding, enhances resolution and sensitivity and provide improved NMR constraints for structure elucidation of oligo-DNA

article published in 1998

Poor hydration enhances the activation energy of the exchange rate of the base-paired imino protons with water at the core part of the DNA duplex

Precipitation of nucleotides by calcium phosphate

scientific article published on 01 May 1982

Quantitation of the Anomeric Effect in Adenosine and Guanosine by Comparison of the Thermodynamics of the Pseudorotational Equilibrium of the Pentofuranose Moiety in N- and C-Nucleosides

scientific article published in 1994

Rapid and quantitative recovery of DNA fragments from gels by displacement electrophoresis (isotachophoresis)

scientific article published on 01 June 1984

Regiospecific synthesis of 2'-deoxy-2',2' -dideuterio nucleosides

Regiospecific synthesis of branched tetranucleotides: U3'p5'A3'p5'U2'p5'G, U3'p5'A3'p5'C2'p5'G, A3'p5'A3'p5'U2'p5'G & A3'p5'A3'p5'C2'p5'G

article published in 1987

Remarkable conformational change promoted by 3′-ethylphosphate at the branch-point of a tetrameric lariat-RNA dictates its self-cleavage reaction modelling some catalytic RNAs (ribozymes)

Reparametrization of Karplus equation relating 3JCCOP to torsion angle

Selective cleavage of the O6-diphenylcarbamoyl group from sugar-modified guanosines for incorporation into oligo-RNA

article by András Földesi et al published October 1999 in Tetrahedron Letters

Significant pKaPerturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA

scientific article published on 01 July 2004

Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern †

scientific article

Site-specific modification of the pyrimidine residue during the deprotection of the fully-protected diuridylic acid

Solid Phase Synthesis of DNA Under a Non-Depurinating Condition with a Base Labile 5′-Protecting Group (Fmoc) Using Phosphiteamidite Approach

Solution conformation of hexameric & heptameric lariat-RNAs and their self-cleavage reactions which give products mimicking those from some catalytic RNAs (ribozymes)

Solution structure of branched U3′p5′A2′p5′G3′p5′C and its comparison with A2′p5′G3′p5′U by 500 MHz NMR spectroscopy

Solution structure of lariat RNA by 500 MHz NMR spectroscopy and molecular dynamics studies in water

scientific article published on October 1993

Solution structure of pentameric and heptameric branched-RNA modelling the lariat structure of group II or nuclear m-RNA introns studied by one- and two-dimensional nmr spectroscopy at 500 mhz

Solution structures of nonameric and decameric branched-RNA modelling the Lariat of group II and nuclear pre-mRNA introns (splicing) by 500 MHz NMR spectroscopy

Some Aspects of Ribonucleoside Chemistry

Spectroscopic, kinetic and semiempirical molecular orbital studies on 8-amino-, 8-methylamino- & 8-dimethylamino-adenosines

Stereoisomeric Selectivity of Human Deoxyribonucleoside Kinases†

scientific article published on 01 December 1999

Steric Effects in the Tuning of the Diastereoselectivity of the Intramolecular Free-Radical Cyclization to an Olefin As Exemplified through the Synthesis of a Carba-Pentofuranose Scaffold

scientific article published on 09 August 2012

Structural analysis of 2′,3′-dideoxyinosine, 2′,3′-dideoxyadenosine, 2′,3′-dideoxyguanosine and 2′,3′-dideoxycytidine by 500-MHz 1H-NMR spectroscopy and ab-initio molecul orbital calculations

scientific article published on 01 December 1992

Structural properties of four isomeric C2'/C3' modified uridines

scientific article published in 1992

Structural studies of anti-HIV 3′-(α-fluorothymidine & 3′-(α-azidothymidine by 500 MHz 1H-NMR spectroscopy & molecular mechanics (MM2) calculations

article

Structural studies of the 5′-phenazinium-tethered matched and G-A-mismatched DNA duplexes by NMR spectroscopy

scientific article published on 01 May 1993

Structural studies on 1-(1-deoxy-β-d-psicofuranosyl)thymine

Structure and reactivity of wyosine (y-nucleoside) and its derivatives. Chemical, kinetic and spectroscopic studies

Structure and toxicity of a peptide hepatotoxin from the cyanobacterium Oscillatoria agardhii

scientific article published in January 1989

Structure of 10-23 DNAzyme in Complex with the Target RNA in silico-A Progress Report on the Mechanism of RNA Cleavage by DNA Enzyme

