Conformational Flexibility Influences Degree of Hydration of Nucleic Acid Hybrids

Abstract

Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes.

Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α

“…The G-quadruplexes formed by RNAs are generally more stable than those formed by equivalent DNA sequences (21–23). Our previous studies indicate that stabilities of G-quadruplexes are higher in the presence of high concentration of cosolute, which might mimic cell-like molecular crowding condition, and encapsulated conditions than in diluted solution (24,25), whereas canonical secondary structures are destabilized in the presence of cosolute, especially solutes decreasing water activity (26,27). In addition, we recently performed that RNA G-quadruplex formed in ORF of mRNA suppressed translation elongation in vitro and reduced protein expression in cells (28).…”

Molecular Crowding Inhibits U-Insertion/Deletion RNA Editing In Vitro: Consequences for the In Vivo Reaction

“…Similarly, the formation of DNA (and perhaps RNA) three-way junctions (TWJ) [25], [26], of G-quadruplex structures [27], [28] and of DNA triple helices [29] are favored in crowded solutions. Next to the excluded volume effect, hydration has been identified as a crucial factor for the stability of RNA molecules in crowded solutions with opposite effects on the stabilities of RNA tertiary and secondary structures [23], [30], [31]. Neutral cosolutes can stabilize the water release reaction of RNA 3D-folds while at the same time disfavor the water-uptake reaction of Watson-Crick base pairs [23].…”

Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription

“…We concluded that crowding conditions induced by the organelle-mimicking liposomes had no effect on structures or stabilities of canonical and non-canonical DNA structures. It has been reported that molecular crowding decreases the stability of a duplex and increases that of the G-quadruplex by decreasing water activity (19–22). The water activities of solution without liposome and with 2.0 mM IM, NM or ER liposomes were not significantly different ( a w = 0.993, where a w is water activity estimated by vapour pressure osmometry).…”

“…We extracted thermodynamic parameters from melting curves as described previously (19–22). The value of Δ G ° 25 (free energy change of the formation of a G-quadruplex at 25°C) for 1cG 3 increased from −3.1 to −1.2 kcal mol −1 when the concentration of POPC was increased from 0 to 2.0 mM (Table 2).…”

“…The formation of G-quadruplexes inhibits biological reactions, such as telomere elongation and transcription (17,18). To better predict whether G-quadruplexes form in cells, the structure and stability of the nucleic acids under conditions of molecular crowding induced by both non-interacting (19–22) and interacting (23) cosolutes have been studied. Formation of the G-quadruplexes is markedly facilitated by cosolutes (19).…”