Research Article: Biomacromolecules as tools and objects in nanometrology—current challenges and perspectives

Date Published: August 14, 2017

Publisher: Springer Berlin Heidelberg

Author(s): Payam Hashemi, Luise Luckau, Petra Mischnick, Sarah Schmidt, Rainer Stosch, Bettina Wünsch.

http://doi.org/10.1007/s00216-017-0554-9

Abstract

Nucleic acids, proteins, and polysaccharides are the most important classes of biopolymers. The inherent properties of biomacromolecules are contrary to those of well-defined small molecules consequently raising a number of specific challenges which become particularly apparent if biomacromolecules are treated as objects in quantitative analysis. At the same time, their specific functional ability of molecular recognition and self-organization (e.g., enzymes, antibodies, DNA) enables us to make biomacromolecules serving as molecular tools in biochemistry and molecular biology, or as precisely controllable dimensional platforms for nanometrological applications. Given the complexity of biomacromolecules, quantitative analysis is not limited to the measurement of their concentration but also involves the determination of numerous descriptors related to structure, interaction, activity, and function. Among the biomacromolecules, glycans set examples that quantitative characterization is not necessarily directed to the measurement of amount-of-substance concentration but instead involves the determination of relative proportions (molar ratios) of structural features for comparison with theoretical models. This article addresses current activities to combine optical techniques such as Raman spectroscopy with isotope dilution approaches to realize reference measurement procedures for the quantification of protein biomarkers as an alternative to mass spectrometry-based techniques. Furthermore, it is explored how established ID-MS protocols are being modified to make them applicable for quantifying virus proteins to measure the HIV viral load in blood samples. As an example from the class of carbohydrates, the challenges in accurate determination of substitution patterns are outlined and discussed. Finally, it is presented that biomacromolecules can also serve as tools in quantitative measurements of dimensions with an example of DNA origami to generate defined dimensional standards to be used for calibration in super-resolution fluorescence microscopy.

Partial Text

Biomacromolecules are naturally occurring macromolecular compounds that make up the essential building blocks of nearly all types of biological systems. Nucleic acids, proteins, and polysaccharides are the most important classes of biopolymers which are formed through condensation of their monomeric units: nucleotides, amino acids, and monosaccharides. The huge number of monomers linked together during polycondensation and the countless combinations that exist for sequencing them lay the foundation for an enormous diversity and structural complexity. Thus, biomacromolecules often exhibit a high degree of functionality and the ability for branching and/or subsequent chemical modification that facilitates the formation of linear and non-linear 2D/3D biopolymer architectures [1].

Over the last two decades, complex biomolecules such as proteins increasingly gained in importance due to their ability to act as biomarker for supporting early diagnosis and monitoring of widespread diseases. The most commonly used standard techniques for their quantification in human body fluids are immunochemical-based test kits. Nevertheless, the high diversity and complexity of protein markers can lead to varying results depending on the assay design. To assure both SI traceability and comparability of the results of routine laboratory tests, reference measurement procedures are urgently needed.

In contrast to proteins and DNA with their identical copies of defined macromolecules, polysaccharides—the most abundant class of biopolymers—usually do not possess a distinct size and sequence. Rather, they show various types of dispersity with respect to molecular weight, structure, and chemistry, including branching, sequence, and average composition of constituents. Furthermore, their polyfunctionality invites to chemical modification to obtain new materials, e.g., for biomedical and construction applications. To elucidate structure-property relationships, the structure has to be described in form of quantitative patterns and profiles with the highest resolution possible. As an example, water-solubility and thermoreversible gelation of methyl cellulose (MC) do not only depend on the average degree of substitution (DS) with methyl groups, but also on their location on the cellulose-constituting monomer, glucose, and on their distribution along and over the macromolecules [19]. Consequently, the analytical challenge is not the determination of absolute concentrations of uniform and defined analytes, but the probabilities of certain structural features, defined by their average degree of polymerization (DP) and DS.

While we have just shown how biomacromolecules can serve as objects, we will now focus on their use as a tool in nanometrology. We therefore discuss DNA origami because they are currently one of the most prominent nanoscopic examples.

The methods and applications discussed in this perspective are developing strategies for the analysis of biomacromolecules at the nanoscale. Quantification of biomacromolecules that serve as diagnostic markers is a challenging task in medical diagnostics. In this context, the availability of reference measurement procedures is of major importance since only those methods are suitable to adequately provide the necessary quality assurance in clinical laboratory medicine. Alternatives to ID-MS-based techniques such as ID-SERS are suitable to complement the portfolio of existing metrological tools. This would in any case be justified, since the huge number, diversity and complexity of potential biomarkers will most probably not be covered by a single universal analytical approach. Further development of existing MS methods towards the determination of viral loads would also help to improve reliability and comparability of routine test procedures for disease monitoring. Both the patients’ well-being and the healthcare system would likewise benefit from the availability of such a metrological basis in clinical chemistry.

 

Source:

http://doi.org/10.1007/s00216-017-0554-9

 

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