Structure of a hepatotoxic pentapeptide from the cyanobacterium Nodularia spumigena

scientific article published in January 1990

Studies on the Stereoselective Synthesis of Deuterated D-Ribose Derivatives

Studies towards the large scale chemical synthesis of the precursors of ribonucleosides-3',4',5',5''-2H4 and -2',3',4',5',5''-2H5.

scientific article

Synthesis and Structure of New Methylene-Bridged Hexopyranosyl Nucleoside (BHNA)

Synthesis and antimycobacterial activity of prodrugs of indeno[2,1-c]quinoline derivatives

scientific article published on 3 February 2011

Synthesis and structure of azole-fused indeno[2,1-c]quinolines and their anti-mycobacterial properties

scientific article published on 7 October 2010

Synthesis and structure of novel conformationally constrained 1',2'-azetidine-fused bicyclic pyrimidine nucleosides: their incorporation into oligo-DNAs and thermal stability of the heteroduplexes

scientific article

Synthesis of 1′#,2′,3′,4′#,5′,5″-2H6-β-D-ribonucleosides and 1′#, 2′,2″,3′,4′#,5′,5″-2H7-β-D-2′-deoxyribonucleosides for selective suppression of proton resonances in partially-deuterated oligo-DNA, oligo-RNA and in 2,5A

Synthesis of 1′-phenazine-tethered psicofuranosyl oligonucleotides: The thermal stability and fluorescence properties of their duplexes and triplexes

Synthesis of 2',4'-propylene-bridged (carba-ENA) thymidine and its analogues: the engineering of electrostatic and steric effects at the bottom of the minor groove for nuclease and thermodynamic stabilities and elicitation of RNase H.

scientific article published on November 2010

Synthesis of 2'-deoxy-2'()-deuterio and 2'-deoxy-2'(r)-deuterio-β-d-nucleosides

Synthesis of 2′,3′-Dideoxy-3′-nitro-2′,3′-didehydrothymidine. Its Use as a General Intermediate for the Preparation of Various 2′,3′-Substituted Nucleosides

Synthesis of 2′,3′-cis-fused pyrrolidino-β-D-nucleosides and their conformational analysis by 500 MHz 1H-NMR

Synthesis of 2′- and 3′-spiro-isoxazolidine derivatives of thymidine & their conversions to 2′,3′-dideoxy-2′,3′-didehydro-3′--substituted nucleosides by radical promoted fragmentation

Synthesis of 5′-polyarene-tethered oligo-DNAs and the thermal stability and spectroscopic properties of their duplexes and triplexes

Synthesis of Branched Oligoribonucleotides ("Lariat")

Synthesis of C-branched spermine tethered oligo-DNA and the thermal stability of the duplexes and triplexes

article published in 1996

Synthesis of Conformationally Constrained 2’-N,4’-C-Ethylene-Bridged Adenosine (aza-ENA-A)

article by Jyoti Chattopadhyaya et al published 2007 in Heterocycles

Synthesis of Conformationally Locked Carba-LNAs through Intramolecular Free-Radical Addition to C═N. Electrostatic and Steric Implication of the Carba-LNA Substituents in the Modified Oligos for Nuclease and Thermodynamic Stabilities

article

Synthesis of Cytidylyl(3′→5′)cytidylyl(3′→5′)-(2′)3′-O-[Lα-alanyl]adenosine

Synthesis of O2'-methyluridine, O2'-methylcytidine, N4,O2'-dimethylcytidine and N4,N4,O2'-trimethylcytidine from a common intermediate

scientific article published on November 1986

Synthesis of [3t̄'(O)→-5t̄'(c)]-oxyacetamido linked nucleosides

Synthesis of [Ru(phen)(2)dppz](2+)-tethered oligo-DNA and studies on the metallointercalation mode into the DNA duplex

scientific article published on April 2001

Synthesis of adenylyl-(3'----5')-guanosine and some analogues as probes to explore the molecular mechanism of stimulation of influenza virus RNA polymerase

scientific article published in January 1985

Synthesis of an mRNA fragment of alanyl-tRNA synthetase gene in Escherichia coli using the 6-methyl-3-pyridyl group for protection of the imide functions of uridine and guanosine

scientific article (publication date: November 1986)

Synthesis of furo[2,3-c]pyran-β-d-nucleosides by radical-cyclization & their conformational analysis by 500 mhz 1h-nmr spectroscopy

