Krishna N. Ganesh

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.

Sensitive dependence of the hydrogen-bonded assemblies in cyanuric acid–4,4′-bipyridyl adducts on the solvent and the structure of the parent acid

Abstract Cyanuric acid (CA) forms a 2:1 hydrogen-bonded adduct with 4,4′-bipyridyl (BP) when co-crystallized from a methanol solution and a 1:1 adduct from an aqueous solution. The sheet structure of the 2:1 adduct involves cyclic hydrogen bonds between the amide units of adjacent CA molecules and N–H⋯N bonds between CA and BP. The 1:1 adduct crystallized from water has a chain structure with single N–H⋯O hydrogen bonds between the adjacent CA molecules. The structures of these hydrogen-bonded assemblies bear a close resemblance to the structures of CA crystallized from the corresponding solvents. N-methylcyanuric acid (MCA) forms a chain structure with single N–H⋯O bonds between the adjacent MCA molecules. The 1:1 hydrogen-bonded adduct of MCA with BP, crystallized from methanol or water solution, retains the chain structure. The structural sensitivity of the hydrogen-bonded assemblies to the solvent of crystallization and the relation between the supramolecular assembly of the adduct and the parent structure of CA are noteworthy.

PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1

To better understand DNA recognition and transcription activity by SATB1, the T-lineage-enriched chromatin organizer and transcription factor, we have determined its optimal DNA-binding sequence by random oligonucleotide selection. The consensus SATB1-binding sequence (CSBS) comprises a palindromic sequence in which two identical AT-rich half-sites are arranged as inverted repeats flanking a central cytosine or guanine. Strikingly, the CSBS half-site is identical to the conserved element ‘TAATA’ bound by the known homeodomains (HDs). Furthermore, we show that the high-affinity binding of SATB1 to DNA is dimerization-dependent and the HD also binds in similar fashion. Binding studies using HD-lacking SATB1 and binding target with increased spacer between the two half-sites led us to propose a model for SATB1–DNA complex in which the HDs bind in an antiparallel fashion to the palindromic consensus element via minor groove, bridged by the PDZ-like dimerization domain. CSBS-driven in vivo reporter analysis indicated that SATB1 acts as a repressor upon binding to the CSBS and most of its derivatives and the extent of repression is proportional to SATB1s binding affinity to these sequences. These studies provide mechanistic insights into the mode of DNA binding and its effect on the regulation of transcription by SATB1.

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.

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 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.

Aminomethylene Peptide Nucleic Acid (am-PNA): Synthesis, Regio-/Stereospecific DNA Binding, And Differential Cell Uptake of (α/γ,R/S)am-PNA Analogues

Inherently chiral, cationic am-PNAs having pendant aminomethylene groups at α(R/S) or γ(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 γ(S)-am PNA superior to α(R/S)-am PNAs and α(R)-am PNA better than the α(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 HeLa cells, and exhibit low toxicity to cells.

Water-induced switching of β-structure to polyproline II conformation in the 4S-aminoproline polypeptide via H-bond rearrangement.

4S-Aminoproline polypeptide 2 forms unusual β-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 β-structure is attributed to competitive pH-dependent (4-NH(3)(+)/NH(2)) stereoelectronic effect (4R vs 4S) and the overriding importance of stereospecific intra/intermolecular H-bonding in (2,4)-cis-4S-aminoproline in contrast to (2,4)-trans-4R-aminoproline oligomers.

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.

Enantioselective enzymatic approach to (+)- and (−)-2-acetoxy/hydroxycyclopentanones

Abstract A new practical enzymatic approach to (+)- and (−)-2-acetoxy/hydroxycyclopentanones with 96–98% ee has been described via enzymatic hydrolysis of the meso-diacetate 2, Swern oxidation of the thus formed (±)-hydroxy acetates 3 and 4, followed by re-enzymatic resolution. Enantiomerically pure (+)- and (−)-2-hydroxycyclopentanones are in equilibrium with enediol 9 and slowly undergo racemisation, a process which could be arrested by protecting the hydroxyl group as the acetate.

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.