Impact of Small Molecules on Intermolecular G-Quadruplex Formation

We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.

Download Full-text

Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level

European Biophysics Journal ◽

10.1007/s00249-010-0587-x ◽

2010 ◽

Vol 39 (9) ◽

pp. 1343-1350 ◽

Cited By ~ 17

Author(s):

A. C. Krüger ◽

M. K. Raarup ◽

M. M. Nielsen ◽

M. Kristensen ◽

F. Besenbacher ◽

...

Keyword(s):

Single Molecule ◽

Hnrnp A1 ◽

Single Molecule Level ◽

G Quadruplex

Download Full-text

G-Quadruplex-Helicase Interactions and the Impact of Small Molecules

Biophysical Journal ◽

10.1016/j.bpj.2018.11.257 ◽

2019 ◽

Vol 116 (3) ◽

pp. 39a

Author(s):

Parastoo Maleki ◽

Hamza Balci

Keyword(s):

Small Molecules ◽

G Quadruplex ◽

The Impact

Download Full-text

Single molecule vs. large area design of molecular electronic devices incorporating an efficient 2-aminepyridine double anchoring group

Nanoscale ◽

10.1039/c9nr05662a ◽

2019 ◽

Vol 11 (34) ◽

pp. 15871-15880 ◽

Cited By ~ 4

Author(s):

L. Herrer ◽

A. Ismael ◽

S. Martín ◽

D. C. Milan ◽

J. L. Serrano ◽

...

Keyword(s):

Electrical Properties ◽

Single Molecule ◽

Electronic Devices ◽

Large Area ◽

Molecular Electronic ◽

Single Molecule Level ◽

Order Of Magnitude ◽

Anchoring Group ◽

Molecular Skeleton ◽

Molecular Electronic Devices

The electrical properties of a bidentate molecule in both large area devices and at the single molecule level have been explored and exhibit a conductance one order of magnitude higher than that of monodentate materials with same molecular skeleton.

Download Full-text

Single Molecule Studies of Physiologically Relevant Telomeric Tails Reveal POT1 Mechanism for Promoting G-quadruplex Unfolding

Journal of Biological Chemistry ◽

10.1074/jbc.m110.205641 ◽

2010 ◽

Vol 286 (9) ◽

pp. 7479-7489 ◽

Cited By ~ 54

Author(s):

Hong Wang ◽

Gerald J. Nora ◽

Harshad Ghodke ◽

Patricia L. Opresko

Keyword(s):

Single Molecule ◽

G Quadruplex ◽

Single Molecule Studies

Download Full-text

The impact of 8-aryl-and 8-heteroaryl-2'-deoxyguanosine derivatives on G-quadruplex formation

Nucleic Acids Symposium Series ◽

10.1093/nass/nrm020 ◽

2007 ◽

Vol 51 (1) ◽

pp. 39-40 ◽

Cited By ~ 3

Author(s):

V. Gubala ◽

M. d. C. Rivera-Sanchez ◽

G. Hobley ◽

J. M. Rivera

Keyword(s):

G Quadruplex ◽

Quadruplex Formation ◽

The Impact

Download Full-text

Nanopore microscope identifies RNA isoforms with structural colors

10.1101/2021.10.16.464631 ◽

2021 ◽

Author(s):

Filip N Boskovic ◽

Ulrich Felix Keyser

Keyword(s):

Single Molecule ◽

Three Dimensional ◽

Rna Structures ◽

Transcript Isoforms ◽

Single Molecule Level ◽

Structural Colors ◽

Rna Targets ◽

Dna Strands ◽

One Step ◽

Simultaneous Identification

Identifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers (IDs) with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colors. Structural colors consist of DNA structures, protein labels, native RNA structures, or a combination of all three. The sequence of structural colors of RNA IDs enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. Our Amplification-free RNA TargEt Multiplex Isoform Sensing (ARTEMIS) reveals structural arrangements in native transcripts in agreement with published variants. ARTEMIS discriminates circular and linear transcript isoforms in a one step, enzyme-free reaction in a complex human transcriptome using single-molecule readout.

Download Full-text

Relevance of single cell and single molecule studies at different biological and physical length scales

10.7287/peerj.preprints.3261 ◽

2017 ◽

Author(s):

Wenfa Ng

Keyword(s):

