Synthetic peptide-DNA created as modular scaffold for variety of applications

Control over distinct properties of soft biomaterials is often difficult to accomplish: changing the chemistry alters the mechanics at the same time. A modular approach to functionality may be offered by the ability to decorate DNA with peptides of interest, thereby encoding the chemistry presented while retaining DNA’s distinct flexibility and compatibility with a wide variety of materials, biosensing and nanomanipulation strategies.

HFSP Program Grant holders Paul Curmi, Nancy Forde, Heiner Linke and Derek Woolfson and colleagues
authored on Tue, 13 January 2015

It is becoming increasingly clear that nano- and microscale chemical and mechanical properties exert a strong influence on cellular fate, macroscale material properties, and biological compatibility. However, to test hypotheses regarding the influence of individual parameters requires modularity in design: the ability to tune local chemistry, for example, without changing mechanics. This challenge has been particularly difficult to overcome in the field of soft fibrous materials, where construction materials such as peptides result in coupling of chemical and structural features, while using DNA as a building block has so far had limited chemical modifications, particularly for lengthy DNA structures.

Recent work sponsored by HFSP has taken initial steps demonstrating one approach to overcoming this hurdle of modularity. Led by researchers at Simon Fraser University, the team used a combination of PCR and click chemistry to construct kilobasepair-long DNA constructs presenting a tunable density of incorporated peptides along their length. Using single-molecule AFM imaging and analysis, they showed that the resulting DNA maintained its characteristic flexibility, even following covalent incorporation of peptides at high density. Furthermore, by linking peptides containing a protease recognition site, their fluorescence measurements demonstrated that trypsin was able to bind and cleave even densely incorporated peptides (1 peptide / 3 basepairs = 1 peptide / nanometer), thereby suggesting that the peptides retained their ability to present information to the enzyme, even when attached to the DNA backbone.

This work demonstrates an important advance towards modular design of soft scaffolds, which have many possible applications. DNA has been used as a scaffold for cell engineering, cell-free translation and drug delivery; this work suggests a straightforward means, using commercially available reagents, by which it can be chemically modified for these and other applications. Because its flexibility is maintained following modification, this type of construct lends itself well to applications with a growing number of nanomanipulation strategies, for example, suggesting its potential use as tracks for directing nanoscale motion. Furthermore, the ability to densely incorporate peptide (or other chemical) signals onto DNA of this length suggests applications to biosensing, where polyvalency arising from a tunable spatial density of peptides can be used to enhance signal.

Reference

Construction and Characterization of Kilobasepair Densely Labeled Peptide-DNA. S. Kovacic, L. Samii, G. Lamour, H. Li, H. Linke, E.H.C. Bromley, D.N. Woolfson, P.M.G. Curmi and N.R. Forde. Biomacromolecules 15, 4065–4072 (2014)

Pubmed link