2023 New's Items

Contact engineering for graphene nanoribbon devices

Mutlu Z
Dinh C
Bokor J
Crommie MF
2023

Graphene nanoribbons (GNRs), when synthesized with atomic precision by bottom–up chemical approaches, possess tunable electronic structure, and high theoretical mobility, conductivity, and heat dissipation capabilities, which makes them an excellent candidate for channel material in post-silicon transistors. Despite their immense potential, achieving highly transparent contacts for efficient charge transport—which requires proper contact selection and a deep understanding of the complex one-dimensional GNR channel-three-dimensional metal contact interface—remains a challenge. In this...

Five-Membered Rings Create Off-Zero Modes in Nanographene

Jacobse PH
Daugherty MC
Crommie MF
2023

The low-energy electronic structure of nanographenes can be tuned through zero-energy π-electron states, typically referred to as zero-modes. Customizable electronic and magnetic structures have been engineered by coupling zero-modes through exchange and hybridization interactions. Manipulation of the energy of such states, however, has not yet received significant attention. We find that attaching a five-membered ring to a zigzag edge hosting a zero-mode perturbs the energy of that mode and turns it into an off-zero mode: a localized state with a...

Thermodynamic behavior of correlated electron-hole fluids in van der Waals heterostructures

Qi R
Wang F
Crommie MF
2023

Coupled two-dimensional electron-hole bilayers provide a unique platform to study strongly correlated Bose-Fermi mixtures in condensed matter. Electrons and holes in spatially separated layers can bind to form interlayer excitons, composite Bosons expected to support high-temperature exciton condensates. The interlayer excitons can also interact strongly with excess charge carriers when electron and hole densities are unequal. Here, we use optical spectroscopy to quantitatively probe the local thermodynamic properties of strongly correlated electron-hole fluids in MoSe2...

Protrusions and contractions generate long-range membrane tension propagation

Belly HD
Yan S
Rocha HBD
Ichbiah S
Town JP
Zager PJ
Estrada DC
Meyer K
Turlier H
Bustamante C
Weiner OD
2023

Membrane tension is thought to be a long-range integrator of cell physiology. Membrane tension has been proposed to enable cell polarity during migration through front-back coordination and long-range protrusion competition. These roles necessitate effective tension transmission across the cell. However, conflicting observations have left the field divided as to whether cell membranes support or resist tension propagation. This discrepancy likely originates from the use of exogenous forces that may not accurately mimic endogenous forces. We overcome this complication by leveraging...

Conformational Change of Nucleosome Arrays prior to Phase Separation

Zhang M
Celis CD
Ren G
Bustamante CJ
2023

Chromatin phase transition serves as a regulatory mechanism for eukaryotic transcription. Understanding this process requires the characterization of the nucleosome array structure in response to external stimuli prior to phase separation. However, the intrinsic flexibility and heterogeneity hinders the arrays’ structure determination. Here we exploit advances in cryogenic electron tomography (cryo-ET) to determine the three-dimensional (3D) structure of each individual particle of mono-, di-, tri-, and tetranucleosome arrays. Statistical analysis reveals the ionic strength changes...

Population-based heteropolymer design to mimic protein mixtures

Ruan Z
Xu T
Bustamante CJ
2023

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed...

A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery

Wee L
Tong AB
Bustamante CJ
2023

In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the...

Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time

Sun M
Heald R
Bustamante CJ
2023

DNA compaction is required for the condensation and resolution of chromosomes during mitosis, but the relative contribution of individual chromatin factors to this process is poorly understood. We developed a physiological, cell-free system using high-speed Xenopus egg extracts and optical tweezers to investigate real-time mitotic chromatin fiber formation and force-induced disassembly on single DNA molecules. Compared to interphase extract, which compacted DNA by ~60%, metaphase extract reduced DNA length by over 90%, reflecting differences in whole-chromosome...

Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism

Shaw A
Bustamante CJ
2023

Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT from Bombyx mori with single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were...

Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy

Onoa B
Díaz-Celis C
Cañari-Chumpitaz C
Lee A
Bustamante C
2023

During replication, expression, and repair of the eukaryotic genome, cellular machinery must access the DNA wrapped around histone proteins forming nucleosomes. These octameric protein·DNA complexes are modular, dynamic, and flexible and unwrap or disassemble either spontaneously or by the action of molecular motors. Thus, the mechanism of formation and regulation of subnucleosomal intermediates has gained attention genome-wide because it controls DNA accessibility. Here, we imaged nucleosomes and their more compacted structure with the linker histone H1 (chromatosomes) using high-...