Quantum Mechanics ◽

Single Cell ◽

Single Molecule ◽

Active Site ◽

Covalent Bond ◽

The Other ◽

Quantum Mechanical ◽

Microfluidic Channels ◽

Other Hand ◽

Single Molecule Studies

Scale transcends multiple levels of biological and physical organization, and is the critical factor that determines success of any scientific investigation. Specifically, the scale at which a question is posed plays a crucial role in influencing the type of experiments and apparatuses needed. Single cell and single molecule experiments came to the fore of experiment science due to its capability at addressing a fundamental problem in biology and physical science: does the same behavior in cells and molecules transcend different length and population scales? Thus far, single cell experiments could be achieved with trapping of single cell using optical tweezer traps and microfluidic channels. The same, however, is not true for single molecule studies, which remains in the realm of theoretical and simulation studies. Specifically, single molecule experiment remains at the hundreds to thousands of molecules level, where possible skew in the population of molecules sampled could provide a false depiction of molecular reality of a larger population. But, what do scientists learn from single cell and single molecule studies? Is it the uncovering of mysteries of the probabilistic behavior at the single entity level, guided by perhaps quantum mechanics? The answer is no for single cell studies, given that cellular decision making require the input of tens to hundreds of molecular sensors and effectors within a cell. Hence, single cell behavior is not random, but directed at a nutrient or concentration gradient or signaling source. On the other hand, enzymatic catalysis of a single molecule substrate with the active site involves a quantum mechanical crosstalk. Thus, reaction between the substrate molecule and the active site proceeds if suitable energy levels (i.e., quantum mechanical states) are found for both parties. Given that distribution of quantum mechanical states is probabilistic, stochasticity rules single molecule interaction such as a covalent bond formation reaction between reactant A and B. Thus, single cell and single molecule studies do hold relevance in biological and physical sciences research if the correct experiment tool is used for a pertinent question at an appropriate length and population scale. For example, while tremendous amount of basic understanding could be derived from single cell experiments, single cell perspective is not relevant to questions examining the interactions between two large subpopulations of cells. Single molecule experiments, on the other hand, remains in the theoretical and simulation realm for highlighting the effect of quantum mechanics in guiding the behavior of molecules at the nanoscale.

Download Full-text

Dark noise and retinal degeneration from D190N-rhodopsin

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2010417117 ◽

2020 ◽

Vol 117 (37) ◽

pp. 23033-23043 ◽

Cited By ~ 2

Author(s):

Daniel Silverman ◽

Zuying Chai ◽

Wendy W. S. Yue ◽

Sravani Keerthi Ramisetty ◽

Sowmya Bekshe Lokappa ◽

...

Keyword(s):

Retinal Degeneration ◽

Single Molecule ◽

Protein Misfolding ◽

Outer Segment ◽

Segment Length ◽

Single Molecule Level ◽

Dark Noise ◽

Order Of Magnitude ◽

Human Mutation ◽

Unclear Etiology

Numerous rhodopsin mutations have been implicated in night blindness and retinal degeneration, often with unclear etiology. D190N-rhodopsin (D190N-Rho) is a well-known inherited human mutation causing retinitis pigmentosa. Both higher-than-normal spontaneous-isomerization activity and misfolding/mistargeting of the mutant protein have been proposed as causes of the disease, but neither explanation has been thoroughly examined. We replaced wild-type rhodopsin (WT-Rho) in RhoD190N/WT mouse rods with a largely “functionally silenced” rhodopsin mutant to isolate electrical responses triggered by D190N-Rho activity, and found that D190N-Rho at the single-molecule level indeed isomerizes more frequently than WT-Rho by over an order of magnitude. Importantly, however, this higher molecular dark activity does not translate into an overall higher cellular dark noise, owing to diminished D190N-Rho content in the rod outer segment. Separately, we found that much of the degeneration and shortened outer-segment length of RhoD190N/WT mouse rods was not averted by ablating rod transducin in phototransduction—also consistent with D190N-Rho’s higher isomerization activity not being the primary cause of disease. Instead, the low pigment content, shortened outer-segment length, and a moderate unfolded protein response implicate protein misfolding as the major pathogenic problem. Finally, D190N-Rho also provided some insight into the mechanism of spontaneous pigment excitation.

Download Full-text

A Novel Complex: A Quantum Dot Conjugated to an Active T7RNA Polymerase

Journal of Nanomaterials ◽

10.1155/2013/468105 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Mette Eriksen ◽

Peter Horvath ◽

Michael A. Sørensen ◽

Szabolcs Semsey ◽

Lene B. Oddershede ◽

...

Keyword(s):

Quantum Dot ◽

Rna Polymerase ◽

Single Molecule ◽

Rna Polymerases ◽

Fluorescent Signal ◽

Single Molecule Level ◽

Single Molecule Studies ◽

Novel Complex ◽

Luminescent Nanoparticle

To perform single-molecule studies of the T7RNA polymerase, it is crucial to visualize an individual T7RNA polymerase, for example, through a fluorescent signal. We present a novel complex combining two different molecular functions, an active T7RNA polymerase and a highly luminescent nanoparticle, a quantum dot. The complex has the advantage of both constituents: the complex can traffic along DNA and simultaneously be visualized, both at the ensemble and at the single-molecule level. The labeling was mediated through anin vivobiotinylation of a His-tagged T7RNA polymerase and subsequent binding of a streptavidin-coated quantum dot. Our technique allows for easy purification of the quantum dot labeled T7RNA polymerases from the reactants. Also, the conjugation does not alter the functionality of the polymerase; it retains the ability to bind and transcribe.

Download Full-text