Structural Alteration from Non-B to B-Form Could Reflect DNase I Hypersensitivity

Abstract

Preferential cleavage of active genes by DNase I has been correlated with a structurally altered conformation of DNA at the hypersensitive site in chromatin. To have a better understanding of the structural requirements for gene activation as probed by DNase I action, digestability by DNase I of synthetic polynucleotides having the ability to adopt B and non-B conformation (like Z-form) was studied which indicated a marked higher digestability of the B-form of DNA. Left handed Z form present within a natural sequence in supercoiled plasmid also showed marked resistance towards DNase I digestion. We show that alternating purine-pyrimidine sequences adopting Z-conformation exhibit DNAse I foot printing even in a protein free system. The logical deductions from the results indicate that 1) altered structure like Z-DNA is not a favourable substrate for DNase I, 2) both the ends of the alternating purine-pyrimidine insert showed hypersensitivity, 3) B-form with a minor groove of 12-13 A is a more favourable substrate for DNase I than an altered structure, 4) any structure of DNA deviating largely from B form with a capacity to flip over to the B-form are potential targets for the DNase I enzymic probes in naked DNA.

Effect of polyamine depletion on chromatin structure in U-87 MG human brain tumour cells

“…In certain polynucleotides, polyamines induce B-Z transitions, which may decrease the sensitivity of chromatin to DNAase I [8,28]. Furthermore, spermine shuts off the DNAase I digestion of poly(dG-me5dC) by inducing a B-Z transition in the polynucleotide (results not shown), but has little effect on the digestion of calf thymus DNA.…”

“…Both enzymes are sensitive to structural changes in DNA and prefer relaxed DNA to condensed DNA [25,26]. In addition, DNAase I is specific for right-handed B-DNA and does not digest left-handed Z-DNA [27,28].…”

The role of extracellular DNA in the formation, architecture, stability, and treatment of bacterial biofilms

“…For example, DNase will not likely work for DNA conformations other than B‐DNA. DNase treatments also are not likely to work against DNA in the Z‐form (Ramesh & Brahmachari, 1989). However, some groups still suggest that any type of DNase can disperse biofilms (Okshevsky et al, 2015).…”

Z-form extracellular DNA is a structural component of the bacterial biofilm matrix

“…DNA in the B-form adopts a right-handed, low energy configuration that is sensitive to nuclease degradation and is the most common DNA configuration under physiologic conditions (Bezanilla et al, 1994;Suck and Oefner, 1986). Conversely, Z-DNA has a left-handed configuration with distinct nucleotide geometry but preserves Watson-Crick base-pairing, is resistant to nuclease degradation (Ramesh and Brahmachari, 1989), and is not abundant intracellularly due to its high intrinsic energy state (Dumat et al, 2016;Ho et al, 1991;Kim et al, 2018). However, Z-DNA-forming sequences are involved in multiple intracellular transactions (Zavarykina et al, 2019;Shin et al, 2016;Zhou et al, 2009;Ray et al, 2013;Wang et al, 2006;van der Vorst et al, 2018).…”

“…Although no studies have provided evidence of non B-form DNA structures involved with biofilm stability (Kassinger and van Hoek, 2020), a recent publication does show the presence of B-form G-quadraplex structures that contribute to the structure of Pseudomonas aeruginosa biofilms (Seviour et al, 2021), thus highlighting the complex architectural eDNA structures of bacterial biofilms. Z-DNA is the most common conformation of DNA that is nuclease-resistant (Ramesh and Brahmachari, 1989;Thomas et al, 1985;Zhang et al, 2019). We thereby hypothesized that in mature bacterial biofilms, eDNA was in the Z-form.…”