Synthesis of heptameric lariat-RNA modelling the lariat introns of group II and nuclear pre-mRNA processing reaction (splicing)

Synthesis of multiply labelled ribonucleosides for sequence-specific labelling of oligo-RNA

article published in 2001

Synthesis of new 2',3'-dideoxy-2',3'-α-fused-heterocyclic uridines, & some 2', 3'-ene-2'-substituted uridines from easily accessible 2',3'- ene-3'phenylselenonyl uridine

Synthesis of new 2′, 3′-modified uridine derivatives from 2′,3′-ene-2′-phenylselenonyl uridine by Michael addition reactions

article

Synthesis of partially-deuterated 2′-deoxyribonucleoside blocks and their incorporation into an oligo-DNA for simplification of overcrowding and selective enhancement of resolution and sensitivity in the 1H-NMR spectra

Synthesis of tetrameric cyclic branched-RNA (lariat) modelling the introns of group II and nuclear pre-mRNA processing reaction (splicing)

Synthesis of the DNA-[Ru(tpy)(dppz)(CH(3)CN)](2+) conjugates and their photo cross-linking studies with the complementary DNA strand

scholarly article published in November 2002

Synthesis of “branched” trinucleotide using the H-phosphonate chemistry

Synthesis of[2′-2H1]-Ribonucleosides

Synthesis, physicochemical and biochemical studies of 1',2'-oxetane constrained adenosine and guanosine modified oligonucleotides, and their comparison with those of the corresponding cytidine and thymidine analogues

scientific article published in September 2004

Synthetic and high-field NMR study of branched tri-, tetra-, penta-, and heptaribonucleotides modelling the lariat-intron in group II splicing.

scientific article published in January 1989

Synthetic siRNA targeting human papillomavirus 16 E6: a perspective on in vitro nanotherapeutic approaches

scientific article published on 31 January 2018

Synthetic studies to improve the deuterium labelling in nucleosides for facilitating structural studies of large RNAs by high-field NMR spectroscopy

scientific article published in April 2001

Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction

scientific article published in February 2003

Temperature-dependent31P n.m.r. shifts to assess the conformations of branched tri- and tetra-nucleotides which are formed as lariats in the splicing reactions

article by A. Sandström et al published 1988 in Journal of the Chemical Society. Chemical communications

The 5-Me of thyminyl (T) interaction with the neighboring nucleobases dictate the relative stability of isosequential DNA-RNA hybrid duplexes.

scientific article published on 29 September 2005

The NMR Structure of Estrone (Es)-tethered Tandem DNA Duplex: [d(5′pCAGCp3′)-Es] + [Es-d(5′pTCCA3′)]: d(5′pTGGAGCTG3′) ⬇️

scientific article published on December 1, 1997

The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR-window' concept]

scientific article published on June 1996

The Protection of The 2′-Hydroxyl Function in Oligoribonucleotide Synthesis

The R-diastereomer of 6′-O-toluoyl-carba-LNA modification in the core region of siRNA leads to 24-times improved RNA silencing potency against the HIV-1 compared to its S-counterpart

article

The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-Phosphate Backbone Torsions in Guanosine 3′,5′-Bisphosphate

article

The application of 2-(4-chlorophenyl)-sulfonylethoxycarbonyl (CPSEC) group in the synthesis of a DNA segment using the phosphotriester approach

The chemical nature of the 2′-substituent in the pentose-sugar dictates the pseudoaromatic character of the nucleobase (pKa) in DNA/RNA

scientific article published on 30 March 2006

The chemical synthesis and antiviral properties of an acyclovir-phospholipid conjugate

scientific article published in January 1985

The cordycepin analogue of 2,5A and its threo isomer. Chemical synthesis, conformation and biological activity

scientific article

The determination of the ionization constants of C-nucleosides

The diastereospecific synthesis of new 2′,3′-Cis-α-fused carbocyclic nucleosides

The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA ('NMR-window') gives complementary structural information

scientific article published on April 1994

The effect of metal ion complex formation on acidic depurination of 2′-deoxyadenosine and 2′-deoxyguanosine

