Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Chirality-Selective Functionalization of Semiconducting Carbon Nanotubes with a Reactivity-Switchable Molecule

Chirality-selective functionalization of semiconducting single-walled carbon nanotubes (SWCNTs) has been a difficult synthetic goal for more than a decade. Here we describe an on-demand covalent chemistry to address this intriguing challenge. Our approach involves the synthesis and isolation of a chemically inert diazoether isomer that can be switched to its reactive form <i>in situ</i> by modulation of the thermodynamic barrier to isomerization with pH and visible light that resonates with the optical frequency of the nanotube. We found that it is possible to completely inhibit the reaction in the absence of light, as determined by the limit of sensitive defect photoluminescence (less than 0.01% of the carbon atoms are bonded to a functional group). This optically driven diazoether chemistry makes it possible to selectively functionalize a specific SWCNT chirality within a mixture. Even for two chiralities that are nearly identical in diameter and electronic structure, (6,5)- and (7,3)-SWCNTs, we are able to activate the diazoether compound to functionalize the less reactive (7,3)-SWCNTs, driving the chemical reaction to near exclusion of the (6,5)-SWCNTs. This work opens opportunities to chemically tailor SWCNTs at the single chirality level for nanotube sorting, on-chip passivation, and nanoscale lithography

Channeling Excitons to Emissive Defect Sites in Carbon Nanotube Semiconductors beyond the Dilute Regime

The exciton photoluminescence of carbon nanotube semiconductors has been intensively exploited for bioimaging, anticounterfeiting, photodetection, and quantum information science. However, at high concentrations, photoluminescence is lost to self-quenching because of the nearly complete overlap of the absorption and emissive states (∼10 meV Stokes shift). Here we show that by introducing sparse fluorescent quantum defects via covalent chemistry, self-quenching can be efficiently bypassed by means of the new emission route. The defect photoluminescence is significantly red-shifted by 190 meV for <i>p</i>-nitroaryl tailored (6,5)-single-walled carbon nanotubes (SWCNTs) from the native emission of the nanotube. Notably, the defect photoluminescence is more than 34 times brighter than the native photoluminescence of unfunctionalized SWCNTs in the most concentrated nanotube solution tested (2.7 × 10¹⁴ nanotubes/mL). Moreover, we show that defect photoluminescence is more resistant to self-quenching than the native state in a dense film, which is the upper limit of concentration. Our findings open opportunities to harness nanotube excitons in highly concentrated systems for applications where photoluminescence brightness and light-collecting efficiency are mutually important

Optical Probing of Local pH and Temperature in Complex Fluids with Covalently Functionalized, Semiconducting Carbon Nanotubes

We show that local pH can be optically probed through defect photoluminescence from semiconducting carbon nanotubes covalently functionalized with aminoaryl groups. Switching between protonated and deprotonated forms of the amino moiety produces an energy shift in the defect state of the functionalized nanotube by as much as 33 meV in the near-infrared region. This unexpected observation enables a new optical pH sensor that features ultrabright near-infrared II (1.1–1.4 μm) photoluminescence, a sensitivity for pH changes as small as 0.2 pH units over a wide working window that covers the entire physiologic pH range, and potentially molecular resolution. Independent of pH, this nanoprobe can simultaneously act as a nanothermometer by monitoring temperature-modulated changes in photoluminescence intensity, which follows the van’t Hoff equation. This work opens new opportunities for quantitative probing of local pH and temperature changes in complex biological systems

Fluorescent Carbon Nanotube Defects Manifest Substantial Vibrational Reorganization

Fluorescent defects have opened up exciting new opportunities to chemically tailor semiconducting carbon nanotubes for imaging, sensing, and photonics needs such as lasing, single photon emission, and photon upconversion. However, experimental measurements on the trap depths of these defects show a puzzling energy mismatch between the optical gap (difference in emission energies between the native exciton and defect trap states) and the thermal detrapping energy determined by application of the van ’t Hoff equation. To resolve this fundamentally important problem, here we synthetically incorporated a series of fluorescent aryl defects into semiconducting single-walled carbon nanotubes and experimentally determined their energy levels by temperature-dependent and chemically correlated evolution of exciton population and photoluminescence. We found that depending on the chemical nature and density of defects, the exciton detrapping energy is 14–77% smaller than the optical gap determined from photoluminescence. For the same type of defect, the detrapping energy increases with defect density from 76 to 131 meV for 4-nitroaryl defects in (6,5) single-walled carbon nanotubes, whereas the optical gap remains nearly unchanged (<5 meV). These experimental findings are corroborated by quantum-chemical simulations of the chemically functionalized carbon nanotubes. Our results suggest that the energy mismatch arises from vibrational reorganization due to significant deformation of the nanotube geometry upon exciton trapping at the defect site. An unexpectedly large reorganization energy (on the order of 100 meV) is found between ground and excited states of the defect tailored nanostructures. This finding reveals a molecular picture for description of these synthetic defects and suggests significant potential for tailoring the electronic properties of carbon nanostructures through chemical engineering