Mechanisms of DNA Adsorption to Soil Particles

Student: Maline Elumelu

Advisor: Dr. Michael Sander
Department of Environmental Sciences, Institute of Biogeochemistry and Pollutant Dynamics
(IBP), Swiss Federal Institute of Technology (ETH), Zurich

Abstract
It has been found that DNA adsorbed to soil particles can be partially protected against
enzymatic degradation. Soils are a very heterogeneous matrix, consisting of various types of
minerals in different sizes and organic matter. The soil surfaces can be positively or
negatively charged. Above pH 5.0, DNA is overall negatively charged. Various soil particles
are negatively charged as well, including clay minerals, quartz, and soil organic matter. Under
certain conditions DNA can overcome this electrostatic repulsion and adsorb to negatively
charged soil particles. The following factors have a major influence on DNA adsorption to
negatively charged soil particles: pH, ligands, ionic strength and valence. At pH 2.0, DNA
was found to adsorb strongly to soil colloids and minerals. An increase in pH leads to a
decrease in DNA adsorption. This pH dependence likely reflects the release of protons by
bases of the DNA molecule, which decreases its positively charged sites. As a consequence, it
is reasonable to expect that more DNA will be adsorbed in acidic than in alkaline soils.
Increasing ionic strength of monovalent cations leads to higher DNA adsorption, because the
cations screen the negative charges between the DNA and the negative surface. Divalent
cations can form complexes with the phosphate backbone DNA and some negatively charged
functional groups of the soil matrix, promoting DNA adsorption even better. The presence of
inorganic ligands, like phosphate, citrate or tartrate, can decrease adsorption due to the
competition between the DNA and the ligands for adsorption sites. On the other hand,
depending on the ligand concentration and the surface type, ligands can also promote DNA
adsorption by dissolving aluminum from soil particles and thus creating new adsorption sites.
The Structure of DNA also has an effect on its adsorption. Linear plasmid DNA adsorbes
better than supercoiled DNA at low ionic strength, at high ionic strength they adsorbed
similar.

1
1 Introduction
Many people are concerned about the evolutionary impact of genetically modified plants and
microorganisms released to the environment. The release could lead to an unwanted spread of
these transgenes and tracer genes, which encode resistance to antibiotics, to native organisms.
However, DNA adsorption in soils must have occurred long before the development of
genetically modified organisms and may have been of fundamental importance for microbial
evolution and ecology.
Lateral gene transfer among bacteria can occur through three different mechanisms:
conjugation, transduction and transformation (13). During conjugation, plasmid DNA is
directly transferred from a donor to a recipient cell. Transduction is a gene exchange mediated
by bacteriophages. The uptake of naked DNA by competent bacterial cells is referred to as
transformation (13). In the latter process, linear and supercoiled DNA, both either
chromosomal or plasmid, can be acquired by the cell (12). Linear DNA is incorporated by
substituting homologous sequences of the recipient’s genome. Contrarily, during plasmid
transformation, a new plasmid replica is established in the recipient cell, where the plasmid
can be replicated autonomously (14). In soil environments DNA molecules are both released
by dying cells and excreted actively by living cells (5). It has been found that DNA adsorbed
to soil particles can be partially protected against enzymatic degradation (1,9).
It is crucial to thoroughly understand the fate of DNA molecules in order to assess whether
transformation can naturally occur, and, if so, its likelihood.

