Vaijayanti A. Kumar

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.

Synthesis of Nα-(purinyl/pyrimidinyl acetyl)-4-aminoproline diastereomers with potential use in PNA synthesis☆

Abstract This paper describes an approach to introduce conformational constraint and chirality into the PNA backbone by bridging the ethylenediamine and glycine components of the same unit by a methylene group which leads to PNA based on 4-aminoprolyl backbone with chirality at C-4 and C-2. The synthesis and characterisation of all four diasteroisomers with thymine (T) as the sidechain nucleobase (3a-d) and the synthesis of one of the stereoisomer (2S, 4R) linked to each of the four nucleobases (10–13) are described. Using these monomeric units, two model dimers (17, 18) containing four chiral centres but differing in stereochemistry at only one site were prepared and CD data on these indicate considerable structural differences in base stacking induced by chiral backbone among these.

Chiral analogues of peptide nucleic acids: synthesis of 4-aminoprolyl nucleic acids and DNA complementation studies using UV/CD spectroscopy

This paper describes chemical synthesis of prolyl PNAs which are a class of conformationally constrained chiral PNA analogues. The monomers are derived from bridging the ethylenediamine and glycine components of the same unit which leads to PNA based on 4-aminoproline backbone with chirality at C-4 and C-2. The modified monomers corresponding to D-trans and L-trans prolyl-T have been incorporated into standard PNA chains, both at the N-terminus and in the interior to generate chiral PNAs. The complementation studies with DNA employing temperature dependent UV spectroscopy indicated that the chiral modifications in PNA:DNA duplexes imparted both stability and orientational preferences. CD spectral studies of chiral PNA:DNA duplexes suggest that the D-trans antiparallel duplexes have the B-DNA conformation while L-trans PNA:DNA duplexes show departure from B-DNA geometry. Thus, inclusion of even a single backbone constrained, distended chiral monomeric unit such as 4-aminoproline into an achiral PNA chain, either at the N-terminus or in the interior, leads to stabilization of the PNA:DNA hybrid. The linking of a polycation such as spermine at the C-terminus of chiral PNA further enhances the thermal stability of duplexes.

Highly Efficient (R-X-R)-Type Carbamates as Molecular Transporters for Cellular Delivery

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.

Chimeric (α-amino acid + nucleoside-β-amino acid)n peptide oligomers show sequence specific DNA/RNA recognition

An α/β-peptide backbone oligonucleotide comprising natural α-amino acids alternating with a β-amino acid component derived from thymidine sequence specifically recognizes and binds to deoxy- and ribo-oligoadenylates in triplex mode.

Ferrocene-linked thymine/uracil conjugates: base pairing directed self-assembly and supramolecular packing.

Ferrocene-linked bis(nucleobase) (1a-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.

Ferrocene-bis(thymine/uracil) conjugates: base pairing directed, spacer dependent self-assembly and supramolecular packing.

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.

(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.

Oligonucleotides with (N-thymin-1-ylacetyl) 1-phenylserinol in backbone: Chiral acyclic analogues that form dna triplexes

Abstract The synthesis of oligonucleotides containing chiral acyclic 2(R/S)-(N-thymin-1-ylacetyl)-amino-1(R/S)-phenyl-1,3-propanediol unit in the backbone (l, RAr) is described. When used as third strand of a triplex with complementary natural duplex, the modified oligonucleotides form stable triplexes with triplex ↔ duplex transition Tm dependent on the number, position and stereochemistry of modification.

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

Abstract 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 (1 S , 2 S ), 4a , and (1 R , 2 R ), 4d , was accomplished under Mitsunobu conditions to get (1 R , 2 S ), 4c , and (1 S , 2 R ), 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 (1 S , 2 S ) being marginally favored over other stereoisomers. The incorporation of these chiral acyclic nucleosides also protected the ODN against enzymatic degradation.