Encyclopedia of Biophysics

Living Edition
| Editors: Gordon Roberts, Anthony Watts, European Biophysical Societies

Absorption Spectroscopy to Probe Ligand Binding

  • Alison RodgerEmail author
Living reference work entry
DOI: https://doi.org/10.1007/978-3-642-35943-9_778-1
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Synonyms

Definition

When a ligand solution is added to a solution of biomacromolecules, if it does not bind to the macromolecules, then the UV–visible spectrum will simply be the sum of the macromolecule spectrum and the ligand spectrum. If the ligand does bind to the macromolecules, then the spectrum of the complex will be (at least slightly) different from the sum spectrum. One should note that the observed spectrum is probably a complicated mixture of the spectrum of bound and unbound ligands and free and complexed macromolecules.

Sometimes there are changes in the spectrum characteristic of the type of interaction. For example, when two planar aromatic molecules bind together, such as an aromatic ligand intercalating between two DNA base pairs, there is usually a characteristic decrease in the ligand-absorbance signal (hypochromism) of up to 50% and a shift to longer wavelength (bathochromic shift) of between ∼2 and 20nm as illustrated in Fig. 1. In this example, the DNA spectrum is also affected by any molecule such as an intercalator which causes a structural change. This makes such spectra a useful probe of DNA–drug interactions but renders absorbance useless for concentration determinations unless the perturbed extinction coefficients are known.
Fig. 1

Absorbance spectrum of an anthracene derivative (B) (illustrated) (5 μM) in water in a 1-cm path length cuvette in the presence of increasing concentrations of DNA (0–84 μM as indicated in the figure). Compound B absorbance intensity decreases and redshifts as the DNA concentration increases. DNA has no absorbance above 320 nm (Tan et al. 2006)

Basic Characteristics

Titrations to Determining Data for Binding Constant Calculations

The term “titration” is used to cover experiments where spectra are collected as a function of concentration, ionic strength, pH, etc. To minimize macromolecule consumption and also (perhaps surprisingly) to minimize concentration errors, the best way to proceed is often to add solution to the cuvette. A simple way to avoid dilution effects is to proceed as follows. Consider a starting sample that has concentration x M of species X. Each time y cm3 of Y is added, also add y cm3 of a 2 x M solution of X. The concentration of X remains constant at x M. Many variants on this theme may be derived though all rely on the species in the solution establishing a new equilibrium. If the binding is extremely strong (e.g., covalent), then independent samples at the required molar ratios will usually need to be made.

Binding Constants

If the shape of the changes (i.e., the spectrum of bound minus spectrum of free) induced into a ligand or macromolecule spectrum remains unchanged during a titration experiment, but the magnitude changes in a manner that is proportional to the concentration of bound ligand, then we can conclude that the ligands are binding in one binding mode or in constant proportions in more than one mode (meaning site, orientation, sequence, etc.). In such cases, spectroscopic data can be used to determine the equilibrium binding constant, K. The data must be of very high quality for absorbance (or any other spectroscopic data) to be used to determine K. A simple plot of change in absorbance versus either total macromolecule or total ligand concentration (whichever is being varied) will probably enable the quality of the data set to be determined. It should be a smooth curve. There are many ways of proceeding from such a curve to a value for K. The one outlined below is designed to indicate the principles rather than necessarily being the best approach.

Whichever data analysis method one chooses, it is very important to check that its assumptions are valid for your situation. For example, the one developed by Schmechel and Crothers (1971) requires one binding site per base pair and small binding ratio. It has been popularized (Pyle et al. 1989) for any situation and so can be misleading.

