The Thermodynamics of DNA Structural Motifs

Figure 1: CRISPR–Cas9-mediated DNA interference in bacterial adaptive immunity. (a) A typical CRISPR locus in a type II CRISPR–Cas system comprises an array of repetitive sequences (repeats, brown dia...

Figure 2: The mechanism of CRISPR–Cas9–mediated genome engineering. The synthetic sgRNA or crRNA–tracrRNA structure directs a Cas9 endonuclease to almost arbitrary DNA sequence in the genome through a...

Figure 3: Overall structure of Streptococcus pyogenes Cas9 (SpyCas9) in the apo state. (a) Ribbon representation of the crystal structure of SpyCas9 (PDB ID 4CMP). Individual Cas9 domains are colored ...

Figure 4: Guide RNA loading enables Cas9 to form a DNA recognition–competent conformation for target search. (a) Ribbon diagram showing the apo structure of SpyCas9 aligned in the same orientation as ...

Figure 5: Structures of CRISPR–Cas9 bound to DNA substrates, showing the same view as in Figure 4c after superposition. (a) Crystal structure of SpyCas9 (surface representation) in complex with sgRNA ...

Figure 6: Schematic representations of the proposed mechanisms of CRISPR–Cas9-mediated target DNA recognition and cleavage. Upon sgRNA loading, Cas9 undergoes a large conformational rearrangement to r...

Figure 7: Structures of Cas9 orthologs reveal both the conserved and divergent structural features among orthologous CRISPR–Cas9 systems. Individual Cas9 domains are colored according to the scheme in...

Figure 1: Z-scheme of photosynthetic electron transfer in plants and cyanobacteria indicating the protein-cofactor complexes bound to the thylakoid membrane. Abbreviations: cyt, cytochrome; Fd, ferre...

Figure 2: Structural arrangement of the cofactors in the reaction center of the photosynthetic bacterium Rhodobacter sphaeroides with the L, M, and H protein subunits. The photosynthetic electron tra...

Figure 3: Light-induced electron transfer (ET) reactions in reaction centers of photosynthetic purple bacteria. The ET times are given for room temperature and are approximated to the nearest power o...

Figure 4: Schematic energy levels and electron transfer routes of photoexcited donor-spacer-acceptor (DsA) complex. The energy level of the RP in the solid matrix indicates the stabilization energy o...

Figure 5: Tensor principal axes system {α, β, γ} and average dimer system {x, y, z} of P865+·. (a) for the g1 tensor, (b) for the g2 tensor. Top: View from the average dimer normal (z direction) onto...

Figure 6: Spin-polarized pulsed W-band EPR spectrum of the correlated coupled radical pair P865+·-QA−· in deuterated Zn-substituted RC of Rb. sphaeroides R-26 in frozen solution together with the sim...

Figure 7: Structures of donor-acceptor model systems selected as examples of time-resolved EPR experiments. For chemical nomenclature, see text and relevant references.

Figure 8: Spin-polarized TREPR spectra of the triplet state, A-B-3*C in a LC, 700 ns after the laser pulse (420 nm) at 150 K. The expanded narrow spectra are those of the RP signal (scan range is 50 ...

Figure 1: Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to crowded medium and standard free energy of (a) association in solu...

Figure 2: Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to confined volume element and standard free energy of (a) associatio...

Figure 3: Dependence of the equilibrium constant for formation of a spherocylindrical dimer from two spherical monomers (R1 = 1) upon the volume fraction φ of hard-sphere crowders and dimer shape at c...

Figure 4: Dependence of the equilibrium constant for binding of a spherical macromolecular ligand to an immobile surface site upon the volume fraction φ of hard-sphere crowders, with MWligand/MWcrowde...

Figure 5: Effect of confinement in a spherical cavity on the free energy of two-state folding, calculated as a function of cavity radius according to the theory of Zhou & Dill (101), for proteins cont...

Figure 1: A photograph of me with the hybrid gull showing its wing feathers, which played the essential role in its identification.

Figure 2: The exchange reaction between a hydrogen atom and a hydrogen molecule. (a) Schematic representation of the reaction with definitions for the distances RAB, RAC, and RBC. (b) Contour plot of ...

Figure 3: The different form of retinal considered in the calculations. The figure has been reproduced, with permission, from Reference 42.

Figure 4: The peptide backbone (α carbons) and disulfide bonds of the bovine pancreatic trypsin inhibitor drawn by Bruce Gelin. (a) X-ray structure. (b) Time-evolved structure after 3.2 ps of dynamica...

Figure 5: Structural model of F0F1-ATP synthase. The figure has been reproduced from Senior AE, Nadanaciva S, Weber J. 2002. Biochim. Biophys. Acta Bioenerg. 1553:188–211

Figure 1: Overview of cellular bodies that are well described as biomolecular condensates. These bodies include large, well-studied structures such as the nucleolus, nuclear speckles, and P-bodies, bu...

Figure 2: Schematic of different types of stickers and spacers for different systems. (a) For folded domains, the mapping of the stickers and spacers is achieved via the physics of patchy colloids, wh...

Figure 3: Schematic of sticker patterning and effective solvation volume. (a) Three distinct sequences of intrinsically disordered proteins with identical numbers of sticker residues distributed in di...

Figure 4: Four examples of multiphase assemblies formed for different multicomponent systems. (a) Three-phase assembly of nucleoli is readily reproduced using a simple stickers-and-spacers model, as s...

Figure 5: General model for emergent stickers formed through oligomerization, linear polymerization, and/or clustering. (a) Depiction of monomers of ARF19 (solid shapes) that correspond to the PB1 dom...