Differential Scanning Calorimetry to Study DNA Aptamer-Thermolabile Ligand Interaction

Abstract

Source: Mittermaier, A. K., et al. Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions. J. Vis. Exp. (2017)

This video demonstrates differential scanning calorimetry — a technique to study the interaction between a biomolecule and a ligand. The binding of a DNA aptamer and a thermolabile ligand is studied by applying repeated heating and cooling cycles to the sample and obtaining scans for thermodynamic analysis.

Protocol

1. Sample Preparation

1. Purify the desired biomolecule.
   NOTE: This protocol uses purchased cocaine-binding DNA aptamer MN4 after exchanging against 2 M NaCl three times followed by three rounds of deionized water using a centrifugal filter with a 3 kDa molecular weight cut-off membrane.
2. Synthesize and purify, or purchase the desired thermolabile ligand.
   NOTE: MN4 binds the thermolabile ligand cocaine. MN4 also binds quinine, which is used as a negative control for ligand thermolability at these experimental temperatures.
3. Prepare buffers for dialysis of the purified biomolecu....

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Sodium chloride	Chem Impex	#00829
Sodium phosphate monobasic dihydrate	Sigma Aldrich	71502
Sodium phosphate dibasic	Sigma Aldrich	S9763
Deioinized water for molecular biology	Millipore	H20MB1001
0.2-micron sterile syringe filters	VWR	CA28145-477
3 kDa centrifugal filters	Millipore	UFC900324
Dialysis tubing 0.5-1.0 kDa cutoff	Spectrum Laboratories	131048
Silicon tubing	VWR	89068-474
Plastic DSC flange caps	TA Instruments	6111
DNA aptamer MN4	Integrated DNA Technologies	https://www.idtdna.com/site/order/menu
Cocaine	Sigma Aldrich	C008
Quinine	Sigma Aldrich	22620
NanoDSC-III microcalorimeter	TA Instruments	http://www.tainstruments.com/nanodsc/
DSCRun software	TA Instruments	http://www.tainstruments.com/support/software-downloads-support/instruments-by-software/
NanoAnalyze software	TA Instruments	http://www.tainstruments.com/support/software-downloads-support/instruments-by-software/
Contrad-70	VWR	89233-152