Atomic layer deposition (ALD) is gaining attention as a thin film deposition method, uniquely suitable for depositing uniform and conformal films on complex three-dimensional topographies. The deposition of a film of a given material by ALD relies on the successive, separated, and self-terminating gas–solid reactions of typically two gaseous reactants. Hundreds of ALD chemistries have been found for depositing a variety of materials during the past decades, mostly for inorganic materials but lately also for organic and inorganic–organic hybrid compounds. One factor that often dictates the properties of ALD films in actual applications is the crystallinity of the grown film: Is the material amorphous or, if it is crystalline, which phase(s) is (are) present. In this thematic review, we first describe the basics of ALD, summarize the two-reactant ALD processes to grow inorganic materials developed to-date, updating the information of an earlier review on ALD [R. L. Puurunen, J. Appl. Phys. 97, 121301 (2005)], and give an overview of the status of processing ternary compounds by ALD. We then proceed to analyze the published experimental data for information on the crystallinity and phase of inorganic materials deposited by ALD from different reactants at different temperatures. The data are collected for films in their as-deposited state and tabulated for easy reference. Case studies are presented to illustrate the effect of different process parameters on crystallinity for representative materials: aluminium oxide, zirconium oxide, zinc oxide, titanium nitride, zinc zulfide, and ruthenium. Finally, we discuss the general trends in the development of film crystallinity as function of ALD process parameters. The authors hope that this review will help newcomers to ALD to familiarize themselves with the complex world of crystalline ALD films and, at the same time, serve for the expert as a handbook-type reference source on ALD processes and film crystallinity.

Crystallinity of inorganic films grown by atomic layer deposition: Overview and general trends

The early detection of cancer can significantly reduce cancer mortality and saves lives. Thus, a great deal of effort has been devoted to the exploration of new technologies to detect early signs of the disease. Cancer biomarkers cover a broad range of biochemical entities, such as nucleic acids, proteins, sugars, small metabolites, and cytogenetic and cytokinetic parameters, as well as entire tumour cells found in the body fluid. They can be used for risk assessment, diagnosis, prognosis, and for the prediction of treatment efficacy and toxicity and recurrence. In this review, we provide an overview of recent advances in cancer biomarker detection. Several representative examples using different approaches for each biomarker have been reviewed, and all these cases demonstrate that the multidisciplinary technology-based cancer diagnostics are becoming an increasingly relevant alternative to traditional techniques. In addition, we also discuss the unsolved problems and future challenges in the evaluation of cancer biomarkers. Clearly, solving these hurdles requires great effort and collaboration from different communities of chemists, physicists, biologists, clinicians, material-scientists, and engineering and technical researchers. A successful outcome will result in the realization of point-of-care diagnosis and individualized treatment of cancers by non-invasive and convenient tests in the future.

Cancer biomarker detection: recent achievements and challenges

https://www2.lbl.gov/tt/publications/2977pub2.pdf

Single cell analysis: the new frontier in ‘omics’

Single cell analysis: the new frontier in ‘Omics’ Daojing Wang 1 and Steven Bodovitz 2 1. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 2. BioPerspectives, San Francisco, CA Corresponding author: Wang, D. (djwang@lbl.gov) Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of ‘Omics’ technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity. Single cell analysis: needs and applications Cellular heterogeneity Cellular heterogeneity within an isogenic cell population is a widespread event [1, 2]. Stochastic gene and protein expression at the single cell level has been clearly demonstrated in different systems using a variety of techniques [3-5]. Therefore, analyzing cell ensembles individually with high spatiotemporal resolutions will lead to a

Single cell analysis: the new frontier in 'Omics'

Lu Shin Wong graduated with a Bachelor of Pharmacy from the University of Nottingham in 1997. He then practiced as a hospital pharmacist for four years while completing his postgraduate diploma in clinical pharmacy from the University of Bradford. Subsequently, he undertook his Ph.D. studies at the University of Southampton with Prof. Mark Bradley on solid-phase organic chemistry, microspectrometry, and solid-supported sensors. Upon completing this in 2005, he joined the Manchester Interdisciplinary Biocentre as a postdoctoral research associate with Prof. Jason Micklefield on the application of chemical biology to surface chemistry and biomolecular-array technologies. Lu Shin is currently an EPSRC Life Science Interface research fellow, and his interests include the combination of chemical biology, surface chemistry, and nanofabrication towards life science applications.
Biography
Farid Khan obtained his Ph.D. from the University of Cambridge (2004), where he studied the folding of GFP using fluorescence and NMR. Previously, he has worked for a number of years at GlaxoSmithKline in fluorescence assay development for drug discovery. He spent two years as a postdoctoral researcher at the Babraham Institute in Cambridge, where he codeveloped novel protein arrays from DNA arrays using cell free synthesis and characterized robust protein immobilization methods. He is currently employed at the University of Manchester as a Systems Biologist at the Manchester Centre of Integrative Systems Biology. His primary role is on the characterizing of enzymes in metabolic pathways, and he is a M.Sc. lecturer in Biotechnology and Enterprise. He is a founder of Lumophore Ltd., a consulting company specializing in applications of protein array technology.
Biography
Jason Micklefield graduated from the University of Cambridge in 1993 with a Ph.D. in Organic Chemistry, working with Prof. Sir Alan R. Battersby to complete the first total synthesis of Haem d1. He then moved to the University of Washington, U.S.A., as a NATO postdoctoral fellow with Prof. Heinz G. Floss, investigating various biosynthetic pathways and enzyme mechanisms. In 1995 he began his independent research career as a Lecturer in Chemistry at Birkbeck College, University of London, before moving to Manchester in 1998, where he is now Chair of Chemical Biology. Prof. Micklefield?s research interests are at the chemistry?biology interface and include the redesign of nucleic acids, small-molecule control of gene expression, biosynthesis and biosynthetic engineering, nonribosomal peptides, biocatalysis, and enzyme mechanism.