The scope of this term paper is to provide a survey of possible interactions between DNA and
soil particle surfaces, and to point out important factors that affect DNA-surface interactions.
First the structure of the DNA molecule and the chemical properties of some main
constituents of soils will be discussed briefly. DNA is negatively charged below pH 5, so
adsorption to positively charged surfaces such as aluminum and iron oxides is very likely.
However, various soil particles are negatively charged, including clay minerals, quartz, and
soil organic matter. To which extent and by what mechanism DNA would adsorb to these
negative surfaces, depends strongly on the solution chemistry of the soil. In particular the
following factors are important and will be addressed: pH, ligands, ionic strength and valence.
A pH below 5 generally promotes DNA adsorption by adding protons to the bases of the
DNA, creating positive sites in the molecule. High ionic strength of monovalent cations also
promotes DNA adsorption, due to charge screening of negatively charged sites within the
molecule and between the molecule and the surface. Divalent cations, especially calcium,
have even a higher promotive effect. Calcium can form “inner-sphere” complexes with the
phosphate groups of the DNA and form bridges between DNA and soil mineral surfaces. The
mechanism of DNA adsorption is expected to strongly influence the desorption behavior and,
therefore, the availability of adsorbed DNA for microbial transformation.

2
2 General description of chemical properties
2. 1 Chemical Properties of DNA and Sites of Interaction with Soil Particles

The DNA molecule consists of the

bases guanine, cytosine, adenine
and thymine linked to pentose
sugars, which are connected to
each other by phosphate. The two
strands of the molecule are hold
together by H-bonds between
complementary base pairs (Figure
1). The pKa value for the
dissociation of H3PO4 to H2PO4- is
2.12 (17). Hence, above pH 2, the
phosphate groups are likely to be
negatively charged. The isoelectric
point of DNA is about 5.0, below
pH 5.0 the bases can accept
protons which creates positive
charged sites in the DNA molecule
(14). If the pH is above 5.0, DNA
is overall negatively charged (6). It
can be considered as a polyanion
(14).
DNA forms a double helix which
Figure 1: Structure formula of DNA (15). can form several conformations (9).
Bacterial DNA can be arranged as a linear or circular molecule. The covalently closed circular
form of bacterial plasmid DNA will spontaneously contort around its own axis, adopting
twisted shape that is referred to as supercoiled.
DNA could, in principle, adsorb to soil particles at various sites. The bases, the phosphate
groups, and free hydroxyl groups of ribose at the end of each DNA strand are possible
candidates for an interaction with soils.

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2.2 Surface Properties of Soil Particles

Soils are a very heterogeneous matrix, consisting of various types of minerals in different
sizes and living or death organic matter. This heterogeneity creates a vast multitude of
surfaces to which DNA can adsorb. These surfaces can be positively or negatively charged.
Iron and aluminum oxides are positively charged at acidic to circumneutral pH and negatively
charged at alkaline pH, so their charge is variable (16). Silicon oxides and the planar surfaces
of clay minerals typically carry a net negative charge above slightly acidic pH.
As both DNA and soil mineral surfaces, except for Al- and Fe-oxides, are negatively charged,
DNA approaching a surface has to overcome electrostatic repulsion.
Quartz, SiO2, the most abundant silica in rocks and soils has a point of zero charge near pH
3.0 (2). Goethite is very abundant iron oxide in soils of temperate climate all over the world.
The PZC of goethite is around pH 8.
Isomorphic substitution in clay minerals leads to a permanent negative surface charge (2). At
the edges of clay minerals, aluminum hydroxide functional groups are exposed to the
environment. These hydroxyl groups can be protonated to carry a positive charge. Kaolinite, a
1:1 sheet silicate with not much isomorphic substitution, has a point of zero charge at pH 3.6
(16). More isomorphic substitution and therefore higher negative surface charges are found in
the 2:1 phyllosilicates illite and montmorillonite. Montmorillonite has a point of zero charge
of 2.5.

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3 Characteristics of DNA Adsorption to Soil

3.1 DNA Adsorption to Various Soil Particles

DNA adsorption to various types of soil particles with different surface properties has been
studied. The main types of soil particles under consideration in this work are different sizes of
clay particles of a clay loamy Brown Soil (Alfisol), quartz (2), the iron oxide goethite, and the
clay minerals kaolinite, illite, and montmorillonite (6,8). The chemical properties of the clay
particles, goethite, the clay minerals kaolinite and montmorillonite are listed in Table 1. By
H2O2-treatement of clay particles substantial parts of organic matter is removed from their
surface, they will further be referred to as inorganic clays.

