Affinity Chromatography

1. AFFINITY CHROMATOGRAPHY
Affinity chromatography is a method of separating biochemical mixtures based on a highly
specific interaction such as that between antigen and antibody, enzyme and substrate, or
receptor and ligand.
PRINCIPLE
The stationary phase is typically a gel matrix; a linear sugar molecule derived from algae.
Usually the tarting point is an undefined heterogeneous group of molecules in solution, such as
blood serum. The molecule of interest will have a well known and defined property, and can be
exploited during the affinity purification process. The process itself can be thought of as an
entrapment, with the target molecule becoming trapped on a solid or stationary phase or
medium. The other molecules in the mobile phase will not become trapped as they do not
possess this property. The stationary phase can then be removed from the mixture, washed
and the target molecule released from the entrapment in a process known as elution. Possibly
the most common use of affinity chromatography is for the purification of recombinant
proteins.

2. PROCEDURE
Step-1: Attach ligand to column matrix
 Binding of the selected ligand to the matrix requires that a covalent bond be formed
between the two.
 This is facilitated by derivatization of the sugar residues' hydroxyl groups.
 It is important to realize that the substrate might not be able to reach the ligand active
site if it is hidden deep within the ligand.
 Most ligands are attached first to spacer arms which are then bonded to the matrix. The
ligand-matrix gel is then loaded into an elution column.

3. STEP 2: Load protein mixture onto column
 Once the column has been prepared, the mixture containing isolate is poured into the
elution column.
 Gravity pulls the solution through the gel, because most of the proteins do not bind to
the ligand-matrix complex.
 When ligand is recognized substrate passes through the gel, it binds to the ligand-matrix
complex, halting its passage through the gel.
 Some of the impurities flow through the gel due to gravity, but most remain, unbound,
in the gel column
STEP 3: Protein bind to ligands
 In order to remove these unbound impurities, a wash of extreme pH, salt concentration,
or temperature is run through the gel.
 It is important to use a strong wash so that all the impurities are removed.
 Once the impurities are washed-out, the only remaining part of the protein mixture
should be the desired isolates.

4. STEP 4: wash column to remove unwanted material
Finally to collect isolate, which is still bound to the ligand-matrix in the gel, a stronger second
wash is run through the column.
STEP 5: Wash off proteins that bind loosely
This second wash relies on the reversible binding properties of the ligand, which allows the
bound protein to dissociate from its ligand in the presence of this stronger wash.
STEP 6: Elute proteins that bind tightly to ligand and collect purified protein of interest
The protein is then free to run through the gel and be collected.

5. INDUSTRIAL APPLICATIONS
 Affinity chromatography is widely used in the pharmaceutical industry to purify and
extract molecules of interest from complex mixtures.
 These molecules tend to be enzymes, proteins or amino acids, but other biological
species can be selectively etained.
 Once isolated, these biological species can be selectively amplified to produce larger
quantities, although at large concentrations.
GEL FILTRATION CHROMATOGRAPHY
Introduction
Gel filtration chromatography is used to separate proteins, peptides and oligo-nucleotides on
the basis of their size only. It is also known as size exclusion chromatography. In gel filtration, as
sample moves through a bed of porous beads, molecules of different size diffuse into the beads
to greater or lesser extent. Small molecules enter further into the beads and thus, elute slowly.
In comparison to that, large molecules enter less or move directly through the void space and
thus, eluting fast. Gel Filtration Chromatography is widely applied for molecular size analysis,
separation of components of a mixture, as well as for desalting and buffer exchange.

6. Principle
The separation of molecules on the basis of their molecular size and shape is achieved by gel
filtration chromatography. It uses the molecular sieve properties of various porous resins. Large
molecules that are completely excluded from the pores pass through the void space, interstitial
spaces between the resin particles and thus, they elute first. While smaller molecules get
distributed between the mobile phase inside and outside the beads and therefore pass through
the column at a slower rate. Thus, they elute in the last. Trapping of the mobile phase inside
the beads solely depends upon the porosity of the resin beads and the size of the molecules to
be separated (figure 1). Thus, the distribution of a molecule in a gel filtration column of
crosslinked beads is determined by the total volume of mobile phase, both inside and outside
the beads. In case of gel filtration chromatography, the distribution coefficient of a molecule
between the inner and outer mobile phase is a function of its molecular size. If a molecule is
sufficiently large to completely exclude from the mobile phase between the beads, then K = 0.
On the other hand, if a molecule is so small that it accesses to the innermost mobile phase deep
in the beads, then K = 1. For others, value of K will vary between 0 and 1. This variation of K
between 0 and 1 makes it possible to separate various molecules present in a mixture within a
narrow molecular size range.
Figure 1: Gel filtration chromatography

