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Suman Das

Publications and source records attributed to Suman Das.

10 recordsLinked to original sources
PubMed2005

Protonated structures of naturally occurring deoxyribonucleic acids and their interaction with berberine.

Protonation-induced conformational changes in natural DNAs of diverse base composition under the influence of low pH, low temperature, and low ionic strength have been studied using various spectroscopic techniques. At pH3.40, 10mM [Na+], and at 5 degrees C, all natural DNAs irrespective of base composition adopted an unusual and stable conformation remarkably different from the canonical B-form conformation. This protonated conformation has been characterized to have unique absorption and circular dichroic spectral characteristics and exhibited cooperative thermal melting profiles with decreased thermal melting temperatures compared to their respective B-form counterparts. The nature of this protonated structure was further investigated by monitoring the interaction of the plant alkaloid, berberine that was previously shown from our laboratory to differentially bind to B-form and H(L)-form of poly[d(G-C)] [Bioorg. Med. Chem.2003, 11, 4861]. Binding of berberine to protonated conformation of natural DNAs resulted in intrinsic circular dichroic changes as well as generation of induced circular dichroic bands for the bound berberine molecule with opposite signs and magnitude compared with B-form structures. Nevertheless, the binding of the alkaloid to both the B and protonated forms was non-linear and non-cooperative as revealed from Scatchard plots derived from spectrophotometric titration data. Steady state fluorescence studies on the other hand showed remarkable increase of the rather weak intrinsic fluorescence of berberine on binding to the protonated structure compared to the B-form structure. Taken together, these results suggest that berberine can detect the formation of significant population of H(L)-form structures under the influence of protonation irrespective of heterogeneous base compositions in natural DNAs.

Animals↗
PubMed2005

Bone tissue engineering using polycaprolactone scaffolds fabricated via selective laser sintering.

Polycaprolactone (PCL) is a bioresorbable polymer with potential applications for bone and cartilage repair. In this work, porous PCL scaffolds were computationally designed and then fabricated via selective laser sintering (SLS), a rapid prototyping technique. The microstructure and mechanical properties of the fabricated scaffolds were assessed and compared to the designed porous architectures and computationally predicted properties. Scaffolds were then seeded with bone morphogenetic protein-7 (BMP-7) transduced fibroblasts and implanted subcutaneously to evaluate biological properties and to demonstrate tissue in-growth. The work done illustrates the ability to design and fabricate PCL scaffolds with porous architecture that have sufficient mechanical properties for bone tissue engineering applications using SLS. Compressive modulus and yield strength values ranged from 52 to 67 MPa and 2.0 to 3.2 Mpa, respectively, lying within the lower range of properties reported for human trabecular bone. Finite element analysis (FEA) results showed that mechanical properties of scaffold designs and of fabricated scaffolds can be computationally predicted. Histological evaluation and micro-computed tomography (microCT) analysis of implanted scaffolds showed that bone can be generated in vivo. Finally, to demonstrate the clinical application of this technology, we designed and fabricated a prototype mandibular condyle scaffold based on an actual pig condyle. The integration of scaffold computational design and free-form fabrication techniques presented here could prove highly useful for the construction of scaffolds that have anatomy specific exterior architecture derived from patient CT or MRI data and an interior porous architecture derived from computational design optimization.

Animals↗
PubMed2005

Binding of (MTR)2Zn2+ complex to chromatin: a comparison with (MTR)2Mg2+ complex.

Mithramycin (MTR), a member of aureolic group of anticancer antibiotic, binds reversibly to double stranded DNA via minor groove with (G.C) base specificity. It leads to inhibition of replication and transcription. Results from different laboratories have shown that at and above physiological pH, Mg2+ is an obligatory factor for the DNA binding and subsequent transcription inhibitory property of mithramycin. Zn2+ is another physiologically important bivalent cation. Its coordination property leads to its important role as a cofactor in different enzymes and nucleosomal DNA binding proteins. Characterization of the complex between mithramycin and Zn2+ using spectroscopic methods shows that the drug forms single type of complex with Zn2+ in the mole ratio of 2:1 in terms of antibiotic: Zn2+. DNA binding properties of the (MTR)2Zn2+ complex has been studied using calf thymus DNA, rat liver chromatin and nucleosome core. (MTR)2Zn2+ complex binds to calf thymus DNA with affinity higher than the corresponding dimer complex with Mg2+ ion. The presence of histone proteins in chromatin and nucleosome reduces the accessibility and hence binding potential of (MTR)2Zn2+ complex to nucleosomal DNA. We have also examined the effect of (MTR)2Zn2+ complex upon the stability of nucleosome core particle. The complex disassembles nucleosome structure leading to the release of nucleosomal DNA. Significance of the results to understand the molecular basis of the action of the drug in vivo is discussed.

Animals↗
PubMed2004

Effect of complex formation between Zn2+ ions and the anticancer drug mithramycin upon enzymatic activity of zinc(II)-dependent alcohol dehydrogenase.

Mithramycin (MTR), a member of the aureolic group of anticancer antibiotics, is a drug that supposedly acts via the inhibition of transcription. It binds to bivalent cations such as Mg(2+) and Zn(2+). In this paper, we report the association of MTR with Zn(2+), a biologically important bivalent cation whose coordination property leads to its important role as a cofactor in different enzymes and nucleosomal DNA-binding proteins. First, we have characterized the complex formation between MTR and Zn(2+) using spectroscopic methods. In the second part, we have examined the effect of the association of Zn(2+) with MTR on the enzymatic activity of a typical zinc(II)-dependent alcohol dehydrogenase (ADH) from yeast. Our data show that MTR forms a single complex with Zn(2+) in a mole ratio of 2:1 in terms of MTR:Zn(2+). We also observe a negative effect for the preincubation of ADH with MTR upon the enzymatic activity. These results indicate that MTR induced structural changes in the enzyme as a sequel to its complex formation with Zn(2+) present in the enzyme, thereby leading to a loss of enzymatic activity.

Alcohol Dehydrogenase↗
PubMed2004

N-terminal tail domains of core histones in nucleosome block the access of anticancer drugs, mithramycin and daunomycin, to the nucleosomal DNA.

Mithramycin (MTR) and daunomycin are two anticancer drugs that bind reversibly to double stranded DNA with (G.C) base specificity leading to inhibition of transcription. MTR is a groove binder of DNA in the presence of a divalent cation such as Mg(2+), while daunomycin intercalates in the double stranded DNA structure. In order to understand the mechanism of action of the two types of transcription inhibitor, namely, groove binder and intercalator, we have studied the effect of N-terminal tail domains in histone proteins of the nucleosome upon the association of both MTR and daunomycin with the nucleosome core particle, because the tails modulate the accessibility to nucleosome during gene expression. Using a combination of spectroscopic, thermodynamic and biochemical studies, we have shown that N-terminal intact and chopped core particles interact differently with the same ligand and the N-terminal tail domains of core histones in the nucleosome stand in the way of free access of these ligands to the nucleosomal DNA. Tryptic removal of N-terminal tail domains of core histones enhances the binding potential and accessibility of both MTR and daunomycin to nucleosomal DNA. They disassemble the nucleosome structure leading to a release of DNA, N-terminal chopped nucleosomes being more susceptible for disruption compared to N-terminal intact nucleosomes. The extent of these effects is more pronounced in case of the intercalator daunomycin. Thus, N-terminal tail domains protect the eukaryotic genome from external agents, such as anticancer drugs, and the degree of protection is dependent upon the mode of binding to DNA.

Animals↗
PubMed2003

Protonated forms of poly[d(G-C)] and poly(dG).poly(dC) and their interaction with berberine.

The pH -induced structural changes on the conformation of homo- and hetero-polymers of guanosine-citydine (G.C) sequences were investigated using spectrophotometric and circular dichroic techniques. At pH 3.40, 10 mM [Na(+)] and 10 degrees C both polynucleotides adopted a unique and stable structural conformation different from their respective B-form structures. The protonated hetero-polymer is established as left-handed structure with Hoogsteen base pairing (H(L)-form) while the homo-polymer favored Watson-Crick base pairing with different stacking arrangements from that of B-form structure as evident from thermal melting and circular dichroic studies. The interaction of berberine, a naturally occurring protoberberine group of plant alkaloid, with the protonated structures was studied using various biophysical techniques. Binding of berberine to the H(L)-form structure resulted in intrinsic circular dichroic changes and generation of extrinsic circular dichroic bands with opposite sign and magnitude compared to its B-form structure while with the homo-polymer of G.C no such reversal of extrinsic circular dichroic bands was seen indicating different stacking arrangement of berberine at the interaction site. Scatchard analysis of the binding data, however, indicated non-cooperative binding to both the protonated forms similar to that of their respective B-form structure. Fluorescence spectral studies, on the other hand, showed remarkable increase in the intrinsic fluorescence of the alkaloid in presence of the protonated forms compared to their respective B-form structure. These results suggest that berberine could be used as a probe to detect the alteration of structural handedness due to protonation and may potentiate its use in regulatory roles for biological functions.

Berberine↗
PubMed2003

Association of chromatin with anticancer antibiotics, mithramycin and chromomycin A3.

