A versatile method for the preparation of conjugates of peptides with DNA/PNA/analog by employing chemo-selective click reaction in water

The specific 1,3 dipolar Hüisgen cycloaddition reaction known as ‘click-reaction’ between azide and alkyne groups is employed for the synthesis of peptide–oligonucleotide conjugates. The peptide nucleic acids (PNA)/DNA and peptides may be appended either by azide or alkyne groups. The cycloaddition reaction between the azide and alkyne appended substrates allows the synthesis of the desired conjugates in high purity and yields irrespective of the sequence and functional groups on either of the two substrates. The versatile approach could also be employed to generate the conjugates of peptides with thioacetamido nucleic acid (TANA) analog. The click reaction is catalyzed by Cu (I) in either water or in organic medium. In water, ∼3-fold excess of the peptide-alkyne/azide drives the reaction to completion in 2 h with no side products

Structure-Editing of Nucleic Acids for Selective Targeting of RNA

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 o several backbone-modified nucleic acid structures. This aticle 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 ound that the six-atom sugar-phosphate backbone could be eplaced by either one-atom extended or one-atom edited epeating units, leading to the folded or extended eometries to maintain the internucleoside distance-complementarity. ther important contributions come from electronegativity of he substituent groups, hydration in the major/minor groove, ase stacking etc

Structure-editing of nucleic acids for selective targeting of RNA

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 sugarphosphate 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 backbonemodified 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

Conformationally constrained PNA analogues: structural evolution toward DNA/RNA binding selectivity

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

(SR/RS)-cyclohexanyl PNAs: conformationally preorganized PNA analogues with unprecedented preference for duplex formation with RNA

PNA oligomers H-GTAGATCAT-lys-NH<SUB>2</SUB> with cis-(1S,2R/1R,2S)-cyclohexyl-T (III) in the backbone form PNA:RNA duplexes with T<SUB>m</SUB>~ 30-50&#176;C higher than that of PNA:DNA duplexes. In comparison, cis-(1S,2R/1R,2S)-cyclopentyl PNA-T (IV) form highly stable duplexes with both RNA and DNA without discrimination

Synthesis and evaluation of (1S,2R/1R,2S)-aminocyclohexylglycyl PNAs as conformationally preorganized PNA analogues for DNA/RNA recognition

Conformationally constrained cis-aminocyclohexylglycyl PNAs have been designed on the basis of stereospecific imposition of 1,2-cis-cyclohexyl moieties on the aminoethyl segment of aminoethylglycyl PNA (aegPNA). The introduction of the cis-cyclohexyl ring may allow the restriction of the torsion angle &#223; in the ethylenediamine segment to 60-70&#176; that is prevalent in PNA2:DNA and PNA:RNA complexes. The synthesis of the optically pure monomers (10a and 10b) is achieved by stereoselective enzymatic hydrolysis of an intermediate ester 2. The chiral PNA oligomers were synthesized with (1S,2R/1R,2S)-aminocyclohexylglycyl thymine monomers in the center and N-terminus of aegPNA. Differential gel shift retardation with one or more units of modified monomer units was observed as a result of hybridization of PNA sequences with complementary DNA sequences. Hybridization studies with complementary DNA and RNA sequences using UV-Tm measurements indicate that PNA with (1S,2R)-cyclohexyl stereochemistry enhances selective binding with RNA over DNA as compared to control aegPNA and PNA with the other (1R,2S) isomer

(1S,2R/1R,2S)-cis-cyclopentyl PNAs (cpPNAs) as constrained PNA analogues: synthesis and evaluation of aeg-cpPNA chimera and stereopreferences in hybridization with DNA/RNA

