Biophysical interaction between lanthanum chloride and (CG)n or (GC)n repeats: A reversible B-to-Z DNA transition.

The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)n and (GC)n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)6 DNA using millimolar concentration of trivalent lanthanide salt LaCl3. The controlled and reversible transition was seen in (CG)12, and (GC)12 DNA employing CD spectroscopy. While LaCl3 failed to induce B-Z transition in shorter oligonucleotides such as (CG)3 and (GC)3, a smooth B-Z transition was recorded for (CG)6, (CG)12 and (GC)12 sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)6 DNA in presence of LaCl3 and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl3-induced Z-DNA is irreversible which suggest a stronger binding of LaCl3 to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La3+ (of LaCl3) with d(CG)8.d(CG)8 is through the minor groove, wherein, 3 out of 11 La3+ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La3+ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl3-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl3 can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition.

Sequence-specific B-to-Z transition in self-assembled DNA: A biophysical and thermodynamic study.

The most remarkable conformational transition in nature is the B-to-Z transition of DNA which not only contributes for epigenetic regulation but also is exploited to create several advanced nanomaterials for sensing and nanomechanics. The present communication focuses on the intrinsic factors that control the La3+/Ce3+-induced B-to-Z transition in self-assembled branched DNA (bDNA) nanostructures. The transition is sensitive even to two nucleotide change in the loop length and overhang sequences. Predominantly, bDNA structures having 3 T loop length are more sensitive towards helical switching than the 5 T bearing structures. Particularly, bDNA US-17, US-19 and US-23 having 3 T in the loop are showing B-Z transition in presence of LaCl3. Interestingly, with 'GATC' overhangs both La3+/Ce3+-induced B-to-Z transition was noticed in bDNA structures US-21 and US-22 (having 3 T and 5 T in the loop, respectively). The lanthanide-induced B-Z transition in bDNA is reversed with treatment of EDTA. Isothermal titration calorimetry (ITC) experiments show that the binding mode of lanthanide salts to bDNA followed an entropically and enthalpically favorable process. Further, for the first time ITC data suggests the B-to-Z transition in bDNA is a cooperative shift from exothermic to endothermic.

Praseodymium promotes B-Z transition in self-assembled DNA nanostructures.

Millimolar concentrations of PrCl3 can induce sequence-specific B-Z transition in various-self-assembled branched DNA (bDNA) nanostructures. Competitive dye binding and thermal kinetics suggest that the phosphate backbone and grooves of bDNA are wrapped with Pr3+ for stabilizing the Z-bDNA. Application of EDTA can convert Z-DNA back to the B-form.

Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of Operon Array.

Since the sulfur specific cleavage is vital for the organic sulfur removal from fossil fuel, we explored potential bacterial strains of MTCC (Microbial Type Culture Collection) to desulfurize the Dibenzothiophene (DBT) through C-S bond cleavage (4-S pathway). MTCC strains Rhodococcus rhodochrous (3552), Arthrobacter sulfureus (3332), Gordonia rubropertincta (289), and Rhodococcus erythropolis (3951) capable of growing in 0.5 mM DBT were examined for their desulfurization ability. The presence of dsz genes as well as the metabolites was screened by polymerase chain reaction (PCR) and HPLC, respectively. All these strains showed > 99% DBT desulfurization with 10 days of incubation in minimal salt medium. From the HPLC analysis it was further revealed that these MTCC strains show differences in the end metabolites and desulfurize DBT differently following a variation in the regular 4-S pathway. These findings are also well corroborating with their respective organization of dszABC operons and their relative abundance. The above MTCC strains are capable of desulfurizing DBT efficiently and hence can be explored for biodesulfurization of petrochemicals and coal with an eco-friendly and energy economical process.

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice.

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices.

Cerium chloride stimulated controlled conversion of B-to-Z DNA in self-assembled nanostructures.

DNA adopts different conformation not only because of novel base pairs but also while interacting with inorganic or organic compounds. Self-assembled branched DNA (bDNA) structures or DNA origami that change conformation in response to environmental cues hold great promises in sensing and actuation at the nanoscale. Recently, the B-Z transition in DNA is being explored to design various nanomechanical devices. In this communication we have demonstrated that Cerium chloride binds to the phosphate backbone of self-assembled bDNA structure and induce B-to-Z transition at physiological concentration. The mechanism of controlled conversion from right-handed to left-handed has been assayed by various dye binding studies using CD and fluorescence spectroscopy. Three different bDNA structures have been identified to display B-Z transition. This approach provides a rapid and reversible means to change bDNA conformation, which can be used for dynamic and progressive control at the nanoscale.