We assume that we can think of the binding as a simple equilibrium:
$$ {L}_f+{S}_f\rightleftharpoons {L}_b $$
(1)
where L f is a free ligand, L b is a bound ligand, and S f is a free site. For DNA, it is often possible to consider it as a series of binding sites of n residues (bases or base pairs) in size. The total site concentration is then Stot = [M]/n, where [M] is the residue concentration of the macromolecule. For proteins, it is usually preferable to think in terms of the concentration of protein molecules rather than residues (amino acids). In this case, Stot = n’[M]; for n’ the number of binding sites per protein should be used. We may write:
$$ K=\frac{nc_b}{c_f\left[M\right]} $$
(2)

where c b is the concentration of bound ligand and c f is the concentration of the free ligand.

There are a large number of methods for determining K using absorbance data. The simplest is the enhancement method. This method is commonly used for fluorescence spectroscopy and may also be used to interpret absorbance data. We write:
$$ {\displaystyle \begin{array}{c}{c}_{\mathrm {tot}}A={c}_f{A}_f+{c}_b{A}_b\\ {}{c}_{\mathrm {tot}}A=\left({c}_{\mathrm {tot}}-{c}_b\right){A}_f+{c}_b{A}_b\\ {}{c}_b=\frac{c_{\mathrm {tot}}\left(A-{A}_f\right)}{A_b-{A}_f}\end{array}} $$
(3)

Application of this equation requires knowledge of the absorbance of free and bound ligand. Determining the latter requires measuring an absorbance spectrum under conditions where it is known that all the ligands are bound to the macromolecules. K may then be determined directly. A more accurate value of K will be achieved if the data are used to perform a Scatchard plot (Scatchard 1949) or fitted directly. The disadvantage of the Scatchard plot is it does not weight all data points equally. Its major advantage is that the curve should be a straight line, so it is obvious to the eye if Eqs. 2 or 3 is not appropriate for the system being studied.

The Scatchard plot is based on rewriting the equation for the equilibrium constant as:
$$ {\displaystyle \begin{array}{c}\frac{r}{c_f}=\frac{KS_f}{\left[M\right]}\\ {}=\frac{K}{n}- rK\end{array}} $$
(4)
where
$$ r=\frac{c_b}{\left[M\right]} $$
(5)

So, a plot of r/c f versus r has slope − K and y-intercept K/n. The x-intercept occurs where r = n.

Other methods commonly used with, for example, circular dichroism or linear dichroism data may be used with normal absorption data if the change in absorbance (the absorbance of the DNA–ligand system minus the absorbance of a free ligand solution of the same ligand concentration) is used in the analysis. Although CD signals induced upon ligand binding to a macromolecule are often much smaller than absorbance signals, they can be more informative, especially for achiral ligands such as the heme group in hemoglobin (Fig. 2).
Fig. 2

Absorbance and circular dichroism spectra of hemoglobin (1.6 mg/mL) in water in a 1-mm path length cuvette. The Soret band at 405 nm gives rise to a circular dichroism couplet at 390 nm and 410 nm upon binding to the protein.

Cross-References

References

  1. Pyle AM, Rehmann JP, Meshoyrer R, Kumar CV, Turro NJ, Barton JK (1989) Mixed-ligand complexes of ruthenium(II): factors governing binding to DNA. J Am Chem Soc 111:3051–3058CrossRefGoogle Scholar
  2. Scatchard G (1949) The attractions of proteins for small molecules and ions. Ann NY Acad Sci 51:660–672CrossRefGoogle Scholar
  3. Schmechel DEV, Crothers DMB (1971) Kinetic and hydrodynamic studies of the complex of proflavine with poly A·poly U. Biolopymers 10:465–480Google Scholar
  4. Tan WB, Bhambhani A, Duff MR, Rodger A, Kumar CV (2006) Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition. Photochem Photobiol 82:20–30CrossRefPubMedGoogle Scholar

Copyright information

© European Biophysical Societies' Association (EBSA) 2018

Authors and Affiliations

  1. 1.Department of Molecular SciencesMacquarie UniversitySydneyAustralia

Section editors and affiliations

  • Alison Rodger
    • 1
  1. 1.Department of Molecular Sciences, Macquarie UniversityNWSAustralia