Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

Abstract

Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize RNA into relatively rigid structures, while flexible non-base-paired regions allow RNA to undergo conformational changes required for function. To advance our understanding of RNA folding and dynamics it is critical to know the flexibility of these un-base-paired regions and how it depends on counterions. Yet, information about nucleic acid polymer properties is mainly derived from studies of ssDNA. Here we measure the persistence lengths (l p ) of ssRNA. We observe valence and ionic strength-dependent differences in l p in a direct comparison between 40-mers of deoxythymidylate (dT 40 ) and uridylate (rU 40 ) measured using the powerful combination of SAXS and smFRET. We also show that nucleic acid flexibility is influenced by local environment (an adjoining double helix). Our results illustrate the complex interplay between conformation and ion environment that modulates nucleic acid function in vivo.single molecule FRET | small angle X-ray scattering | worm-like chain | ion-nucleic acid interactions N ucleic acids in the cell are dynamic and undergo structural changes as they transmit and process genetic information. Dynamic processes related to biological function (e.g., transcription for DNA and recognition and folding for RNA) involve nonbase-paired regions that confer flexibility to the overall structure. For RNAs like riboswitches that exchange between multiple structures in equilibrium (1), conformational disorder is often an intrinsic property of the molecule and important for biological function. Even relatively stable molecules like catalytic introns and transfer RNA must pass through a disordered phase while folding. Thus, progress toward a mechanistic understanding of RNA folding and dynamics will require detailed knowledge of nucleic acid chain flexibility and its dependence on base content, solution conditions, and molecular context.In light of its importance to biology, it is surprising that RNA flexibility has not been studied in as much detail as DNA flexibility. Despite the chemical similarity of the RNA and DNA backbone, there is ample evidence from X-ray crystallography that the identity of the sugar (ribose vs. deoxy-ribose) affects backbone conformations (2). However, researchers have used the properties of DNA to understand RNA folding (3) because corresponding information for RNA was lacking. This difficulty motivates our present efforts to measure and directly compare the flexibilities of single-stranded nucleic acids (ssRNA and ssDNA).In the cell, RNA and DNA interact with cations that screen the negatively charged phosphate backbone. Both diffuse and specifically bound ions are important for RNA folding (4), and divalent ions are almost always required to stabilize RNA tertiary structures (5-8). A full mechanistic description of these ion effects is complicated by the fact that ions can interact with RNA differently during various stages of folding (9, ...

Activation of PKR by short stem–loop RNAs containing single-stranded arms

“…For both ppp-15-15-15 and ppp-0-15-0, which lacks single-stranded tails, the binding affinities decrease strongly in AU60/5 Mg (Supplemental Table S4). This observation is consistent with previous studies indicating that Mg 2+ is ∼100-fold more efficient at charge screening for RNAs compared to monovalent cations (Bizarro et al 2012;Chen et al 2012). As indicated by a similar reduction in the maximum RP 2 for the two RNAs, there are no specific Mg 2+ effects conferred by the single-stranded tails.…”

Enhancing miRNAs Capture on Polydimethylsiloxane Surface with Nanostructuration

“…The estimated length of persistence of a single-chain nucleic acid having similar number of nucleotides of miRNA-21 (which has 22 ntd), was of 0.4-0.7 nm [34,35]. Based on miRNA molecules dimensions, we attempted to fabricate a nano-hole pattern of about 5 nm in depth to obtain both improved surface to volume ratio and a size range similar to the tested molecules.…”

Correlation Force Spectroscopy for Single Molecule Measurements

“…ssDNA is an essential intermediate in many DNA metabolic processes such as replication, recombination, repair, and transcription, and it is specifically recognized by many DNA-binding proteins, and thus its behavior is of growing interest to the scientific community [124][125][126][127][128][129][130][131][132][133].…”

“…Thus, the current work addresses the important area of short, heteropolymeric ssDNA. Most previous work on heteropolymeric ssDNA utilized spectroscopic techniques such as Förster resonance energy transfer (FRET) or scattering techniques small angle X-ray scattering (SAXS) [51,133,134,136].…”

“…For example, the Worm-like Chain (WLC) model of polymer elasticity has been successful in describing the properties of nucleic acids and polypeptides [50][51][52]. The force required to extend a polymer chain in the WLC model was given as equation (3.1) [49] [51,135], valence [133], and number of nucleotides [135,137]. Other recent attempts to measure p l of ssDNA include transient electric birefringence (TEB) [135], AFM imaging [138], and Monte Carlo simulation [139,140].…”