Selective covalent protein immobilization: strategies and applications.

Parylene is a family of chemically vapour deposited polymer with material properties that are attractive for biomedicine and nanobiotechnology. Chemically inert parylene “peel-off” stencils have been demonstrated for micropatterning biomolecular arrays with high uniformity, precise spatial control down to nanoscale resolution. Such micropatterned surfaces are beneficial in engineering biosensors and biological microenvironments. A variety of substituted precursors enables direct coating of functionalised parylenes onto biomedical implants and microfluidics, providing a convenient method for designing biocompatible and bioactive surfaces. This article will review the emerging role and applications of parylene as a biomaterial for surface chemical modification and provide a future outlook.

/pdf/surface-engineering-and-patterning-using-parylene-for-3pq4d2ky60.pdf

Surface engineering and patterning using parylene for biological applications

Epigenetic states are governed by DNA methylation and a host of modifications to histones bound with DNA. These states are essential for proper developmentally regulated gene expression and are perturbed in many diseases. There is great interest in identifying epigenetic mark placement genome wide and understanding how these marks vary among cell types, with changes in environment or according to health and disease status. Current epigenomic analyses employ bisulfite sequencing and chromatin immunoprecipitation, but query only one type of epigenetic mark at a time, DNA methylation, or histone modifications and often require substantial input material. To overcome these limitations, we established a method using nanofluidics and multicolor fluorescence microscopy to detect DNA and histones in individual chromatin fragments at about 10 Mbp/min. We demonstrated its utility for epigenetic analysis by identifying DNA methylation on individual molecules. This technique will provide the unprecedented opportunity...

Single Molecule Epigenetic Analysis in a Nanofluidic Channel

Nanomechanical resonators have shown potential application for mass sensing and have been used to detect a variety of biomolecules. In this study, a dynamic resonance-based technique was used to detect prion proteins (PrP), which in conformationally altered forms are known to cause neurodegenerative diseases in animals as well as humans. Antibodies and nanoparticles were used as mass labels to increase the mass shift and thus amplify the frequency shift signal used in PrP detection. A sandwich assay was used to immobilize PrP between two monoclonal antibodies, one of which was conjugated to the resonator's surface while the other was either used alone or linked to the nanoparticles as a mass label. Without additional mass labeling, PrP was not detected at concentrations below 20 μg/mL. In the presence of secondary antibodies the analytical sensitivity was improved to 2 μg/mL. With the use of functionalized nanoparticles, the sensitivity improved an additional 3 orders of magnitude to 2 ng/mL.

Prion protein detection using nanomechanical resonator arrays and secondary mass labeling.

We present “Print-and-Peel”, a high-throughput method to generate multicomponent biomolecular arrays with sub-100 nm nanoscale feature width. An inkjet printer is first aligned to a parylene template containing nanoscale openings. After printing, the parylene is peeled off to reveal uniformly patterned nanoscale features, despite the imperfect morphologies of the original inkjet spots. We further patterned combinatorial nanoarrays by performing a second print-run superimposed over the first, thereby extending the multiplexing capability of the technique.

Nanoscale Resolution, Multicomponent Biomolecular Arrays Generated By Aligned Printing With Parylene Peel-Off

Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification. In this work, we present a proof-of-principle demonstration for a new method using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state. This device evaluates the fluorescence from labeled epigenetic modifications to actuate sorting. This technology has demonstrated up to 98% accuracy in molecule sorting and has achieved postsorting sample recovery on femtogram quantities of genetic material. We have applied it to sort methylated DNA molecules using simultaneous, multicolor fluorescence to identify methyl binding domain protein-1 (MBD1) bound to full-duplex DNA. The functionality enabled by this nanofluidic platform now provides a workflow for color-multiplexed detection, sorting, and recovery of single molecules toward subsequent DNA sequencing.

Christine P. Tan

Papers

Surface engineering and patterning using parylene for biological applications

Single Molecule Epigenetic Analysis in a Nanofluidic Channel

Prion protein detection using nanomechanical resonator arrays and secondary mass labeling.

Nanoscale Resolution, Multicomponent Biomolecular Arrays Generated By Aligned Printing With Parylene Peel-Off

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel