Crowding-induced Cooperativity in DNA Surface Hybridization

Abstract

High density DNA brush is not only used to model cellular crowding, but also has a wide application in DNA-functionalized materials. Experiments have shown complicated cooperative hybridization/melting phenomena in these systems, raising the question that how molecular crowding influences DNA hybridization. In this work, a theoretical modeling including all possible inter and intramolecular interactions, as well as molecular details for different species, is proposed. We find that molecular crowding can lead to two distinct cooperative behaviours: negatively cooperative hybridization marked by a broader transition width, and positively cooperative hybridization with a sharper transition, well reconciling the experimental findings. Moreover, a phase transition as a result of positive cooperativity is also found. Our study provides new insights in crowding and compartmentation in cell, and has the potential value in controlling surface morphologies of DNA functionalized nano-particles.

Solid-Phase Nucleic Acid Sequence-Based Amplification and Length-Scale Effects during RNA Amplification

“…These are often referred to as crowding, confinement, or proximity phenomena. They have been studied in the context of oligonucleotide hybridization in microarrays and solid-phase detection platforms. − More recent work has addressed the additional complications introduced by solid-phase amplification. Kim et al, for example, used cone-shaped dendron molecules to define specific distances, varying from about 1 to 6 nm, between tethering sites on a surface and showed that the elongation of separated primers was more efficient than that on a fully saturated surface.…”

Fluorescence In Situ Hybridization of 16S rRNA in Escherichia coli Using Multiple Photo‐Cross‐Linkable Probes

“…From these results, the number of assistant probes is not essential, and it is necessary to position the optimum 14.7 � 3.1 56 A6,A7,A8 9.2 � 1.1 [a] Relative Cy3 fluorescence intensity is the value based on Cy3 intensity of E. coli stained by only probe D without photoirradiation assistant probe at the same time as the detection probe in order to break the higher-order structure. [36][37][38][39] As shown in Figure 3, the relative fluorescence intensity when using 8 types of assistant probes is 39.9, which is not much different from the highest relative fluorescence intensity of 35.5 when using 3 types of assistant probes. Therefore, it is important to design an optimal assistant probe for the detection of RNA that forms a higher-order structure.…”

“…In addition, an increase in Cy3 fluorescence intensity was confirmed in all the patterns when the assistant probe was added to the combination with the lowest fluorescence intensity. From these results, the number of assistant probes is not essential, and it is necessary to position the optimum assistant probe at the same time as the detection probe in order to break the higher‐order structure [36–39] . As shown in Figure 3, the relative fluorescence intensity when using 8 types of assistant probes is 39.9, which is not much different from the highest relative fluorescence intensity of 35.5 when using 3 types of assistant probes.…”

Assembling Nanoparticle Clusters by Kinetic Control Using Weakly Interacting DNA

“…Further, DNA-mediated assembly was confirmed through thermal denaturation of the A-L-B linkages where subsequent disassembly of the clusters was performed with temperature and monitored via UV-vis. [54][55][56][57][58] Figure S1 plots the Tm for each linker system which were determined to be 32°C, 48°C, 54°C and 58°C for L6-L15, respectively. We next compared the apparent assembly kinetics as monitored by SPR change.…”