The effect of protecting groups of the nucleobase and the sugar moieties on the acidic hydrolysis of the glycosidic bond of 2deoxyadenosine: a kinet

article by Gerald Remaud et al published January 1987 in Tetrahedron

The first example of a Hoogsteen base-paired DNA duplex in dynamic equilibrium with a Watson-Crick base-paired duplex--a structural (NMR), kinetic and thermodynamic study

scientific article published in June 2001

The first example of sequence-specific non-uniformly 13C5 labelled RNA: Synthesis of the 29mer HIV-1 TAR RNA with 13C Relaxation Window

article

The first experimental evidence for a larger medium-dependent flexibility of natural β--nucleosides compared to the α--nucleosides

article

The hydrogen bonding and hydration of 2'-OH in adenosine and adenosine 3'-ethyl phosphate

scientific article

The identification of the A-type RNA helices in a 55mer RNA by selective incorporation of deuterium-labelled nucleotide residues (Uppsala NMR-window concept)

scientific article published on 01 March 2000

The interaction of the 2′-OH group with the vicinal phosphate in ribonucleoside 3′-ethylphosphate drives the sugar-phosphate backbone into unique (S,ω−) conformational state

article by J. Plavec et al published October 1995 in Tetrahedron

The pK(a)'s of 2'-hydroxyl group in nucleosides and nucleotides

scientific article published in March 2001

The pKaof the Internucleotidic 2‘-Hydroxyl Group in Diribonucleoside (3‘→5‘) Monophosphates

scientific article published on 01 March 2003

The quantitation of the competing energetics of the stereoelectronic and steric effects of the 3′-OH and the aglycone in the α-versus & by 1H-NMR

The residence time of the bound water in the hydrophobic minor groove of the carbocyclic-nucleoside analogs of Dickerson-Drew dodecamers

scientific article

The self-cleavage of lariat-RNA

The solution conformation of a carbocyclic analog of the Dickerson-Drew dodecamer: comparison with its own X-ray structure and that of the NMR structure of the native counterpart

scientific article

The solution structure of a 3'-phenazinium (Pzn) tethered DNA-RNA duplex with a dangling adenosine: r(5'G-AUUGAA3'):d(5'TCAATC3'-Pzn)

scientific article published on December 1994

The synthesis and conformation of 2′- and 3′-hypermodified tricyclic nucleosides and their use in the synthesis of novel 2′- or 3′-isomeric 4(7)-substituted isoxazolidine-nucleosides

The synthesis and reactivity of new 2-(N,N-diisopropylamino)-3-methylsulfonyl-1,3,2-benzoxazaphospholes. The utility of the 5-chloro analogue in the one-pot synthesis of oligothiophosphates: [ApsppA, ApspppA, ppp5′A2′ps5′A, m7GpsppA, Apspppp, A

The synthesis of deuterionucleosides

scientific article

The synthesis of new 3′-bis--substituted-3′-deoxy-3′-dehydro-[3.3.0]-α-fused thymidines by intramolecular radical trapping by tethered acetylenes

The synthesis of therapeutic locked nucleos(t)ides.

scientific article

The tunable transmission of the aromatic character of the aglycone through the anomeric effect in C-nucleosides drives its own sugar conformation: A thermodynamic study

article

The use of 15N-NMR spectroscopy for assigning the structures of isomeric N7- and N9-substituted purines

The use of non-uniform deuterium labelling ['NMR-window'] to study the NMR structure of a 21mer RNA hairpin

scientific article published on April 1996

Total Synthesis of 2‘,3‘,4‘,5‘,5‘ ‘-2H5-Ribonucleosides: The Key Building Blocks for NMR Structure Elucidation of Large RNA

scientific article published on 01 October 2001

Unusual Strain-Releasing Nucleophilic Rearrangement of a Bicyclo[2.2.1]heptane System to a Cyclohexenyl Derivative

scientific article published on 24 October 2012

Unusual radical 6-endo cyclization to carbocyclic-ENA and elucidation of its solution conformation by 600 MHz NMR and ab initio calculations.

scientific article published on 27 October 2008

Why Carba-LNA-modified oligonucleotides show considerably improved 3'-exonuclease stability compared to that of the LNA modified or the native counterparts: A Michaelis-Menten kinetic analysis.

scientific article published on April 2010

Why do all lariat RNA introns have adenosine as the branch point nucleotide ? Conformational studies on the implication of the branch-point modification by guanine, uracil or cytosine in the naturally.occurring branched tetranucleotide by 1H- & 31p-N

article published in 1989

Why do all lariat RNA introns have adenosine as the branch-point nucleotide? Conformational study of naturally-occuring branched trinucleotides and its eleven analogues by 1H-, 31P-NMR and CD spectroscopy

scientific article published on 01 February 1989

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