7. Process of gel filtration
Buffer selection – Any buffer in which the analyte to be separated is stable can be used as pH,
ionic strength and composition do not significantly affect resolution, though the buffer should
maintain the buffering capacity and constant pH . Low strength salt can be added to the buffer
to avoid any interaction with gel particle or if there is an ionic interaction between molecules to
be separated. The sample buffer does not have to be the same buffer as the column, but prior
to running the column should be equilibrated with sample buffer. Extreme pH conditions and
ionic strengths should be avoided because it may affect the gel as well as separation. Prior to
using, all buffers should be filtered through a 0.22µm membrane. Some commonly used buffers
are Tris-HCl and phosphate.
Sample preparation & loading – The sample should not be diluted as it may cause band
broadening. Thus, it should be concentrated; however it should not be that concentrated that it
precipitates. Ideally, 1% of bed volume of sample should be loaded onto the column. The
sample should be clear, free of any debris; therefore it should be filtered prior to loading. To
load the sample manually, remove the upper adapter and remove the excess of the buffer on
the top of the gel without disturbing the gel surface. Then, gently pipette in the sufficient
amount of sample and allow the sample to pass through the surface. At the time, take care that
the surface of the gel does not dry. Finally, add little buffer to the column and set the upper
adapter. The above processes can also be done by automated sample injector.
Flow rate – Ideally the flow rate should be slow in the range 6-12mL/hr. The slower flow rate
may cause diffusion and high flow rate may cause poor resolution.
Elution – A fraction collector is attached to the system to collect the fractions of the elution.
The sample is eluted isocratically using a single buffer system. The length of tubing connected
to fraction collector should be small and small fractions of size 1mL or less should be collected
to avoid mixing of peaks. The detector connected to the fraction collector analyses the
separation. The total elution should be equal to or more than one bed volume. The volume of
the buffer that elutes from the column before a particular peak in the elution profile appears is
called elution volume (Ve). The distribution coefficient (Kd) of an analyte in gel filtration

8. chromatography can be mathematically defined as Kd =Ve –V0/ Vt – V0 After completion of
each run, the column should be washed thoroughly to remove any analytes left in the gel.
Ideally, it should be done by 1-2 bed volumes of buffer. For long term storage, antimicrobial
agents should be added to the buffer.
Applications
(i) Molecular weight determination - Gel filtration chromatography is widely applied for
determination of the molecular weight of proteins. The molecular weight of a given protein is
estimated by comparing its elution volume with that of known protein standards. The standard
curve is constructed by plotting logarithm of the molecular weights of standard proteins against
their respective ratios of elution volume to column void volume (Ve/V0). This standard curve is
then used to determine the molecular weight of unknown proteins.
(ii) Desalting - Salt molecules and buffer components are several times smaller in comparison
to macromolecules. For this reason, gel filtration chromatography using a resin with smaller
sizeexclusion limits can be used for desalting and buffer exchange applications. Desalting is the
process of salt removal from a protein sample, while in buffer exchange a protein solution is
replaced by more appropriate buffer. This is one of the most applied applications of gel
filtration chromatography. The separation limits for resins are generally in range of up to 10
kDa. Resins with large exclusion limits are not suitable for buffer exchange and desalting
application.
(iii) Separation of macromolecules – Gel filtration chromatography is commonly applied in
research laboratories for separation of proteins and peptides. It is applied for detection and
separation of oligomers.
(iv) Group separation - Gel filtration chromatography is also applied for fractionation of crude
samples into low and high molecular weight protein groups.

9. References
 Fundamentals of Analytical Chemistry(D.A. Skoog and D.M. West)
 www.ucl.ac.uk
 www.sigmaaldrich.com/content
 quimica.udea.edu.co
 www.thomassci.com
 mymission.lamission.edu