PNAs grafted with (α/γ, R/S)-aminomethylene pendants: regio and stereo specific effects on DNA binding and improved cell uptake.

PNAs grafted with cationic aminomethylene (am) pendants on the backbone at the glycyl (α) or ethylenediamine (γ) segments show regio (α/γ) and stereochemistry (R/S) dependent binding with complementary DNA. These are efficiently taken up by cells, with γ(S-am) aeg-PNA being the best in all properties.

Lived spaces in history: a study in human geography in the context of Sangam texts.

There has been considerable research work on early South India, particularly early Tamilakam, using archaeological, epigraphical and literary sources. Earlier, studies on early Tamilakam was almost exclusively based on the early Tamil texts, called as heroic or bardic poetry. However, a wealth of material has been generated by archaeological exploration, that have unearthed a mass of material from paleolithic, mesolithic, neolithic and the iron age megalithic, bordering on the early historic ages. A number of Tamil Brahmi label inscriptions have also been discovered. However, the largest number of archaeological finds have been megalithic burial sites and habitation sites are only in the process of being discovered. There are also difficulties in corroborating archaeological and epigraphic material with the enormous corpus of early Tamil texts. As a result, there is a tendency to dismiss the early Tamil texts as not conducive to historical analysis. The present article argues that we will still be able to use the material of the early Tamil texts using the tools provided by human geography, and suggests a methodology for making use of the literary material for further explorations in the early history of Tamilakam.

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 SATB1's 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.

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.

Efficacy of piperonyl butoxide (PBO) as a synergist with deltamethrin on five species of mosquitoes.

Development of insecticide resistance has been a challenging problem for a long time and new solutions are yet to emerge. In this regard, the use of synergist with the insecticide is thought to play a key role in reducing the resistance levels. Present study demonstrates the efficacy of PBO with deltamethrin against the field collected mosquito larvae of five species of Aedes, Anopheles and Culexfrom in and around Mysore.

Pyrethroid susceptibility & enzyme activity in two malaria vectors, Anopheles stephensi (Liston) &. A. culicifacies (Giles) from Mysore, India.

BACKGROUND & OBJECTIVES: Anopheles stephensi and A. culicifacies are the two major vectors of malaria in Karnataka. These mosquito populations are continuously being exposed directly or indirectly to different insecticides including the most effective pyrethroids. Therefore, there is a threat of insecticide resistance development. We subjected these vectors to larval bioassay using two popular pyrethroids viz deltamethrin and permethrin. An attempt was also made to correlate the activities of certain detoxifying enzymes such as A- esterase, B-esterase, glutathione-S transferase (GST) and glucose-6-phosphate dehydrogenase (G6PD) with the tolerance levels of the two vectors. METHODS: Larval bioassay was carried out following the standard WHO procedure on field-collected larvae. The LC50 and LC90 values were calculated following Probit analysis. Biochemical estimations were done with a U V spectrophotometer and the isozyme studies employing native polyacrylamide gel electrophoresis (PAGE). RESULTS: The results of the larval bioassay revealed that A. stephensi has more tolerance to deltamethrin than A. culicifacies and vice versa for permethrin. Biochemical estimations revealed significantly (P < 0.05) higher levels of A-esterase and GST activity in A. stephensi whereas A. culicifacies showed significantly higher (P < 0.05) levels of B-esterase and G6PD activity. The total larval protein assayed was found to be more (P < 0.05) in A. stephensi. The isozyme profiles also revealed difference in mobility, intensity and the number of bands. INTERPRETATION & CONCLUSION: As these malaria vectors are exposed to different kinds of insecticides, they develop increased enzyme activities to overcome the insecticide pressure. This has enhanced the tolerance level against the pyrethroids tested. Thus, A. stephensi was found to be tolerant to deltamethrin depicting a higher activity of A-esterase and GST enzymes, whereas the higher activity of B-esterase and G6PD has resulted in the development of tolerance to permethrin in A. culicifacies.

Structural changes enhance the activity of Chainia xylanase in low urea concentrations.

