A novel low energy electron microscope for DNA sequencing and surface analysis

• Published in: Ultramicroscopy Vol. 145; pp. 36 - 49
• Main Authors: Mankos, M., Shadman, K., Persson, H.H.J., N’Diaye, A.T., Schmid, A.K., Davis, R.W.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2014; Elsevier
• Subjects: Aberration; Aberration correction; Computer Simulation; Contrast; Deoxyribonucleic acid; DNA Sequencing; DNA, B-Form - chemistry; DNA, B-Form - ultrastructure; Dual beam illumination; Electrons; Energy filtering; Equipment Design; Gene sequencing; High-Throughput Nucleotide Sequencing - instrumentation; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - statistics & numerical data; Illumination; Image contrast; Imaging; Low energy; Low energy electron microscopy; Microscopy, Electron - instrumentation; Microscopy, Electron - methods; Microscopy, Electron - statistics & numerical data; Monochromator; Monochromators; Nanostructures; Optical Devices; Optical Phenomena; OTHER INSTRUMENTATION; Photoelectron Spectroscopy; Sequence Analysis, DNA - instrumentation; Sequence Analysis, DNA - methods; Sequence Analysis, DNA - statistics & numerical data; Surface Properties; Low energy electron microscopy; Dual beam illumination; Monochromator; Aberration correction; Energy filtering; DNA Sequencing; Contrast
• ISSN: 0304-3991; 1879-2723
• DOI: 10.1016/j.ultramic.2014.01.007

Monochromatic, aberration-corrected, dual-beam low energy electron microscopy (MAD-LEEM) is a novel technique that is directed towards imaging nanostructures and surfaces with sub-nanometer resolution. The technique combines a monochromator, a mirror aberration corrector, an energy filter, and dual beam illumination in a single instrument. The monochromator reduces the energy spread of the illuminating electron beam, which significantly improves spectroscopic and spatial resolution. Simulation results predict that the novel aberration corrector design will eliminate the second rank chromatic and third and fifth order spherical aberrations, thereby improving the resolution into the sub-nanometer regime at landing energies as low as one hundred electron-Volts. The energy filter produces a beam that can extract detailed information about the chemical composition and local electronic states of non-periodic objects such as nanoparticles, interfaces, defects, and macromolecules. The dual flood illumination eliminates charging effects that are generated when a conventional LEEM is used to image insulating specimens. A potential application for MAD-LEEM is in DNA sequencing, which requires high resolution to distinguish the individual bases and high speed to reduce the cost. The MAD-LEEM approach images the DNA with low electron impact energies, which provides nucleobase contrast mechanisms without organometallic labels. Furthermore, the micron-size field of view when combined with imaging on the fly provides long read lengths, thereby reducing the demand on assembling the sequence. Experimental results from bulk specimens with immobilized single-base oligonucleotides demonstrate that base specific contrast is available with reflected, photo-emitted, and Auger electrons. Image contrast simulations of model rectangular features mimicking the individual nucleotides in a DNA strand have been developed to translate measurements of contrast on bulk DNA to the detectability of individual DNA bases in a sequence. •We present a LEEM with a monochromator, aberration corrector, energy filter and two electron beams.•We analyze objective lens aberrations up to 5th order with and without aberration correction.•A pentode mirror corrector combined with a monochromator greatly reduces blur.•We present experimental data from bulk DNA specimens demonstrating that base specific contrast is available with X-ray photoemission, Auger, and reflected electrons.•Contrast simulations utilizing the minimum experimental contrast predict that images will yield a relatively low error rate are obtainable.