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. © 2022 Elsevier B.V

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

Screening of <i>dsz</i> genes in different MTCC strains <i>Rhodococcus rhodochrous</i> (3552), <i>Artrobacter sulfureus</i> (3332), <i>Gordonia rubropertincta</i> (289) and <i>Rhodococcus erythropolis</i> (3951) enriched with DBT.

<p>The different lanes are showing the amplified products of different genes <i>dszA</i>, <i>dszB</i>, <i>dszC</i> and <i>dszD</i>.</p

List of organisms comparing their desulfurizing efficiency in percentage removal of sulfur from literature with reference to the present study.

<p>List of organisms comparing their desulfurizing efficiency in percentage removal of sulfur from literature with reference to the present study.</p

Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of Operon Array - Fig 4

<p>HPLC graph showing the retention time of (a) DBT and (b) 2-HBP. (c) The control DBT without microorganism also shows same retention time with respect to the standard DBT without any degradation.</p

Standardization of PCR product of <i>dsz</i> genes and 16s rRNA with different annealing temperatures.

<p>The PCR products with different annealing temperature were electrophoresed in agaraose gel against 100 bp DNA ladder.</p

Possible bacterial strains containing <i>dszABC</i> operon.

<p>Possible bacterial strains containing <i>dszABC</i> operon.</p

Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of Operon Array - Fig 5

<p>Chromatogram showing the DBT desulfurization after 10 days of growth with different MTCC strains (a) <i>Rhodococcus rhodochrous</i> (3552), (b) <i>Artrobacter sulfureus</i> (3332), (c) <i>Gordonia rubropertincta</i> (289) and (d) <i>Rhodococcus erythropolis</i> (3951).</p

4S-Pathway of biodesulfurization of dibenzothiophene (DBT).

<p>Four enzymes (DszA, DzsB, DszC and DszD) are involved in the pathway where the first three steps catalyzed by flavin mononucleotide reduced (FMNH₂)-dependent monooxygenases, those leading to DBT-sulfoxide (DBTO), DBT-dioxide (DBTO₂) and hydroxyphenyl benzenesulfinate (HPBS), respectively. The final desulfurization step to 2-hydroxybiphenyl (2-HBP) is catalyzed by desulfinase.</p