Table 1: selected properties of soil colloids and minerals studied.a Data and figure legend
taken from (6) (….) and (8)(….).
soil colloid or mineral O.M. SESA PZC CEC composition
-1 2 -1 -1
(g kg ) (m g ) (cmol kg )
Total Clay (<2µm) 71.0 64.4 2.1 57.6 hydromica (55%)
vermiculite (30%),
kaolinite (15%)
H2O2-Treated 9.6 77.1 3.3 47.9
Coarse Clay (0.2-2µm) 67.6 31.7 2.4 46.2 hydromica (45%),
vermiculite (35%),
kaolinite (20%)
H2O2-Treated 5.9 37.5 3.5 41.2
Fine Clay (<0.2µm) 74.4 97.1 1.8 68.9 hydromica (60%)
vermiculite (30%),
kaolinite (10%)
H2O2-Treated 13.3 116.5 3.0 54.5
montmorillonite - 73.6 2.5 90.2 montmorillonite
kaolinite - 22.9 3.6 7.1 kaolinite
goethite - 83.0 8.7 0 goethite
a
Clay mineral was determined by X-ray diffraction analysis. Organic matter (O.M.), point of
zero charge (PZC), cation exchange capacity (CEC) and specific external surface area
(SESA) were analyzed by K2Cr2O7 digestion and N2 adsorption method, respectively.

5
A Langmuir isotherm for the adsorption of DNA to various soil colloid fractions and minerals
has been found by Cai et al. (Figure 2). The properties of the soil particles are listed in Table
1. The soil particles were inoculated with salmon sperm DNA. Adsorption was calculated
indirectly by depletion of DNA from solution.

Figure 2: Equilibrium adsorption of DNA from salmon sperm DNA (25-350 µg) on 10 mg of
soil colloids and kaolinite and 1 mg of montmorillonite. Inorganic clays have been H2O2-
treated to remove organic matter from their surface. Figure and figure legend taken from 8.

The adsorption maxima derived from Langmuir fits decreased with the following order:
montmorillonite, fine inorganic clay, fine organic clay, kaolinite, coarse inorganic clay, coarse
organic clay.
Fine clays adsorbed 4-7 times more DNA than coarse clays per mg (Figure 2). However, note
that the mass of adsorbed DNA is normalized to the mass rather than the surface area of
sorbent (see Figure 2). This point will be discussed further in the outlook section.
The difference between inorganic clays and organic clays in the amount of adsorbed DNA
was not as big as between fine and coarse clays. However inorganic clays could adsorb more
nucleic acid than organic clays. This larger adsorption in inorganic clays as been attributed to
surfaces of Fe-Al oxides, which were exposed after the organic material has been removed by
H2O2 (7).
In inorganic clays and kaolinite, DNA is thought to adsorb mainly on the clay edges by ligand
exchange. Aluminum hydroxides and hydroxyl-aluminum-clay complexes can adsorb organic
ligands by this mechanism (7). It has been suggested that the hydroxyl groups of the ribose
and the phosphate groups at the two ends of the DNA molecule are involved in ligand
exchange. During ligand exchange strong bonds are formed. Therefore, DNA adsorbed with
higher affinity to inorganic clays and kaolinite than to organic clays and montmorillonite.
Because the coarse clay fraction comprised more kaolinite and the fine clay fraction in this
study, the adsorption affinity was higher for coarse clays than for fine clays.
Cai et al. (8) suggest that DNA adsorption to organic clays and montmorillonite occurs on the
planar surface (of clays) by electrostatic interactions and that these interactions allow weak
bonds and lead to a lower adsorption affinity. However, this explanation seems questionable
in light of the fact that both DNA and surfaces are negatively charged. This point will be
further discussed in the outlook section.
According to Cai et al. (7) the strong bonds formed during ligand exchange made DNA
adsorption to inorganic clays exothermic. For coarse inorganic clay it was even more
exothermic than for fine inorganic clays. That the adsorption to organic clays was

6
endothermic, was explained by higher electrostatic repulsion between DNA and organic clays
(7). Adsorption enthalpies of DNA were measured by a TAM air isothermal calorimeter.

