hydrophobic associations. Interaction of amino acids with ribonucleic acids is an
important and relevant subject to understand prebiotic scenarios [80].
3.3.1 Electrostatic Interactions
The most obvious interaction force is electrostatic, due to charged amino acids on
proteins and the presence of ionizable structures within the chain of nucleic acids.
Both are zwitterions since they can switch from acidic character to alkaline ones,
depending on the environmental pH. For a large pH range (e.g., between 4–5 and
12), nucleic acids are dominantly acidic and have a clear propensity to interact
electrostatically with proteins. The latter have mostly a dominant positive charge
above pH 5, thus generating a natural attraction between these entities.
Subsequent to this first “molecular meeting,” other interactions take place
progressively. In an interesting article, Rohs et al. [81] subdivided the nucleic
acid-protein interaction in two main categories of dockings: the first is named
“base readout” where the protein simply recognizes the signature of DNA bases
and the second named “shape readout” in which the interaction is sequencedependent and therefore much more specific. It comprises, at the same time, hydrogen bonds and hydrophobic associations, both described below.
Distinguishing between specific and non-specific electrostatic interaction was the
purpose of a paper published by Privalov et al. [82]. This classification was specified
by the sensibility of the interaction in the presence of salts. It was concluded that the
electrostatic binding energy was fully entropic, as opposed to the enthalpy of binding
when the interaction was not sensitive to the presence of salts. With this interpretation, it is admitted that electrostatic interaction is relatively secondary to the specificity of the complex formation, but contributes mostly at the initial stage of the
interaction process, and therefore to the affinity between proteins and nucleic acids.
3.3.2 Hydrogen Bonding
Hydrogen bonding occurs when two electronegative atoms share or compete for a
hydrogen atom. The electronegativity of involved atoms, which increases when
more than one electron is exposed to the external electron shell, triggers the type
of hydrogen bond. Not all molecules that have hydrogen atoms form hydrogen
bonds; however, considering the complex composition of both, aptamer and proteins, a large variety of hydrogen bonds can be present. The formation of a hydrogen
bond must occur when few conditions are satisfied: first, when the proton donor
group and the acceptor come into close proximity (typically around 0.3 nm), and
second, when the hydrogen atom faces the electron pair. Although there are some
restrictions to prevent the formation of such bonds between two identical entities,
ideal configurations are generally easily reached with distinct molecules. This
corresponds to the case of both aptamers and proteins. The angle and the distance
of a hydrogen bond between the proton acceptor and the hydrogen atom are
Aptamer-Based Affinity Chromatography for Protein Extraction and Purification
103
important and relevant subject to understand prebiotic scenarios [80].
3.3.1 Electrostatic Interactions
The most obvious interaction force is electrostatic, due to charged amino acids on
proteins and the presence of ionizable structures within the chain of nucleic acids.
Both are zwitterions since they can switch from acidic character to alkaline ones,
depending on the environmental pH. For a large pH range (e.g., between 4–5 and
12), nucleic acids are dominantly acidic and have a clear propensity to interact
electrostatically with proteins. The latter have mostly a dominant positive charge
above pH 5, thus generating a natural attraction between these entities.
Subsequent to this first “molecular meeting,” other interactions take place
progressively. In an interesting article, Rohs et al. [81] subdivided the nucleic
acid-protein interaction in two main categories of dockings: the first is named
“base readout” where the protein simply recognizes the signature of DNA bases
and the second named “shape readout” in which the interaction is sequencedependent and therefore much more specific. It comprises, at the same time, hydrogen bonds and hydrophobic associations, both described below.
Distinguishing between specific and non-specific electrostatic interaction was the
purpose of a paper published by Privalov et al. [82]. This classification was specified
by the sensibility of the interaction in the presence of salts. It was concluded that the
electrostatic binding energy was fully entropic, as opposed to the enthalpy of binding
when the interaction was not sensitive to the presence of salts. With this interpretation, it is admitted that electrostatic interaction is relatively secondary to the specificity of the complex formation, but contributes mostly at the initial stage of the
interaction process, and therefore to the affinity between proteins and nucleic acids.
3.3.2 Hydrogen Bonding
Hydrogen bonding occurs when two electronegative atoms share or compete for a
hydrogen atom. The electronegativity of involved atoms, which increases when
more than one electron is exposed to the external electron shell, triggers the type
of hydrogen bond. Not all molecules that have hydrogen atoms form hydrogen
bonds; however, considering the complex composition of both, aptamer and proteins, a large variety of hydrogen bonds can be present. The formation of a hydrogen
bond must occur when few conditions are satisfied: first, when the proton donor
group and the acceptor come into close proximity (typically around 0.3 nm), and
second, when the hydrogen atom faces the electron pair. Although there are some
restrictions to prevent the formation of such bonds between two identical entities,
ideal configurations are generally easily reached with distinct molecules. This
corresponds to the case of both aptamers and proteins. The angle and the distance
of a hydrogen bond between the proton acceptor and the hydrogen atom are
Aptamer-Based Affinity Chromatography for Protein Extraction and Purification
103