Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching

2007 ◽  
Vol 4 (6) ◽  
pp. 517-522 ◽  
Author(s):  
Ioana D Vladescu ◽  
Micah J McCauley ◽  
Megan E Nuñez ◽  
Ioulia Rouzina ◽  
Mark C Williams
Keyword(s):  
Single Molecule ◽  
Dna Intercalation ◽  
Zero Force

Determining the Zero-Force Binding Energetics of an Intercalated DNA Complex by a Single-Molecule Approach

ChemPhysChem ◽  
2009 ◽  
Vol 10 (16) ◽  
pp. 2791-2794 ◽  
Author(s):  
Tzu-Sen Yang ◽  
Yujia Cui ◽  
Chien-Ming Wu ◽  
Jem-Mau Lo ◽  
Chi-Shiun Chiang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Zero Force ◽  
Binding Energetics ◽  
Dna Complex

Single-molecule determination of chemical equilibrium of DNA intercalation by electrical conductance

2021 ◽  
Author(s):  
Lu Zhang ◽  
Satoshi Kaneko ◽  
Shintaro Fujii ◽  
Manabu Kiguchi ◽  
Tomoaki Nishino
Keyword(s):  
Single Molecule ◽  
Chemical Equilibrium ◽  
Electrical Conductance ◽  
Dna Intercalation ◽  
Molecule Reaction ◽  
Association Reaction

We investigated a single-molecule reaction of DNA intercalation as an example of a bimolecular association reaction. Single-molecule conductance values of the product and reactant molecules adsorbed on an Au surface...

scholarly journals Differential contribution of basic residues to HIV-1 nucleocapsid protein’s nucleic acid chaperone function and retroviral replication

2013 ◽  
Vol 42 (4) ◽  
pp. 2525-2537 ◽  
Author(s):  
Hao Wu ◽  
Mithun Mitra ◽  
M. Nabuan Naufer ◽  
Micah J. McCauley ◽  
Robert J. Gorelick ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Zinc Finger ◽  
Single Molecule ◽  
Chaperone Activity ◽  
Dna Intercalation ◽  
Structural Basis ◽  
Retroviral Replication ◽  
Hiv 1

Abstract The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein contains 15 basic residues located throughout its 55-amino acid sequence, as well as one aromatic residue in each of its two CCHC-type zinc finger motifs. NC facilitates nucleic acid (NA) rearrangements via its chaperone activity, but the structural basis for this activity and its consequences in vivo are not completely understood. Here, we investigate the role played by basic residues in the N-terminal domain, the N-terminal zinc finger and the linker region between the two zinc fingers. We use in vitro ensemble and single-molecule DNA stretching experiments to measure the characteristics of wild-type and mutant HIV-1 NC proteins, and correlate these results with cell-based HIV-1 replication assays. All of the cationic residue mutations lead to NA interaction defects, as well as reduced HIV-1 infectivity, and these effects are most pronounced on neutralizing all five N-terminal cationic residues. HIV-1 infectivity in cells is correlated most strongly with NC’s NA annealing capabilities as well as its ability to intercalate the DNA duplex. Although NC’s aromatic residues participate directly in DNA intercalation, our findings suggest that specific basic residues enhance these interactions, resulting in optimal NA chaperone activity.

scholarly journals Two-Step DNA Intercalation by Threading of the Flexible Ruthenium Dimer Studied by the Single Molecule DNA Stretching

2015 ◽  
Vol 108 (2) ◽  
pp. 397a-398a
Author(s):  
Ioulia Rouzina ◽  
Meriem Bahira ◽  
Ali Almaqwashi ◽  
Micah McCauley ◽  
Fredrik Westerlund ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Intercalation ◽  
Dna Stretching

Single molecule DNA intercalation in continuous homogenous elongational flow

Lab on a Chip ◽  
2014 ◽  
Vol 14 (19) ◽  
pp. 3881-3893 ◽  
Author(s):  
Joshua W. Griffis ◽  
Mikhail M. Safranovitch ◽  
Shilpi P. Vyas ◽  
Sean Gerrin ◽  
Ekaterina Protozanova ◽  
...  
Keyword(s):  
Single Molecule ◽  
Elongational Flow ◽  
Dna Intercalation

Single molecule DNA intercalation in continuous elongational flow.