3.2 Influence of Solution Chemistry on DNA Adsorption

3.2.1 pH Dependent Adsorption

Figure 3: Equilibrium adsorption of 200 µg of salmon sperm DNA on 10 mg of soil colloids

and minerals in the range of pH from 2.0 to 9.0. Figure and figure legend taken from (8).

At pH 2.0, all of the added DNA was found to adsorb to soil colloids and minerals. Increasing
pH from 2.0 to 5.0 resulted in a dramatic adsorption decrease from 20 to 0.51-2.98 µg mg-1
for organic clays and montmorillonite and from 20 to 5.26-6.98 µg mg-1 for inorganic clays
and kaolinite (8). This pH dependence likely reflects the release of protons by bases of the
DNA molecule, which decreases its positive charge. A further increase in pH from 5.0 to 9.0,
still leads to less DNA adsorbed, but the decrease is not as steep. As a consequence, it is
reasonable to expect that more DNA is adsorbed in acidic than in alkaline soils.
With high salt concentrations, in the presence of divalent cations, the pH dependent
adsorption behavior of DNA changes dramatically. Lorenz et al. (10) found that in presence
of magnesium adsorption to sea sand was highest under alkaline conditions due to cation
bridging.

7
3.2.2 Influence of Ligands on DNA Adsorption

In soil environments, especially in the rhizosphere, various organic and inorganic ligands are
present. It is important to know how these ligands affect DNA adsorption in order to make
statements about the fate of DNA in soils.
Cai et al. (6) investigated the adsorption of salmon sperm DNA to soil particles in the
presence of phosphate and the inorganic acids citrate and tartrate. Citrate and tartrate can
occur in the rhizosphere in concentrations up to 10-20mM, the concentration of phosphate can
be even higher, especially in fertilized agricultural land.

Figure 4: Adsorption of DNA on soil

colloids and minerals in the presence of
increasing concentration of organic acids
and phosphate. Figure and figure legend
taken from 6.

Geothite, organic and inorganic clay as

sorbents: For goethite, as well as
inorganic and organic clays, adsorption
decreased with increasing citrate, tartrate
and phosphate concentrations. This
inhibition of adsorption by ligands was
attributed to competition between the
DNA and the ligands for adsorption sites.
Furthermore increasing ligand
concentrations increased the negative
charge on the surface and hence increased
the electrostatic repulsion between DNA
and soil colloids. Phosphate was found to
have the highest ability to decrease DNA
adsorption onto goethite and soil colloids,
followed by citrate and tartrate. Adding
DNA to the system before adding the
ligands, led to higher adsorption, than
simultaneous addition. Lowest adsorption
was observed, when the ligand was added
first followed by DNA.
Montmorillonite and kaolinite as
sorbents: The amount of DNA adsorbed
to montmorillonite and kaolinite
decreased with increasing ligand
concentration in the range of 0-5mM.
DNA adsorption was then enhanced again
with increasing concentrations of tartrate
and citrate from 5 to 80 mM and
increasing phosphate concentration from
5 to 200 mM. The authors speculated that at high ligand concentrations, the ligands could
promote DNA adsorption to montmorillonite and kaolinite by dissolving aluminum from

8
kaolinite and thus creating new adsorption sites. The formation of aluminum-phosphate
precipitates and bridging of soluble Al3+ between the negatively charged mineral surfaces and
the phosphate backbone was further suggested as explanation for an enhanced adsorption
process. In the cases in which the ligand was added first, adsorption was higher than in cases
in which DNA and ligand simultaneously or DNA first (6).