Conformationally constrained chiral PNA analogues were designed on the basis of stereospecific imposition of a 1,2-cis-cyclopentyl moiety on an aminoethyl segment of aegPNA. It is known that the cyclopentane ring is a relatively flexible system in which the characteristic puckering dictates the pseudoaxial/pseudoequatorial dispositions of substituents. Hence, favorable torsional adjustments are possible to attain the necessary hybridization-competent conformations when the moiety is imposed on the conventional PNA backbone. The synthesis of the enantiomerically pure 1,2-cis-cyclopentyl PNA monomers (10a and 10b) was achieved by stereoselective enzymatic hydrolysis of a key intermediate ester 2. The chiral (1S,2R/1R,2S)-aminocyclopentylglycyl thymine monomers were incorporated into PNA oligomers at defined positions and through the entire sequence. Hybridization studies with complementary DNA and RNA sequences using UV-Tm measurements indicate that aeg-cpPNA chimera form thermally more stable complexes than aegPNA with stereochemistry-dependent selective binding of cDNA/RNA. Differential gel shift retardation was observed on hybridization of aeg-cpPNAs with complementary DNA

BisPNA targeting to DNA: effect of neutral loop on DNA duplex strand invasion by aepPNA-N7G/aepPNA-C substituted peptide nucleic acids

N7-Alkyl-substituted guanine (N7G) as a CH<SUP>+</SUP> mimic has been introduced into aminoethylglycyl PNA (aegPNA) forming a hairpin through a neutral linker derived from bis(tetraethylene) glycol (teg-teg). These form pH-independent PNA<SUB>2</SUB>:DNA triplexes with complementary DNA sequences. The introduction of chiral, cationic aminoethylprolyl (aep) units with C and the CH<SUP>+</SUP> mimic N7G in the backbone of the hairpin bisPNAs with a neutral teg-teg linker, influenced the recognition of complementary DNA in an orientation-selective manner. Fluorescence assay was used to examine the process of strand invasion of the target DNA duplex by the modified hairpin bisPNAs with the neutral teg linker and comparison of results of previous studies employing cationic linkers suggested the triplex formation to be a two-step process, with the preferred formation of HG bonds in the first step

Oligonucleotides with (N-thymin-1-ylacetyl)-1-arylserinol backbone: chiral acyclic analogs with restricted conformational flexibility

All four threo/erythro stereoisomers of 2(R/S)-(N-thymin-1-ylacetyl)-amino-1(R/S)-aryl-1,3-propanediol were synthesized from 2(R/S)-amino-1(R/S)-aryl-1,3-propanediol in 45-50% overall yield. The inversion of the C1 hydroxyl group in (1S, 2S), 4a, and (1R, 2R), 4d, was accomplished under Mitsunobu conditions to get (1R, 2S), 4c, and (1S, 2R), 4e isomers, respectively. Compounds 4a-f were individually converted into their respective amidite synthons 5a-f. All these stereoisomers were individually incorporated into oligonucleotides (ODNs) at pre-determined positions and various biophysical studies of their hybrids with complementary DNA were carried out. All the four stereoisomers when present at 3'/5' terminal positions in the ODNs were almost equally efficient in their binding capacity as the natural oligomers, with (1S, 2S) being marginally favored over other stereoisomers. The incorporation of these chiral acyclic nucleosides also protected the ODN against enzymatic degradation

N7-guanine as a C<SUP>+</SUP> mimic in hairpin aeg/aepPNA-DNA triplex: probing binding selectivity by UV-T<SUB>m</SUB> and kinetics by fluorescence-based strand-invasion assay

N7-substituted guanine (N7G) has been introduced into aminoethylglycyl bisPNA (7) as a C<SUP>+</SUP> mimic to achieve pH-independent triplex formation with complementary DNA sequences. The introduction of chiral, cationic aminoethylprolyl units with C<SUP>+</SUP> and C<SUP>+</SUP> mimic N7G in the backbone of bisPNAs (8, 9) influenced the recognition of complementary DNA in an orientation-selective manner. A simple fluorescence assay is developed to examine the process of strand invasion of target DNA duplex by these modified bisPNAs and comparative results of the study employing triplex forming polypyrimidine (C/T) (6, 8) and purine-pyrimidine (N7G/T) mixmer-bisPNAs (7, 9) are presented