title: A novel low energy electron microscope for DNA sequencing and surface analysis.
abstract: 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.
authors: Electron Optica Inc., 1000 Elwell Court ♯110, Palo Alto, CA 94303, USA. Electronic address: marian@electronoptica.com.
authors: M
authors: M
authors: Mankos
authors: Electron Optica Inc., 1000 Elwell Court ♯110, Palo Alto, CA 94303, USA.
authors: K
authors: K
authors: Shadman
authors: Stanford Genome Technology Center, Stanford University School of Medicine, 855 California Avenue, Palo Alto, CA 94304, USA.
authors: H H J
authors: HH
authors: Persson
authors: Electron Optica Inc., 1000 Elwell Court ♯110, Palo Alto, CA 94303, USA; NCEM, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: A T
authors: AT
authors: N'Diaye
authors: NCEM, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors: A K
authors: AK
authors: Schmid
authors: Stanford Genome Technology Center, Stanford University School of Medicine, 855 California Avenue, Palo Alto, CA 94304, USA.
authors: R W
authors: RW
authors: Davis
mesh_terms: D003198:Computer Simulation; D059371:DNA, B-Form / Q000737:chemistry / Q000648:ultrastructure; D004583:Electrons; D004867:Equipment Design; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data; D008854:Microscopy, Electron / Q000295:instrumentation* / Q000379:methods / Q000706:statistics & numerical data; D049329:Nanostructures; D055096:Optical Devices; D055620:Optical Phenomena; D056951:Photoelectron Spectroscopy; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods / Q000706:statistics & numerical data; D013499:Surface Properties
chemical_list: D059371:DNA, B-Form
keywords: Aberration correction; Contrast; DNA Sequencing; Dual beam illumination; Energy filtering; Low energy electron microscopy; Monochromator