3.2.3 Influence of Salts on DNA Adsorption: Ionic Strength and Valence

A quartz crystal microbalance with dissipation was used by Nguyen et al. (2) to measure
adsorption rates of supercoiled plasmid DNA to a quartz surface (Figure 5). The attachment
efficiency α is the ratio of the measured adsorption rate under different experimental
conditions to the diffusion-controlled (i.e. maximum) adsorption rate of negatively charged
DNA to a positively charged surface. At pH 6 and pH 8 the plasmid DNA and the silica
surface are both negatively charged. It is therefore likely that solution chemistry has a strong
effect on the electrostatic repulsion, which has to be overcome for a successful adsorption.

Figure 5: Adsorption kinetics and

attachment efficiency of plasmid DNA unto
silica surfaces at pH 6 and 8 (a) as a
function of NaCl concentration (b) as a
function of CaCl2 concentration. Total
ionic strength was kept at 10 mM by
proper addition of NaCl. Plasmid DNA
concentrations during the experiments
were 170mg/L and the temperature was
25°C. Error bars indicate standard
deviations of at least two replicate
measurements. The horizontal dashed line
indicates the detection limit of the quartz
crystal microbalance with dissipation
measurements. Figure taken from 2.

Increasing Na+ concentrations lead to higher adsorption rates and attachment efficiencies,
because the cations screen the negative charges between the DNA and the silica surface.
Charge screening allows the DNA molecule to approach the negative surface close enough for
adsorbing by van der Waals forces at a distance from the surface, where electrostatic
interactions are small.
The authors report that adsorption rates and attachment efficiencies in solutions containing
NaCl were much lower than in CaCl2 containing solutions.
The adsorption rates were 10 times higher in systems that had an aqueous concentration of at
least 0.5mM Ca2+ (total ionic strength 10mM) than in systems with a concentration of 300mM
Na+. Calcium is believed to have the following promoting effects on DNA adsorption: (i)
cation bridging, (ii) charge screening between the surfaces and DNA molecules (iii) condense
the structure of DNA itself. Ca2+ forms “inner-sphere” complexes with the phosphate
backbone of plasmid DNA, which decreases the net negative charge and hence decreases the
electrostatic repulsion between phosphates and results in a more compact structure of the
plasmid molecule and a higher diffusion coefficient.

9
Ca2+ also binds to silanol groups, which reduces the negative charge of the silica surface.
-SiOH + Ca2+ + H2O=-SiOCa+ + H3O+ log K= -7.3
2+
As it binds to both phosphate and silanol groups, Ca can act as bridge between the two
groups.
According to the authors, this is the main reason why the attachment efficiency reaches a
value close to 1 in the presence of Ca2+ (2).

Similar investigations have been made about the role of cations in plasmid DNA adsorption to
a natural organic matter-coated silica surface.
The highest attachment efficiencies have again been found in the presence of Ca2+. Ca2+ forms
“inner-sphere” complexes with both plasmid DNA and COOH-groups of natural organic
matter, therefore bridges between the natural organic matter and the plasmid DNA are
formed.
Adsorption efficiencies in the presence of Mg2+ were lower than in the presence of Ca2+. This
was attributed to the fact that Mg2+ forms weaker “outer-sphere” complexes with the
phosphate backbone and the natural organic matter. Charge neutralization of plasmid DNA's
phosphate groups and the carboxyl groups of the natural organic matter decreases the
electrostatic repulsion between the sorbent and the sorbate. Na+ competes with Mg2+, which
led to to incomplete charge neutralization, therefore lower adsorption rates and attachment
efficiencies are observed in a solution containing both Na+ and Mg2+. In Ca2+-dependent
adsorption process the presence of Na+ didn’t decrease the attachment efficiency significantly
(4).

