Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface

Payne, Andrew; Andregg, Michael; Kemmish, Kent; Hamalainen, Mark; Bowell, Charlotte; Bleloch, Andrew; Klejwa, N.; Lehrach, Wolfgang; Schatz, Ken; Stark, Heather; Marblestone, Adam H.; Church, George M.; Own, Christopher S.; Andregg, William

doi:10.1371/journal.pone.0069058

Cited by 5 publications

(5 citation statements)

References 42 publications

(46 reference statements)

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“…The thymine bases in ssDNA were labelled with osmium atoms by staining ssDNA with a thymidine-selective osmium tetroxide 2–29 bipyridine (osbipy) contrast-enhancing label. The ssDNA strands were prepared by the ‘‘molecular threading’’ method - a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules 30 . DNA was stretched into air at a liquid-air interface and subsequently deposited onto a dry substrate isolated from solution.…”

Section: Sample Preparationmentioning

confidence: 99%

Direct visualization of charge transport in suspended (or free-standing) DNA strands by low-energy electron microscopy

Latychevskaia

Escher

Andregg³

et al. 2019

Sci Rep

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Low-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be employed for imaging charges as small as a fraction of one elementary charge. The combination of these properties makes low-energy electrons an exciting tool for imaging charge transport in individual biomolecules. Here we demonstrate the imaging of individual deoxyribonucleic acid (DNA) molecules at the resolution of about 1 nm with simultaneous imaging of the charging of the DNA molecules that is of the order of less than one elementary charge per nanometer. The cross-correlation analysis performed on different sections of the DNA network reveals that the charge redistribution between the two regions is correlated. Thus, low-energy electron microscopy is capable to provide simultaneous imaging of macromolecular structure and its charge distribution which can be beneficial for imaging and constructing nano-bio-sensors.

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Section: Sample Preparationmentioning

confidence: 99%

Direct visualization of charge transport in suspended (or free-standing) DNA strands by low-energy electron microscopy

Latychevskaia

Escher

Andregg³

et al. 2019

Sci Rep

Self Cite

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“…A recent development of molecular combing uses a microneedle to pull out DNA molecules from solution into air and stretch them mechanically on a desired surface. Despite the low-throughput of the method, it facilitates imaging on clean surfaces isolated from the sample and allows one to choose the properties of the surface . Approaches involving DNA stretching without fixation include (1) DNA stretching in nanochannels, driven by confinement due to the small dimensions of the channels; , (2) stretching by confinement in nanoslits; − and (3) stretching by stagnation point flow …”

Section: Vocabularymentioning

confidence: 99%

Toward Single-Molecule Optical Mapping of the Epigenome

et al. 2013

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The last decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity on the population level. The complex composition of the genome has made it an ideal system to study on the single-molecule level and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nano-scale and enhanced optical resolving power for analysis of genomic information. In the very last years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation.

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“…Understanding DNA chemical behaviors at air interfaces is critical to the development of materials science applications and biotechnologies. DNA positioning at air–solid interfaces is useful for nanofabrication of DNA-based nanostructures on solid substrates, , quantitative physical mapping of genes, − and transmission electron microscopy DNA sequencing . Despite being a strongly polar, hydrophilic biomacromolecule, DNA significantly adsorbs at the hydrophobic air–water interface in millimolar salt buffer or upon DNA condensation from picomolar DNA concentrations in a bulk aqueous solution .…”

Section: Introductionmentioning

confidence: 99%

Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces

2022

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Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure−function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air−water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C−H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C−H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.

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Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface

Cited by 5 publications

References 42 publications

Direct visualization of charge transport in suspended (or free-standing) DNA strands by low-energy electron microscopy

Direct visualization of charge transport in suspended (or free-standing) DNA strands by low-energy electron microscopy

Toward Single-Molecule Optical Mapping of the Epigenome

Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces

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