Plasmid DNA mediated transfer of the herpes simplex virus thymidine kinase gene to a new bromodeoxyuridine resistant variant of human primary lung carcinoma cells

A human primary lung carcinoma cell line (HPL-R1) established from the tumor biopsy of a lung cancer patient, lacking in cytochrome P1-450 [aryl hydrocarbon (benzo[a]pyrene) hydroxylase (AHH)], was cloned and used to obtain variants deficient in the expression of thymidine-kinase via treatment with 5-bromo-2'-deoxyuridine, and selection for drug resistance phenotype. The variant cell line, precharacterized for thymidine kinase negative phenotype, was transfected with the thymidine kinase gene bearing p R-tk and px1-tk plasmids. Transfections from both the plasmids, demonstrated a frequency of 5.5 X 10(-5). The transfectants showed a 76-100% retention of the transferred phenotype. These data suggest that transfection in variant human cells can approach significant levels of stability observed with rodent cell recipients.

DNA photocleavage and anticancer activity of terpyridine copper(II) complexes having phenanthroline bases

Copper(II) complexes Cu(ph-tpy)(B)](ClO4) (1-3), where ph-tpy is (4'-phenyl)-2,2':6',2 `'-terpyridine and B is N,N-donor phenanthroline base, viz. 1,10-phenanthroline (phen, 1), dipyridoquinoxaline (dpq, 2), and dipyridophenazine (dppz, 3), were prepared and characterized from analytical and spectral data. Complex 1, characterized by X-ray crystallography, shows a distorted square-pyramidal (4 + 1) CuN5 coordination geometry having the tridentate ph-tpy ligand at the basal plane and bidentate phen bound to the axial-equatorial sites. The complexes display a d-d band near 650 nm in aqueous DMF. The complexes are avid binders to calf thymus DNA giving the binding order: 3 (dppz) > 2 (dpq) > 1 (phen). The dpq and dppz complexes show photo-induced DNA cleavage activity in red light via photo-redox pathway forming hydroxyl radicals. The cytotoxicity of the dppz complex 3 was studied by MTT assay in HeLa cancer cells. The IC50 values are 3.7 and 12.4 mu M in visible light of 400-700 nm and dark, respectively. (C) 2010 Elsevier Ltd. All rights reserved.

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

DNA Photocleavage and Cytotoxic Properties of Ferrocene Conjugates

Ferrocenyl conjugates 2-ferrocenylimidazophenanthroline (1) and 2-ferrocenylimidazophenanthrene (2) were prepared, characterized, and their photoinduced DNA cleavage and photocytotoxic activity were studied. 2-Phenylimidazophenanthroline (3) was used as a control species. Compound 2 was characterized by X-ray crystallography. The interaction of the compounds with double-stranded calf thymus DNA (CT DNA) was studied. The compounds show good binding affinity to CT DNA with K-b values of approximately 10(5) M-1. Thermal denaturation data suggest the groove binding nature of the compounds. The redox-active compounds show poor chemical nuclease activity in the presence of hydrogen peroxide and glutathione (GSH). Compound 1 exhibits significant DNA photocleavage activity in visible light of 476 and 532 nm. Compound 3 shows only moderate DNA cleavage activity. The positive effect of the ferrocenyl moiety is demonstrated by the DNA photocleavage data. Mechanistic investigations reveal the formation of superoxide as well as hydroxyl radicals as the active species. The photocytotoxicity of the compounds in HeLa cells was studied upon irradiation with visible light (400-700 nm). Compound 1 shows efficient photocytotoxic activity with an IC50 value of 13 mu M, while compounds 2 and 3 are less active with IC50 values of > 50 and 22 mu M, respectively.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Photocytotoxicity and DNA photocleavage activity of La(III) and Gd(III) complexes of phenanthroline bases