Desorption and Structure:

Changes in the viscoelastic properties of the adsorbed DNA layer onto silica and natural
matter-coated silica and adsorption reversibility have been measured by Nguyen et al. (2,4).
For both types of silica surface the adsorption of DNA in the presence either 1mM Ca2+ or
Mg2+ or a moderately high ionic strength of 300mM Na+ is irreversible.
When DNA layers formed with Ca2+ in presence of Na+ were rinsed sequentially with
solutions of lower ionic strength and deionized water, they acquired a less compact structure.
This structural change, which describes an increase in the thickness of the adsorbed DNA
layer and a decrease of its viscosity, is referred to as softening. Na+ is thought to charge shield
phosphate groups, which are not complexed with Ca2+, therefore with decreasing Na+ in the
solution electrostatic repulsion increases, which leads to softening. DNA layers pre-adsorbed
with Ca2+, but without Na+, do not soften, when they are rinsed (2,4).

Pastrè et al. (11) found in a theoretical and experimental study, that divalent or higher valence
cations can generate high attraction forces between DNA molecules and mica, which have
comparable surface charges. In their study the addition of monovalent cations also lead to a
decrease in adsorption affinity.

10
3.3 Effect of DNA Structure on its Adsorption: Differences between Supercoiled
and Linear Plasmid DNA

Adsorption of linear and supercoiled plasmid DNA on natural organic matter-coated silica
have been compared by Nguyen et al. (3) using a quartz crystal microbalance with dissipation.
The attachment efficiency α of linear plasmid DNA at low ionic strength is higher than that of
supercoiled DNA (see Figure 6). The electrostatic repulsion between the phosphate groups
leads to an extended conformation of the linear DNA. It is thought that the ends of linear
DNA can approach the natural organic matter layer more easily, because the extended
conformation makes linear DNA more flexible. As Na+ concentration is increased, charge
screening allows the phosphate groups to get closer. At high ionic strength both supercoiled
and linear DNA had comparably compact conformation and adsorbed similar.

Figure 6: Attachment efficiencies of linear

and supercoiled plasmid DNA onto silica
surfaces coated with natural organic matter
at pH 5.8 at different solution ionic strengths.
Plasmid DNA concentrations during the
experiments were 120 mg/L and the
temperature was 25°C. Error bars indicate
standard deviations of at least two replicate
measurements. Figure taken from (3).

At low ionic strength (1mM NaCl) linear plasmid DNA was found to have lower diffusion
coefficients than supercoiled DNA. This was attributed to the loose conformation (i.e., the
large molecular size) of the linear plasmid DNA. With increasing ionic strength the overall
size of the DNA molecule decreases, which led to higher diffusion coefficients. At a ionic
strength of 300 mM NaCl the diffusion coefficient of both linear and supercoiled plasmid
DNA are statistically the same.

Poly et al. (12) investigated the adsorption of linear calf thymus DNA and supercoiled
plasmid DNA to homoionic, calcium saturated montmorillonite, kaolinite and illite.
Adsorption isotherms for both linear and supercoiled DNA showed a high affinity stage to
Ca-illite, Ca-kaolinite and Ca-montmorillonite at low DNA concentrations in pure water and
in a solution containing free Ca2+. In this high affinity stage all DNA was completely
adsorbed. Adsorption increased with increasing concentrations of linear DNA. However,
adsorption decreased with DNA concentrations for the supercoiled form. As the phosphate
groups are thought to play the major role in the adsorption to Ca-saturated clays, the density
and availability of these groups have to be considered. Poly et al. (12) hypothesize that in
plasmid DNA only groups at the maximum bending of the supercoiled molecule may
participate in the binding for steric considerations. In linear DNA, on the other hand, the
negative charges of the phosphate groups are distributed all along the molecule, allowing a
multi-loci contact with the Ca2+ cations on the clay mineral surfaces. The higher tendency of
supercoiled DNA to self-aggregate in presence of Ca2+ with increasing concentration could
also account for the decrease in the amount of DNA supercoiled adsorbed. Self-aggregation
was observed by Low-Temperature Scanning Electron Microscopy, which conserves the
hydrated structure of the sample (Figure 7).

