Primers

Puzzarini and colleagues explore the computational characterization of medium-sized molecular systems using different spectroscopic techniques. The Primer provides essential information about the characteristics, accuracy and limitations of current computational approaches used for modelling spectroscopic phenomena with a focus on estimating error bars, limitations and coupling interpretability to accuracy.

Bian et al. discuss the utility of different variants of scanning probe microscopy, with a focus on scanning tunnelling microscopy and atomic force microscopy. They summarize how the tools are used in the life and physical sciences.

This Primer on in situ electron paramagnetic resonance spectroscopy describes various experimental set-ups to acquire spectral information on the paramagnetic state of chemical species with unpaired electrons present during catalytic reactions, with the goal of unravelling catalytic mechanisms and optimizing catalyst activity.

This Primer discusses methods for characterizing the subcellular location and organization of cellular proteins. The authors outline methods for generating spatially resolved proteomics data and describe tools and considerations for data analysis, before discussing the applications of these methods for investigating protein trafficking, identifying multi-localized proteins and localizing proteins at sub-organelle resolution.

The underlying mechanisms and optimal conditions that drive biorthogonal reactions and the utility of these for applications in medicinal chemistry and protein synthesis to polymers and materials science are described in this Primer. Current reproducibility standards and how current reaction limitations are driving new research efforts are also discussed.

This Primer on parallel nuclear magnetic resonance describes various parallelization techniques ranging from hardware design to pulse sequence development that allow concurrent acquisition of different signals and lead to an increase in both data acquisition speeds and sensitivity when elucidating molecular structures.

This Primer on optical tweezers describes the instrumentation and experimental designs used in most single-molecule optical tweezers assays and discusses optical tweezers measurements in systems of biophysical interest such as DNA elasticity, protein and RNA folding, and molecular motors.

This Primer summarizes the most relevant aspects of chemical synthesis in this information age for those looking to understand the software, hardware and data and how these are used to enable retrosynthetic logic, reaction prediction and automation.

This Primer discusses the basic concepts, experimental considerations and diverse applications of spatially offset Raman spectroscopy (SORS). The authors describe available SORS modalities and their advantages and disadvantages, outline strategies for analysing SORS data and discuss future directions and applications for this novel spectroscopic technique.

Ule and colleagues discuss cross-linking and immunoprecipitation (CLIP) methods for characterizing the RNA binding partners of RNA-binding proteins and explore the data analysis workflows, best practices and applications for these techniques. The Primer also considers methods for characterizing the protein binding partners of specific RNAs and discusses how data from these complementary methods can be integrated into CLIP workflows.

This Primer on X-ray computed tomography explores the different experimental configurations for three-dimensional data acquisition as well as the fundamentals of three-dimensional data reconstruction, segmentation and analysis with examples across the physical and life sciences.

This Primer outlines the best ways to find, handle and analyse ancient DNA from various sources. The authors summarize ethical considerations and the importance of working closely with all stakeholders, including archaeologists, curators and descendant communities.

Dey et al. discuss the design and implementation of DNA origami, as well as the techniques used to analyse quality and construction. They summarize exciting new research areas where DNA nanotechnology is being used and future directions for the field.

This Primer on chromatin accessibility profiling methods discusses differences in the methods commonly used to determine chromatin states in different cell types, including ATAC-seq and ChIP–seq. The authors summarize applications in different areas of research, from single cells to tissues and whole organisms.

This Primer on chemical vapour deposition summarizes current and emerging experimental set-ups as well as common characterization approaches used to determine thin film formation and quality as applied to graphene and other novel 2D materials.

This Primer on Bayesian statistics summarizes the most important aspects of determining prior distributions, likelihood functions and posterior distributions, in addition to discussing different applications of the method across disciplines.

This Primer by Wannier and colleagues summarizes the methodology, analysis and utility of recombineering and multiplex automated genome engineering (MAGE) in microbial species. In addition, this Primer examines advanced techniques that pair MAGE with other tools to improve editing efficiency.

This Primer on solid-state nuclear magnetic resonance spectroscopy summarizes the most common experiments and data analysis approaches used to determine the structure and dynamics of solids and semi-solids as applied to biology, chemistry and materials sciences.