Mithramycin and chromomycin A(3) are two anticancer antibiotics, which inhibit protein biosynthesis via transcription inhibition. They bind reversibly to DNA with (G.C) base specificity. At and above physiological pH in the absence of DNA, they form two types of complexes with Mg(2+), complex I (1:1 in terms of antibiotic: Mg(2+)) and complex II (2:1 in terms of antibiotic: Mg(2+)). These are the DNA binding ligands. In vivo, the antibiotics interact with chromatin, a protein-DNA complex. In order to understand the mode of action of these antibiotics at molecular level, we have carried out spectroscopic, gel electrophoretic and UV melting studies of complex I of these antibiotics with rat liver chromatin, nucleosome core particle and DNA stripped of all chromosomal proteins. Analysis of the results has led us to propose that the antibiotic: Mg(2+) complex binds to both nucleosomal and linker DNA in native chromatin. Histone proteins reduce the binding potential and accessibility of the complexes to the minor groove of (G.C) rich regions of chromosomal DNA. The antibiotic: Mg(2+) complex stabilizes DNA duplex and histone- DNA contacts in chromatin fiber. It also leads to the aggregation of chromatin fibers. From a comparison of the association of the antibiotic: Mg(2+) complexes with different levels of chromatin structure and their effects upon the structure, we suggest that the sugar moieties of the antibiotics play a role in the binding process. Significance of these results to understand the molecular basis of the transcription inhibition potential of the antibiotics in eukaryotes is discussed.

Animals↗
PubMed2003

Spectroscopic and thermodynamic studies on the binding of sanguinarine and berberine to triple and double helical DNA and RNA structures.

A comparative study on the interaction of sanguinarine and berberine with DNA and RNA triplexes and their parent duplexes was performed, by using a combination of spectrophotometric, UV thermal melting, circular dichroic and thermodynamic techniques. Formation of the DNA and RNA triplexes was confirmed from UV-melting and circular dichroic measurements. The interaction process was characterized by increase of thermal melting temperature, perturbation in circular dichroic spectrum and the typical hypochromic and bathochromic effects in the absorption spectrum. Scatchard analysis indicated that both the alkaloids bound to the triplex and duplex structures in a non-cooperative manner and the binding was stronger to triplexes than to parent duplexes. Thermal melting studies further indicated that sanguinarine stabilized the Hoogsteen base paired third strand of both DNA and RNA triplexes more tightly compared to their Watson-Crick strands, while berberine stabilized the third strand only without affecting the Watson-Crick strand. However, sanguinarine stabilized the parent duplexes while no stabilization was observed with berberine under identical conditions. Circular dichroic studies were also consistent with the observation that perturbations of DNA and RNA triplexes were more compared to their parent duplexes in presence of the alkaloids. Thermodynamic data revealed that binding of sanguinarine and berberine to triplexes (T.AxT and U.AxU) and duplexes (A.T and A.U) showed negative enthalpy changes and positive entropy changes but that of sanguinarine to C.GxC(+) triplex and G.C duplex exhibited negative enthalpy and negative entropy changes. Taken together, these results suggest that both sanguinarine and berberine can bind and stabilize the DNA and RNA triplexes more strongly than their respective parent duplexes.

Alkaloids↗
PubMed2002

Influence of DNA structures on the conversion of sanguinarine alkanolamine form to iminium form.

Sanguinarine exhibits pH dependent structural equilibrium between iminium form (structure I) and alkanolamine form (structure II) with a pKa of 7.4 as revealed from spectrophotometric titration. The titration data show that the compound exists almost exclusively as structure I and structure II in the pH range 1 to 6 and 8.5 to 11, respectively. The interaction of structure I and structure II to several B-form natural and synthetic double and single stranded DNAs has been studied by spectrophotometric, spectrofluorimetric and circular dichroic measurements in buffers of pH 5.2 and pH 10.4 where the physicochemical properties of DNA remain in B-form structure. The results show that structure I bind strongly to all B-form DNA structures showing typical hypochromism and bathochromism of the alkaloid's absorption maximum, quenching of steady-state fluorescence intensity and perturbations in circular dichroic spectrum. The structure II does not bind to DNA, but in presence of large amount of DNA significant population of structure I is generated, which binds to DNA and forms a structure I-DNA intercalated complex. The nature and magnitude of the spectral pattern are very much dependent on the structure as well as base composition of each DNA. The generation of the structure I from structure II is significantly affected by increasing ionic strength of the medium. The conversion of structure II to structure I in presence of high concentration of DNA in solution is explained through formation of a binding equilibrium process between structure II and structure I-DNA intercalated complex.

Alkaloids↗