11
 Figure 7: Cryoscanning electron micrographs
showing Blue script plasmid DNA. (A) Plasmid DNA
in 5 mM CaCl2, DNA molecules aggregated to form a
net (N) or filaments consisting of several plasmid
molecules (F) (bars= 10 µ m). (B) Plasmid DNA
adsorbed on homoionic kaolinite acting as a bridge
(arrows) between clay and platelets (bars= 1 µ m).
Figure and figure legend taken from 12.

The concentration of 5 mM Ca2+ lies in a range that

can be expected for neutral soils. Panel A shows the adsorption of free plasmid DNA
deposited on aluminum foil. Several supercoiled plasmid DNA molecules band together to
form filaments and web like structures. It is likely that free supercoiled DNA forms similar
structures in natural soil environments.
As can be observed in panel B, supercoiled plasmid DNA adsorbed to kaolinite forms bridges
between the edges of kaolinite crystals. Linear DNA was found to lie on montmorillonite,
adsorbing partly or completely to the clay edges and surface (12). Consequently, linear and
supercoiled DNA do not adsorb by the same mechanisms, which implies also different
degrees of protection against degradation. Its higher tendency to stay in solution and the fact
that it adsorbs only at few sites, makes supercoiled DNA sterically more accessible to
degradation than linear DNA, where only one strain is exposed.

12
4 Conclusion & Outlook

Free DNA is rapidly degraded in soils by enzymes, but adsorbed DNA can be protected
against this degradation for extended time periods (14). In some cases, DNA adsorbs to soil
surfaces even if electrostatics are unfavorable. Environmental factors such as cations, pH and
ligands have a high influence on DNA adsorption. Consequently, DNA can be conserved in a
variety of different soils. However, it has been reported that DNA adsorption is irreversible.
This would imply that even though DNA is protected in soils bacterial transformation is not
very likely to occur, because the DNA cannot be desorbed easily.
There are a few unclear points in the papers I read that I would like to discuss.
First of all, sorbed concentrations of DNA to sorbents are commonly expressed as mass of
DNA adsorbed per mass of sorbent (6, 7, 8, 12). However, the normalization to mass is
misleading as it is not the mass but rather the surface area plays an important role an
adsorption processes. Consequently, higher adsorption to fine clays than to coarse clays as
reported by Cai et al. may simply reflect that fine clays have larger surface areas than coarse
clays (see Figure 2 and Table 1).
In addition, Cai et al. (8) reported that DNA adsorption to organic clays and montmorillonite
occurs on the planar surface of clays, which is negatively charged, by electrostatic
interactions. These interactions are suggested to allow weak bonds between the negatively
charged DNA molecules and the surfaces. This explanation seems questionable, because as
both DNA and surfaces are negatively charged, the interactions should be repulsive rather
than attractive. How and between which functional groups could weak bonds then be formed?

The influence of pH, ionic strength and valence of cations have excessively been studied.
Another variable that could be considered when investigating soil environments is the redox
potential. For example weather a decrease in redox potential when soils are flooded would
influence DNA adsorption by changing the surface properties of soil colloids.
DNA adsorption to soil surfaces has been investigated so far by using one of two main
methods. Either adsorption has been indirectly measured by measuring depletion of the DNA
concentration in the solution or it has been directly measured by sophisticated surface
techniques, where detailed data about viscoelastic properties and conformational changes of
adsorbed DNA can be obtained. For further research I suggest to combine both methods to get
a more holistic view of the mechanisms involved.
Further research should also place more emphasis on desorption of DNA from soil particles.
Whether DNA can be desorbed actively by bacteria for desorption gives high implications on
the possibility of bacterial transformation.