Lanthanide(II) complexes La(B)(acac)(3)] (1-3) and Gd(B)(acac)(3)] (4-6), where B is a N,N-donor phenanthroline base, viz., 1,10-phenanthroline (phen in 1, 4), dipyrido3,2-d:2',3'-f]quinoxaline (dpq in 2, 5) and dipyrido3,2-a:2',3'-c]phenazine (dppz in 3, 6), have been prepared and characterized. The Gd(111) complexes 4 6 are structurally characterized by single crystal X-ray crystallography. The complexes display GdO6N2 coordination with the ligands showing bidentate chelating mode of bonding. The complexes are non-electrolytic in aqueous DMF and exhibit ligand-centered absorption bands in the UV region. The dppz complexes show a band at 380 nm in DMF. The La(111) complexes are diamagnetic. The Gd(III) complexes are paramagnetic with magnetic moment that corresponds to seven unpaired electrons. The Complexes are avid binders to calf thymus DNA giving K-b values in the range of 4.7 x 10(4) 6.1 x 10(5) M-1 with a relative binding order: 3, 6 (dppz) > 2, 5 (dpq) > 1, 4 (phen). The binding data suggest DNA surface and/or groove binding nature of the complexes. The dpq and dppz complexes efficiently cleave SC DNA to its nicked circular form in UV-A light of 365 nm via formation of both singlet oxygen (O-1(2)) and hydroxyl radical (HO center dot) species. The dppz complexes 3 and 6 exhibit significant PDT effect in He La cervical cancer cells giving respective IC50 value of 460(+/- 50) and 530(+/- 30) nM in UV-A light of 365 rim, and are essentially non-toxic in dark with an IC50 value of >100 mu M. The dppz ligand alone is cytotoxic in dark and UV-A light. A significant decrease in the dark toxicity of the dppz base is observed on binding to the Ln(III) ion while retaining its photocytotoxicity.

Dicopper(II) complexes showing DNA hydrolase activity and monomeric adduct formation with bis(4-nitrophenyl)phosphate

Ferromagnetic dicopper(II) complexes [Cu(2)(mu-O(2)CCH(3))(mu-OH)(L)(2)(mu-L(1))](PF(6))(2), where L = 1,10-phenanthroline (phen), L(1) = H(2)O in 1 and L = dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), L(1) = CH(3)CN in 2, are prepared and structurally characterized. Crystals of 1 and 2 belong to the monoclinic space group of P2(1)/n and P2(1)/m, respectively. The copper(II) centers display distorted square-pyramidal geometry having a phenanthroline base and two oxygen atoms of the bridging hydroxo and acetate group in the basal plane. The fifth coordination site has weak axially bound bridging solvent molecule H(2)O in 1 and CH(3)CN in 2. The Cu center dot center dot center dot Cu distances are 3.034 and 3.046 angstrom in 1 and 2, respectively. The complexes show efficient hydrolytic cleavage of supercoiled pUC19 DNA as evidenced from the mechanistic studies that include T4 DNA ligase experiments. The binuclear complexes form monomeric copper(II) adducts [Cu(L)(2)(BNPP)](PF(6)) (L = phen, 3; dpq, 4) with bis(4-nitrophenyl)phosphate (BNPP) as a model phosphodiester. The crystal structures of 3 and 4 reveal distorted trigonal bipyramidal geometry in which BNPP binds through the oxygen atom of the phosphate. The kinetic data of the DNA cleavage reactions of the binuclear complexes under pseudo- and true-Michaelis-Menten conditions indicate remarkable enhancement in the DNA hydrolysis rate in comparison to the control data. (C) 2011 Elsevier B.V. All rights reserved.

MODLEX: A Multi Objective Data Layout EXploration Framework for Embedded Systems-on-Chip

The memory subsystem is a major contributor to the performance, power, and area of complex SoCs used in feature rich multimedia products. Hence, memory architecture of the embedded DSP is complex and usually custom designed with multiple banks of single-ported or dual ported on-chip scratch pad memory and multiple banks of off-chip memory. Building software for such large complex memories with many of the software components as individually optimized software IPs is a big challenge. In order to obtain good performance and a reduction in memory stalls, the data buffers of the application need to be placed carefully in different types of memory. In this paper we present a unified framework (MODLEX) that combines different data layout optimizations to address the complex DSP memory architectures. Our method models the data layout problem as multi-objective genetic algorithm (GA) with performance and power being the objectives and presents a set of solution points which is attractive from a platform design viewpoint. While most of the work in the literature assumes that performance and power are non-conflicting objectives, our work demonstrates that there is significant trade-off (up to 70%) that is possible between power and performance.

