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Nature Sep 2023The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and...
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
Topics: Humans; Base Sequence; Chromosomes, Human, Y; DNA, Satellite; Genetic Variation; Genetics, Population; Genomics; Heterochromatin; Multigene Family; Reference Standards; Segmental Duplications, Genomic; Sequence Analysis, DNA; Tandem Repeat Sequences; Telomere
PubMed: 37612512
DOI: 10.1038/s41586-023-06457-y -
The Journal of Organic Chemistry Sep 2023Free-base corroles have long been known to be acidic, readily undergoing deprotonation by mild bases and in polar solvents. The conjugate base, however, has not been...
Free-base corroles have long been known to be acidic, readily undergoing deprotonation by mild bases and in polar solvents. The conjugate base, however, has not been structurally characterized until now. Presented here is a first crystal structure of a free-base corrole anion, derived from tris(-cyanophenyl)corrole, as the tetrabuylammonium salt. The low-temperature (100 K) structure reveals localized hydrogens on a pair of opposite pyrrole nitrogens. DFT calculations identify such a structure as the global minimum but also point to two tautomers only 4-7 kcal/mol above the ground state. In terms of free energy, however, the tautomers are above or essentially flush with the -to- barrier so the cis tautomers are unlikely to exist or be observed as true intermediates. Thus, the hydrogen bond within each dipyrrin unit on either side of the molecular pseudo- axis through C (i.e., between pyrrole rings A and B or between C and D) qualifies as or closely approaches a low-barrier hydrogen bond. Proton migration across the pseudo- axis entails much higher activation energies >20 kcal/mol, reflecting the relative rigidity of the molecule along the C-C pyrrole-pyrrole linkage.
PubMed: 37647416
DOI: 10.1021/acs.joc.3c01125 -
Nature Jun 2023Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases. Nonsense mutations convert a sense codon that is decoded by tRNA into...
Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
Topics: Animals; Mice; Amino Acids; Codon, Nonsense; Cystic Fibrosis Transmembrane Conductance Regulator; RNA, Transfer; Base Pairing; Anticodon; Protein Biosynthesis; Nasal Mucosa; Ribosome Profiling
PubMed: 37258671
DOI: 10.1038/s41586-023-06133-1 -
Proceedings of the National Academy of... Jul 2023Exosomes (EXOs) have been proven as biomarkers for disease diagnosis and agents for therapeutics. Great challenge remains in the separation of EXOs with high-purity and...
Exosomes (EXOs) have been proven as biomarkers for disease diagnosis and agents for therapeutics. Great challenge remains in the separation of EXOs with high-purity and low-damage from complex biological media, which is critical for the downstream applications. Herein, we report a DNA-based hydrogel to realize the specific and nondestructive separation of EXOs from complex biological media. The separated EXOs were directly utilized in the detection of human breast cancer in clinical samples, as well as applied in the therapeutics of myocardial infarction in rat models. The materials chemistry basis of this strategy involved the synthesis of ultralong DNA chains via an enzymatic amplification, and the formation of DNA hydrogels through complementary base-pairing. These ultralong DNA chains that contained polyvalent aptamers were able to recognize and bind with the receptors on EXOs, and the specific and efficient binding ensured the selective separation of EXOs from media into the further formed networked DNA hydrogel. Based on this DNA hydrogel, rationally designed optical modules were introduced for the detection of exosomal pathogenic microRNA, which achieved the classification of breast cancer patients versus healthy donors with 100% precision. Furthermore, the DNA hydrogel that contained mesenchymal stem cell-derived EXOs was proved with significant therapeutic efficacy in repairing infarcted myocardium of rat models. We envision that this DNA hydrogel-based bioseparation system is promising as a powerful biotechnology, which will promote the development of extracellular vesicles in nanobiomedicine.
Topics: Humans; Rats; Animals; Exosomes; Hydrogels; MicroRNAs; Mesenchymal Stem Cells
PubMed: 37399419
DOI: 10.1073/pnas.2303822120