13
5 References

1. Demanèche, S.; L. Jocteur-Montrozier; H. Quiquampoix & P. Simonet: evaluation of

biological and physical protection against nuclease degradation of clay-bound plasmid DNA,
Applied and Environmental Microbiology 2001, 67, 293-299.

2. Nguyen, T.H. & M. Elimelech: Plasmid DNA adsorption on silica: Kinetics and
conformational changes in monovalent and divalent salts, Biomacromolecules 2007, 8, 24-32.

3. Nguyen, T.H.& M. Elimelech: Adsorption of plasmid DNA to a natural organic matter-

coated silica surface: Kinetics, conformation, and reversibility, Langmuir 2007, 23, 3273-
3279.

4. Nguyen, T.H. & K. L. Chen: Role of divalent cations in plasmid DNA adsorption to natural
organic matter-coated silica surface, Environmental Science & Technology 2007, 42, 5370-
5375

5. Cai, P.; Q. Huang; W. Chen; D. Zhang; K. Wang; D. Jiang & W. Liang:

Soil colloids-bound plasmid DNA: Effect on transformation of E. coli and resistance to
DNase I degradation, Soil Biology & Biochemistry, 39, 1007-1013.

6. Cai, P.; Q. Huang; J. Zhu; X. Zhou; D. Jiang; X. Rong & W. Liang: Effects of low-
molecular-weight organic ligands and phosphate on DNA adsorption by soil colloids and
minerals, Colloids and Surfaces B-Biointerfaces 2007, 54, 53-59.

7. Cai, P.; Q. Huang; D. Jiang; X. Rong & W. Liang: Microcalorimetric studies on the
adsorption of DNA by soil colloidal particles, Colloids and Surfaces B-Biointerfaces 2006,
49, 49-54.

8. Cai, P.; Q. Huang; X. Zhang; & H. Chen: Adsorption of DNA on clay minerals and various
colloidal particles from an Alfisol, Soil Biology & Biochemistry 2006, 38,471-476.

9: Cai, P.; QY. Huang & XW. Zhang: Interactions of DNA with clay minerals and soil
colloidal particles and protection against degradation by DNase, Environmental Science &
Technology 2006, 40, 2971-2976.

10. Lorenz, M.G. & W. Wackernagel: Adsorbtion of DNA to sand and variable degradation
rates of adsorbed DNA, Applied and environmental microbiology 1987, 53, 2948-2952.

11. Pastre, D.; O. Pietrement; P. Fusil; F. Landousy; J. Jeusset; MO. David; C. Hamon; E. Le
Cam & A. Zozim: Adsorption of DNA to mica mediated by divalent counterions: A
theoretical and experimental study, Biophysical Journal 2003, 85, 2507-2518.

12. Poly, F.; C Chenu; P. Simonet; J. Rouiller & LJ Monrozier: Differences between linear
chromosomal and supercoiled plasmid DNA in their mechanisms and extent of adsorption on
clay minerals, Langmuir 2000, 16, 1233-1238.

13. Droge, M.; A. Puhler & W. Selbitschka: Horizontal gene transfer among bacteria in
terrestrial and aquatic habitats as assessed by microcosm and field studies, Biology and
Fertility of Soils 1999, 29 (3), 221-245.

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14. Trevors, J.T.: DNA in soil: adsorbtion, genetic transformation, molecular evolution and
genetic microchip; Antonie van Leeuwenhoek 1996, 70, 1-10.

15. http://oak.cats.ohiou.edu/~ballardh/pbio475/Heredity/DNA-double-helix.JPG

16. Scheffer F. & P. Schachtschabel: Lehrbuch der Bodenkunde, Spektrum, Akademischer

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17. Atkins P.W.: Physical Chemistry, 6th edition, Oxford University Press, Oxford, 1998.

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