Direct Measurement of the Rates and Barriers on Forward and Reverse Diffusions of Intramolecular Collision in Overhang Oligonucleotides

Abstract

The dynamics of end-to-interior (Type I) and end-to-end (Type II) collisions in a dangling overhang anchored on a double-stranded DNA (dsDNA) was studied by monitoring the fluorescence quenching of tetramethylrhodamine (TMR) by guanosine residues through combining photoinduced electron transfer (PET) with fluorescence correlation spectroscopy (FCS) at different temperatures. TMR and guanosine residues are separated by a double helix with dangling bases ranging from 2 to 16. By analyzing the FCS data, we obtained the forward and reverse intrachain diffusion rate constants and respective barriers. For both Type I and Type II collisions, the intrachain diffusion rates followed the scaling law of the Gaussian chain model. Especially, the reverse intrachain diffusion rate was insensitive to the base length of separation. Both the activation enthalpy and activation entropy of the forward and reverse diffusions were length independent. The comparison between Type I and Type II collisions shows that the collision rate of end-to-interior is slower than that of end-to-end. The phenomenon is further checked in detail by a series of dangling DNA with the same separation length but different tail lengths (Type III).

Universality in the Timescales of Internal Loop Formation in Unfolded Proteins and Single-Stranded Oligonucleotides

“…When the tail is longer than~35% of the loop length, the loop formation times become independent of the length of the tail. Such saturation in the tail length dependence has been anticipated by theory (46), observed in previous simulations (47,48) and demonstrated in a recent experimental study (45). In this long-tail limit, the loop length dependence of the IE loop formation time follows a power law of the form of Eq.…”

“…In an effort to better understand the dynamics of unstructured biopolymers, a number of groups have studied the dynamics of end-to-end collisions using both theoretical (2,(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37) and experimental (1,3,27,(38)(39)(40)(41)(42) approaches. In contrast, studies of the rate with which two internal positions in a chain collide, or a terminus collides with an internal position, remain limited (43)(44)(45)(46)(47)(48)(49)(50)(51). Here, we explore this specific dynamic property of an unfolded biopolymer via simulations, experiments, and theory.…”

Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation

“…The FCS experiments were conducted on a modified Nikon TE2000 microscopy as previously described (24). The samples were excited by a CW 532 nm laser (SUW Tech., China) with 300 μW of power.…”

Steady‐state and time‐resolved fluorescence of tetramethylrhodamine attached to DNA: correlation with DNA sequences

“…Novel fluorophores, such as quantum dots (6), lanthanide chelates (7), and transition metal-ligand complexes (8) have been introduced into fluorescence-based techniques due to narrow emission spectra or long fluorescent lifetime. However, taking the advantages of high quantum yield, photo-stability, easy synthesis and labeling, traditional organic dyes are still the preferred fluorescence probes (9)(10)(11)(12)(13). Among organic dyes commonly used, tetramethylrhodamine (TAMRA) is one of the most frequently used fluorescence probes.…”

“…Fluorescence quenching has been reported when TAMRA was labeled on DNA (11,14,15). However, it is difficult to characterize the quenching effect as the interactions between TAMRA and DNA often display sequence-dependent properties (16).…”