Low concentrations of urea (1.2 M) stimulated the activity of endo-xylanase from Chainia by 30%. Subtle structural changes in the monomeric protein were reflected in the secondary and tertiary structure of the enzyme as monitored by fluorescence and circular dichroism. Changes in lambda(max) of emission, the fluorescence intensity and the Stern-Volmer quenching constants for acrylamide, measured in the presence of urea, indicated changes in the microenvironment of the Trp residues, suggesting alterations in tertiary structure. The ellipticity changes at 220 nm and Selcon analysis reflected changes in the content of beta-sheet while both the near- and far-UV CD spectra indicated alterations in the secondary and tertiary structure of the protein in presence of urea. The dissociation constant values (K(d)) show very little change in the affinity of the enzyme for the substrate while the k(cat) values suggest enhanced turnover of the substrate in presence of urea. We suggest that low urea concentrations perturb the conformational state of xylanase leading to an open and a more flexible structure, resulting in enhanced catalytic rates.

Role of esterases and monooxygenase in the deltamethrin resistance in Anopheles stephensi Giles (1908), at Mysore.

Field collected An. stephensi larvae were colonized in the laboratory for 15 generations and acclimatized. An isofemale line was raised from this colony and the larvae were subjected to continuous deltamethrin selection pressure. LC50 and LC90 values were calculated at every generation. The values indicated that at the end of seventh generation the larvae have developed 87 fold tolerance in terms of LC50 value compared with the first generation. The reason for this kind of resistance was analyzed on the basis of differential activity of A-esterase, B-esterase, glutathione s-transferase (GST) and glucose 6-phosphate dehydrogenase (G6PD). A significant correlation (P < 0.05) was observed with B-esterase and G6PD activity with the rise in the LC50 and LC90 values. However no significant rise were observed in the other enzymes tested such as A-esterase and GST. The isozyme analysis of the A-esterase and B-esterase using polyacrylamide gel electrophoresis (PAGE) have shown differential profiles.

Engineering preferences of hairpin PNA binding to complementary DNA: effect of N7G in aeg/aep PNA backbone.

AegPNA and aepPNA monomeric units bearing the N7-guanine nucleobase as a substitute for C+ have been demonstrated to bind to a GC base-pair of a duplex in a pH-independent manner when placed in the third strand. The aepPNA backbone exerts a preference for binding in the antiparallel Hoogsteen mode over the parallel Hoogsteen mode.

Synthesis and evaluation of prolyl carbamate nucleic acids (PrCNA).

Carbamate linked prolyl nucleic acids are obtained in high yield and purity under mild conditions in solution and solid phase. p-Nitrophenylchloroformate is used as the activating reagent for alcohol. Homooligomers of PrCNA do not bind to DNA. The introduction of this modification in PNA sequences destabilizes the triplexes, inspite of enhancement in the base stacking.

Constrained flexibility in PNA: DNA binding studies with bridged aminopropylglycyl PNA.

Introduction of methylene bridges in aegPNA and apgPNA molecules give rise to cyclic five and six membered ring structures. Synthesis of a new six membered cyclic PNA monomer, aminopipecolyl PNA (pipPNA) is reported. Incorporation of pipPNA into PNA oligomers and comparative binding with target DNA sequences is studied.

Deltamethrin tolerance & associated cross resistance in Aedes aegypti from Mysore.

BACKGROUND & OBJECTIVES: The indiscriminate use of insecticides in public health and agriculture has led to the development of resistance to these insecticides in the vector mosquitoes. To understand the development of resistance to synthetic pyrethroids, selection studies on Aedes aegypti were done at Mysore. METHODS: Ae. aegypti collected from the field were subjected to selection experiment with deltamethrin for 16 generations in the laboratory. Cross resistance test was conducted against permethrin and fenvalerate. RESULTS: Tolerance level was found to increase by 333.83 folds in terms of its LC50 values. Cross resistance of this deltamethrin selected line was tested against permethrin and fenvalerate. The results show that the selected line has developed cross resistance as much as 5.19 and 5.92 folds respectively against permethrin and fenvalerate. INTERPRETATION & CONCLUSIONS: The findings show a continuous elevation in tolerance in Ae. aegypti with increase in deltamethrin selection pressure, and development of cross resistance to other insecticides of the same class. The natural or developed tolerance has its implications in the control of these mosquitoes.

Pyrrolidyl polyamines: branched, chiral polyamine analogues that stabilize DNA duplexes and triplexes.