Impact of metal on the DNA photocleavage activity and cytotoxicity of ferrocenyl terpyridine 3d metal complexes

Ferrocenyl terpyridine 3d metal complexes and their analogues, viz. [M(Fc-tpy)(2)](ClO(4))(2) (1-4), [Zn(Ph-tpy)(2)](ClO(4))(2) (5) and [Zn(Fc-dpa)(2)]X(2) (X = ClO(4), 6; PF6, 6a), where M = Fe(II) in 1, Co(II) in 2, Cu(II) in 3 and Zn(II) in 4, Fc-tpy is 4'-ferrocenyl-2,2': 6', 2 `'-terpyridine, Ph-tpy is 4'-phenyl-2,2': 6', 2 `'-terpyridine and Fc-dpa is ferrocenyl-N,N-dipicolylmethanamine, are prepared and their DNA binding and photocleavage activity in visible light studied. Complexes 2, 4, 5 and 6a that are structurally characterized by X-ray crystallography show distorted octahedral geometry with the terpyridyl ligands binding to the metal in a meridional fashion, with Fc-dpa in 6a showing a facial binding mode. The Fc-tpy complexes display a charge transfer band in the visible region. The ferrocenyl (Fc) complexes show a quasi-reversible Fc(+)-Fc redox couple within 0.48 to 0.66 V vs. SCE in DMF-0.1 M TBAP. The DNA binding constants of the complexes are similar to 10(4) M(-1). Thermal denaturation and viscometric data suggest DNA surface binding through electrostatic interaction by the positively charged complexes. Barring the Cu(II) complex 3, the complexes do not show any chemical nuclease activity in the presence of glutathione. Complexes 1-4 exhibit significant plasmid DNA photocleavage activity in visible light via a photoredox pathway. Complex 5, without the Fc moiety, does not show any DNA photocleavage activity. The Zn(II) complex 4 shows a significant PDT effect in HeLa cancer cells giving an IC(50) value of 7.5 mu M in visible light, while being less toxic in the dark (IC(50) = 49 mu M).

Chimeras of Escherichia coli and Mycobacterium tuberculosis Single-Stranded DNA Binding Proteins: Characterization and Function in Escherichia coli

Single stranded DNA binding proteins (SSBs) are vital for the survival of organisms. Studies on SSBs from the prototype, Escherichia coli (EcoSSB) and, an important human pathogen, Mycobacterium tuberculosis (MtuSSB) had shown that despite significant variations in their quaternary structures, the DNA binding and oligomerization properties of the two are similar. Here, we used the X-ray crystal structure data of the two SSBs to design a series of chimeric proteins (m beta 1, m beta 1'beta 2, m beta 1-beta 5, m beta 1-beta 6 and m beta 4-beta 5) by transplanting beta 1, beta 1'beta 2, beta 1-beta 5, beta 1-beta 6 and beta 4-beta 5 regions, respectively of the N-terminal (DNA binding) domain of MtuSSB for the corresponding sequences in EcoSSB. In addition, m beta 1'beta 2(ESWR) SSB was generated by mutating the MtuSSB specific `PRIY' sequence in the beta 2 strand of m beta 1'beta 2 SSB to EcoSSB specific `ESWR' sequence. Biochemical characterization revealed that except for m beta 1 SSB, all chimeras and a control construct lacking the C-terminal domain (Delta C SSB) bound DNA in modes corresponding to limited and unlimited modes of binding. However, the DNA on MtuSSB may follow a different path than the EcoSSB. Structural probing by protease digestion revealed that unlike other SSBs used, m beta 1 SSB was also hypersensitive to chymotrypsin treatment. Further, to check for their biological activities, we developed a sensitive assay, and observed that m beta 1-beta 6, MtuSSB, m beta 1'beta 2 and m beta 1-beta 5 SSBs complemented E. coli Delta ssb in a dose dependent manner. Complementation by the m beta 1-beta 5 SSB was poor. In contrast, m beta 1'beta 2(ESWR) SSB complemented E. coli as well as EcoSSB. The inefficiently functioning SSBs resulted in an elongated cell/filamentation phenotype of E. coli. Taken together, our observations suggest that specific interactions within the DNA binding domain of the homotetrameric SSBs are crucial for their biological function.

Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps 1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA protein interactions under the same set of conditions.

Testing concordance in species boundaries using acoustic, morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea, Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species-specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency.

Photo-induced DNA cleavage activity and remarkable photocytotoxicity of lanthanide(III) complexes of a polypyridyl ligand

Lanthanide(III) complexes [Ln(pyphen)(acac)(2)(NO3)] (1, 2), [Ln(pydppz)(acac)(2)(NO3)] (3, 4) and [La(pydppz)(anacac)(2)(NO3)] (5), where Ln is La(III) (in 1, 3, 5) and Gd(III) (in 2, 4), pyphen is 6-(2-pyridyl)-1,10-phenanthroline, pydppz is 6-(2-pyridyl)-dipyrido[3,2-a:2',3'-c] phenazine, anacac is anthracenylacetylacetonate and acac is acetylacetonate, were prepared, characterized and their DNA photocleavage activity and photocytotoxicity studied. The crystal structure of complex 2 displays a GdO6N3 coordination. The pydppz complexes 3-5 show an electronic spectral band at similar to 390 nm in DMF. The La(III) complexes are diamagnetic, while the Gd(III) complexes are paramagnetic with seven unpaired electrons. The molar conductivity data suggest 1 : 1 electrolytic nature of the complexes in aqueous DMF. They are avid binders to calf thymus DNA giving K-b in the range of 5.4 10(4)-1.2 x 10(6) M-1. Complexes 3-5 efficiently cleave supercoiled DNA to its nicked circular form in UV-A light of 365 nm via formation of singlet oxygen (O-1(2)) and hydroxyl radical (HO center dot) species. Complexes 3-5 also exhibit significant photocytotoxic effect in HeLa cancer cells giving respective IC50 value of 0.16(+/- 0.01), 0.15(+/- 0.01) and 0.26 +/-(0.02) mu M in UV-A light of 365 nm, while they are less toxic in dark with an IC50 value of >3 mu M. The presence of an additional pyridyl group makes the pydppz complexes more photocytotoxic than their dppz analogues. FACS analysis of the HeLa cells treated with complex 4 shows apoptosis as the major pathway of cell death. Nuclear localization of complex 5 having an anthracenyl moiety as a fluorophore is evidenced from the confocal microscopic studies.

Synthesis, X-ray crystal structure, DNA binding, antioxidant and cytotoxicity studies of Ni(II) and Pd(II) thiosemicarbazone complexes

New complexes, [Ni(HL)(PPh3)]Cl (1), [Pd(L)(PPh3)](2), and [Pd(L)(AsPh3)](3), were synthesized from the reactions of 4-chloro-5-methyl-salicylaldehyde thiosemicarbazone [H2L] with [NiCl2(PPh3)(2)], [PdCl2(PPh3)(2)] and [PdCl2(AsPh3)(2)]. They were characterized by IR, electronic, H-1-NMR spectral data. Further, the structures of the complexes have been determined by single crystal X-ray diffraction. While the thiosemicarbazone coordinated as binegative tridentate (ONS) in complexes 2 and 3, it is coordinated as mono negative tridentate (ONS) in 1. The interactions of the new complexes with calf thymus DNA was examined by absorption and emission spectra, and viscosity measurements. Moreover, the antioxidant properties of the new complexes have also been tested against DPPH radical in which complex 1 exhibited better activity than that of the other two complexes 2 and 3. The in vitro cytotoxicity of complexes 1-3 against A549 and HepG2 cell lines was assayed, and the new complexes exhibited higher cytotoxic activity with lower IC50 values indicating their efficiency in killing the cancer cells even at very low concentrations.