The method of replication affects metal film granularity and resolution

1989 ◽  
Vol 47 ◽  
pp. 708-709
Author(s):  
George C. Ruben
Keyword(s):  
Electron Beam ◽  
High Resolution ◽  
Film Thickness ◽  
Single Molecule ◽  
Metal Film ◽  
Vertical Surface ◽  
High Resolution Imaging ◽  
Controllable Factors ◽  
Resolution Imaging

Single molecule resolution in electron beam sensitive, uncoated, noncrystalline materials has been impossible except in thin Pt-C replicas ≤ 150Å) which are resistant to the electron beam destruction. Previously the granularity of metal film replicas limited their resolution to ≥ 20Å. This paper demonstrates that Pt-C film granularity and resolution are a function of the method of replication and other controllable factors. Low angle 20° rotary , 45° unidirectional and vertical 9.7±1 Å Pt-C films deposited on mica under the same conditions were compared in Fig. 1. Vertical replication had a 5A granularity (Fig. 1c), the highest resolution (table), and coated the whole surface. 45° replication had a 9Å granulartiy (Fig. 1b), a slightly poorer resolution (table) and did not coat the whole surface. 20° rotary replication was unsuitable for high resolution imaging with 20-25Å granularity (Fig. 1a) and resolution 2-3 times poorer (table). Resolution is defined here as the greatest distance for which the metal coat on two opposing faces just grow together, that is, two times the apparent film thickness on a single vertical surface.

Single molecule optical diffraction: A tool for understanding the structure of triple stranded left-hand helical cellulose

1989 ◽  
Vol 47 ◽  
pp. 1024-1025
Author(s):  
George C. Ruben ◽  
William Krakow
Keyword(s):  
Single Molecule ◽  
Helical Structure ◽  
Optical Diffraction ◽  
Maximum Diameter ◽  
Primary Cell Wall ◽  
Cellulose Synthesis ◽  
Left Hand ◽  
Left Handed ◽  
Freeze Dried ◽  
Diffraction Patterns

Tobacco primary cell wall and normal bacterial Acetobacter xylinum cellulose formation produced a 36.8±3Å triple-stranded left-hand helical microfibril in freeze-dried Pt-C replicas and in negatively stained preparations for TEM. As three submicrofibril strands exit the wall of Axylinum , they twist together to form a left-hand helical microfibril. This process is driven by the left-hand helical structure of the submicrofibril and by cellulose synthesis. That is, as the submicrofibril is elongating at the wall, it is also being left-hand twisted and twisted together with two other submicrofibrils. The submicrofibril appears to have the dimensions of a nine (l-4)-ß-D-glucan parallel chain crystalline unit whose long, 23Å, and short, 19Å, diagonals form major and minor left-handed axial surface ridges every 36Å.The computer generated optical diffraction of this model and its corresponding image have been compared. The submicrofibril model was used to construct a microfibril model. This model and corresponding microfibril images have also been optically diffracted and comparedIn this paper we compare two less complex microfibril models. The first model (Fig. 1a) is constructed with cylindrical submicrofibrils. The second model (Fig. 2a) is also constructed with three submicrofibrils but with a single 23 Å diagonal, projecting from a rounded cross section and left-hand helically twisted, with a 36Å repeat, similar to the original model (45°±10° crossover angle). The submicrofibrils cross the microfibril axis at roughly a 45°±10° angle, the same crossover angle observed in microflbril TEM images. These models were constructed so that the maximum diameter of the submicrofibrils was 23Å and the overall microfibril diameters were similar to Pt-C coated image diameters of ∼50Å and not the actual diameter of 36.5Å. The methods for computing optical diffraction patterns have been published before.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

Sign in / Sign up

Export Citation Format

Share Document