[figure: see text] Pyrrolidyl polyamines (III-VI) are conformationally restricted, chiral analogues of linear spermine elaborated by the addition of aminopropyl chains to yield branched diastereomers. It is demonstrated that in concentrations as low as 0.01 mM, these compounds remarkably stabilize DNA duplexes and triplexes through strong electrostatic interactions. The synthesized compounds are potential dendrons with a chiral pyrrolidine core, and such molecules may have potential as DNA delivery and transfection agents.

Cyanurate mimics of hydrogen-bonding patterns of nucleic bases: crystal structure of a 1:1 molecular complex of 9-ethyladenine and N-methylcyanuric acid.

[figure: see text] 9-Ethyladenine forms a unique molecular complex with N-methylcyanuric acid consisting of homomeric and heteromeric hydrogen-bonding patterns. Also, the homomeric hydrogen bond pattern is different than that observed in its pure crystal structures.

Solid state NMR of a molecular self-assembly: multinuclear approach to the cyanuric acid-melamine system.

[see structure]. Trinuclear MAS NMR, involving naturally abundant (13C, 15N) and easily deuterated (2H) nuclei, is shown to offer newer opportunities to study molecular self-assembly in noncrystalline supramolecular systems.

Pyrrolidine nucleic acids: DNA/PNA oligomers with 2-hydroxy/aminomethyl- 4-(thymin-1-yl)pyrrolidine-N-acetic acid.

Synthesis of pyrrolidine-based chiral positively charged DNA analogues is reported. The synthesis of (2S,4S) and (2R,4R) thymin-1-ylpyrrolidine-N-acetic acid, its site specific incorporation in PNA:DNA chimera and PNA, and the study of their binding properties with complementary DNA/RNA sequences is presented.

Aminoethylprolyl (aep) PNA: mixed purine/pyrimidine oligomers and binding orientation preferences for PNA:DNA duplex formation.

[structure in text] The synthesis of (2S,4S)- and (2R,4S)-aepPNA monomers of adenine, guanine, and cytosine (3-5) and their incorporation at appropriate positions into aegPNA sequence 7 leads to mixed aeg-aep backbone/mixed nucleobase PNAs 8-11. The thermal stabilities of the derived duplexes with DNA are found to be dependent on nucleobase and backbone stereochemistry.

Cyanuryl-PNA monomer: synthesis and crystal structure.

[structure: see text] The chemical synthesis and crystal structure of the peptide nucleic acid (PNA) monomer 11 having cyanuric acid as the nucleobase is reported. The crystal structure of 11 shows molecular tapes arising from continuous intermolecular dimeric hydrogen bonding, with successive tapes held by single hydrogen bonds in the backbone.

Recognition of 5-aminouracil (U(#)) in the central strand of a DNA triplex: orientation selective binding of different third strand bases.

A necessary feature of the natural base triads for triplex formation is the requirement of a purine (A or G) in the central position, since only these provide sets of two hydrogen bond donors/acceptors in the major groove of the double helix. Pyrimidine bases devoid of this feature have incompatible complementarity and lead to triplexes with lower stability. This paper demonstrates that 5-aminouracil (U#) (I), a pyrimidine nucleobase analogue of T in which 5-methyl is replaced by 5-amino group, with hydrogen bonding sites on both sides, is compatible in the central position of triplex triad X*U# x A, where X = A/G/C/T/2-aminopurine (AP), and * and x represent Hoogsteen and Watson-Crick hydrogen bonding patterns respectively. A novel recognition selectivity based on the orientation (parallel/antiparallel) of the third strand purines A, G or AP with A in the parallel motif (A(p)*U# x A), and G/AP in the antiparallel motif (G(ap)/AP(ap)*U# x A) is observed. Similarly for pyrimidines in the third strand, C is accepted only in a parallel mode (C(p)*U(#) x A). Significantly, T is recognised in both parallel and antiparallel modes (T(p)/T(ap)*U(#) x A), with the antiparallel mode being stable compared to the parallel one. The 'U(#)' triplexes are also more stable than the corresponding control 'T' triplexes. The results expand the lexicon of triplex triads with a recognition motif consisting of pyrimidine in the central strand.