Antagonistic effects of natural osmolyte mixtures and hydrostatic pressure on the conformational dynamics of a DNA hairpin probed at the single-molecule level

Abstract

Organisms are thriving in the deep sea at pressures of up to the 1 kbar level. To withstand such harsh conditions, they accumulate particular osmolyte mixtures to counteract the pressure stress imposed. We explored the combined effects of pressure and osmolyte mixtures known from deep sea organisms on the closed-to-open conformational transition of a DNA hairpin (Hp). To this end, single-molecule Förster resonance energy transfer (smFRET) experiments were carried out in an optimized high-pressure capillary optical cell. In the absence of osmolytes, pressure shifts the conformational equilibrium of the DNA Hp towards the open, unfolded state owing to a volume decrease of about -20 cm3 mol-1. We show that the deep-sea osmolyte mixture, largely composed of TMAO, is able to rescue the DNA Hp from unfolding even up to almost 1 kbar, which is supposed to be essentially due to a distinct excluded volume effect.

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

“…For DNA, elevated pressure induced the B/Z conformational change and affected stability of non‐canonical structures (G‐quadruplex and i‐motif) . Such changes were found to be strongly dependent on the sequence and solvent . Similar observations were reported for RNA .…”

Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study

“…The driving forces dictating pressure-induced conformational shifts are the release of packing defects or voids and changes in hydration (e.g. upon exposure of charged residues), resulting in an overall smaller volume of the system (1,8,9–17).…”

“…Even though HHP studies have become a common biophysical technique in studying the thermodynamics and kinetics of biomolecular systems, pressure studies on nucleic acids are still relatively scarce (9,12,14–21). In particular, the effect of cosolutes, such as salts, osmolytes and crowding agents mimicking intracellular conditions, on the folding landscape and structural dynamics of nucleic acids are still largely under research (17,18,21–24).…”

The Deep Sea Osmolyte TrimethylamineN‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex from Urea and Pressure Stress

“…The single‐molecule fluorescence resonance energy transfer (smFRET) technique as used herein allows to distinguish different folded conformations . Recently, we were also able to setup a HHP smFRET stage (Figure S1 in the Supporting Information) allowing us to reach pressures up to ∼2 kbar (200 MPa), covering the whole relevant pressure range on Earth . We used a DNA construct comprised of a duplex stem and a single stranded region containing the human telomeric repeats (Figure ), which was also previously used in ambient pressure smFRET studies …”

“…[23][24][25][26] Recently,w ew ere also able to setup aH HP smFRET stage ( Figure S1 in the Supporting Information) allowing us to reach pressures up tõ 2kbar (200 MPa), covering the whole relevant pressure range on Earth. [27,28] We used aD NA construct comprised of ad uplex stem and as ingle stranded region containing the human telomeric repeats ( Figure 1), which was also previously used in ambient pressure smFRET studies. [9,11,[29][30][31] High-resolution structural data indicated that the human telomeric oligonucleotide adopts ap arallel stranded propeller conformation in the presenceo fK + and an antiparallel basket structure in the presence of Na + .…”