The mechanical stability of tRNAs contributes to their biological activities.The mitochondrial tRNAArg from Romanomermis culicivorax is the shortest tRNA ever known.This tRNA lacks D-and T-arms,represents a stem-bulge...The mechanical stability of tRNAs contributes to their biological activities.The mitochondrial tRNAArg from Romanomermis culicivorax is the shortest tRNA ever known.This tRNA lacks D-and T-arms,represents a stem-bulge-stem architecture but still folds into a stable tertiary structure.Although its structure had been reported,studies on its mechanical folding and unfolding kinetic characteristics are lacking.Here,we directly measured the single-molecule mechanical folding and unfolding kinetics of the armless mt tRNAArg by using optical tweezers in different solution conditions.We revealed a two-step reversible unfolding pathway:the first and large transition corresponds to the unfolding of acceptor stem and bulge below 11 pN,and the second and small transition corresponds to the unfolding of anticodon arm at 12 pN-14 pN.Moreover,the free energy landscapes of the unfolding pathways were reconstructed.We also demonstrated that amino acid-chelated Mg^(2+)(aaCM),which mimics the intracellular solution condition,stabilizes the bulge of mitochondrial tRNAArg possibly by reducing the topological constraints or stabilizing the possible local non-canonical base pairings within the bulge region.Our study revealed the solution-dependent mechanical stability of an armless mt tRNA,which may shed light on future mt tRNA studies.展开更多
Van der Waals(vdW)contact,dominated by weak but ubiquitous vdW interactions,plays a significant role in diverse fields such as supramolecular chemistry,nanotechnology,and surface science.Accurate characterization of v...Van der Waals(vdW)contact,dominated by weak but ubiquitous vdW interactions,plays a significant role in diverse fields such as supramolecular chemistry,nanotechnology,and surface science.Accurate characterization of vdW contact at the single-molecule level remains challenging.Herein,we combine the scanning tunneling microscope break junction technique with first-principles calculations to study the mechanical and electrical characteristics of the alkane/Au vdW contact in an in-situ solution environment.The step-like conductance plateaus indicate a gradual desorption of alkyl chains in units of two methylene groups under force stretching.Two distinct charge transport channels,through the shortest C–H/Au pathway and the entire adsorbed alkyl chain,are identified.Furthermore,we discover that a higher electric field leads to increased conductance and stronger bonding of the alkane/Au vdW contact.These results unveil the intrinsic properties of vdW contact at the molecular and even atomic levels,which are crucial for exploring noncovalent interactions and advancing molecular sciences.展开更多
Molecular machines transduce energy from one form to another through controlled motion in response to stimuli.Despite the ubiquitous use of molecular machines in biology,understanding the detailed mechanisms of such c...Molecular machines transduce energy from one form to another through controlled motion in response to stimuli.Despite the ubiquitous use of molecular machines in biology,understanding the detailed mechanisms of such complex structures remains challenging.Recent progress in studying the modes of operation of synthetic small-molecule machines at the single-molecule level has shed new light on the mechanisms of nano-machinery.In this mini-review,we focus on the study of artificial small-molecule machines using single-molecule techniques,including single-molecule force spectroscopy,single-molecule electrical spectroscopy,and single-molecule optical spectroscopy.We survey the techniques used to monitor single-molecule behavior to date and describe the latest studies on small-molecule machines,highlighting their common features and challenges that need to be overcome to realize the potential of these techniques in unraveling the behavior of small molecule systems.展开更多
基金supported by the Natural Science Foundation of Guangdong Province,China(Grant No.2017A030310085)the Science and Technology Planning Project of Guangdong Province,China(Grant No.2018A050506034).
文摘The mechanical stability of tRNAs contributes to their biological activities.The mitochondrial tRNAArg from Romanomermis culicivorax is the shortest tRNA ever known.This tRNA lacks D-and T-arms,represents a stem-bulge-stem architecture but still folds into a stable tertiary structure.Although its structure had been reported,studies on its mechanical folding and unfolding kinetic characteristics are lacking.Here,we directly measured the single-molecule mechanical folding and unfolding kinetics of the armless mt tRNAArg by using optical tweezers in different solution conditions.We revealed a two-step reversible unfolding pathway:the first and large transition corresponds to the unfolding of acceptor stem and bulge below 11 pN,and the second and small transition corresponds to the unfolding of anticodon arm at 12 pN-14 pN.Moreover,the free energy landscapes of the unfolding pathways were reconstructed.We also demonstrated that amino acid-chelated Mg^(2+)(aaCM),which mimics the intracellular solution condition,stabilizes the bulge of mitochondrial tRNAArg possibly by reducing the topological constraints or stabilizing the possible local non-canonical base pairings within the bulge region.Our study revealed the solution-dependent mechanical stability of an armless mt tRNA,which may shed light on future mt tRNA studies.
基金financial support from the National Key R&D Program of China(grant nos.2021YFA1200102,2021YFA1200101,and 2022YFE0128700)the National Natural Science Foundation of China(grant nos.22173050,22150013,21727806,21933001,and 11974106)+3 种基金the New Cornerstone Science Foundation through the XPLORER PRIZE,the Natural Science Foundation of Beijing(grant no.2222009)Beijing National Laboratory for Molecular Sciences(grant no.BNLMS202105)the Fundamental Research Funds for the Central Universities(grant no.63223056)the Frontiers Science Center for New Organic Matter at Nankai University(grant no.63181206).
文摘Van der Waals(vdW)contact,dominated by weak but ubiquitous vdW interactions,plays a significant role in diverse fields such as supramolecular chemistry,nanotechnology,and surface science.Accurate characterization of vdW contact at the single-molecule level remains challenging.Herein,we combine the scanning tunneling microscope break junction technique with first-principles calculations to study the mechanical and electrical characteristics of the alkane/Au vdW contact in an in-situ solution environment.The step-like conductance plateaus indicate a gradual desorption of alkyl chains in units of two methylene groups under force stretching.Two distinct charge transport channels,through the shortest C–H/Au pathway and the entire adsorbed alkyl chain,are identified.Furthermore,we discover that a higher electric field leads to increased conductance and stronger bonding of the alkane/Au vdW contact.These results unveil the intrinsic properties of vdW contact at the molecular and even atomic levels,which are crucial for exploring noncovalent interactions and advancing molecular sciences.
基金supported the National Natural Science Foundation of China(grant no.22001074 to L.Z.)the Natural Science Foundation of Shanghai(grant no.22ZR1479400 to L.Z.).
文摘Molecular machines transduce energy from one form to another through controlled motion in response to stimuli.Despite the ubiquitous use of molecular machines in biology,understanding the detailed mechanisms of such complex structures remains challenging.Recent progress in studying the modes of operation of synthetic small-molecule machines at the single-molecule level has shed new light on the mechanisms of nano-machinery.In this mini-review,we focus on the study of artificial small-molecule machines using single-molecule techniques,including single-molecule force spectroscopy,single-molecule electrical spectroscopy,and single-molecule optical spectroscopy.We survey the techniques used to monitor single-molecule behavior to date and describe the latest studies on small-molecule machines,highlighting their common features and challenges that need to be overcome to realize the potential of these techniques in unraveling the behavior of small molecule systems.
