Binding abilities of polyaminocyclodextrins: Polarimetric investigations and biological assays

Article abstract of DOI:10.3762/bjoc.13.271

Three polyaminocyclodextrin materials, obtained by direct reaction between heptakis(6-deoxy-6-iodo)-β-cyclodextrin and the proper linear polyamines, were investigated for their binding properties, in order to assess their potential applications in biologi

Full text of DOI:10.3762/bjoc.13.271

Binding abilities of polyaminocyclodextrins:
polarimetric investigations and biological assays
Marco Russo1, Daniele La Corte1, Annalisa Pisciotta1, Serena Riela1, Rosa Alduina1
and Paolo Lo Meo*1,2
Full Research Paper
Open Access
Address:
Beilstein J. Org. Chem. 2017, 13, 2751–2763.
1Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e
Farmaceutiche (STEBICEF), University of Palermo, V.le delle Scienze
ed. 17, 90128 Palermo, Italy and 2ATeNCenter, University of
Palermo, V.le delle Scienze ed. 18, 90128 Palermo, Italy
doi:10.3762/bjoc.13.271
Received: 23 August 2017
Accepted: 09 December 2017
Published: 18 December 2017
Email:
Paolo Lo Meo* - paolo.lomeo@unipa.it
Associate Editor: H. Ritter
* Corresponding author
© 2017 Russo et al.; licensee Beilstein-Institut.
License and terms: see end of document.
Keywords:
aminocyclodextrins; binding properties; nitroanilines; pDNA;
polarimetry; supramolecular chemistry
Abstract
Three polyaminocyclodextrin materials, obtained by direct reaction between heptakis(6-deoxy-6-iodo)-β-cyclodextrin and the
proper linear polyamines, were investigated for their binding properties, in order to assess their potential applications in biological
systems, such as vectors for simultaneous drug and gene cellular uptake or alternatively for the protection of macromolecules. In
particular, we exploited polarimetry to test their interaction with some model p-nitroaniline derivatives, chosen as probe guests. The
data obtained indicate that binding inside the host cavity is mainly affected by interplay between Coulomb interactions and confor-
mational restraints. Moreover, simultaneous interaction of the cationic polyamine pendant bush at the primary rim was positively
assessed. Insights on quantitative aspects of the interaction between our materials and polyanions were investigated by studying the
binding with sodium alginate. Finally, the complexation abilities of the same materials towards polynucleotides were assessed by
studying their interaction with the model plasmid pUC19. Our results positively highlight the ability of our materials to exploit both
the cavity and the polycationic branches, thus functioning as bimodal ligands.
Introduction
Polyamine macromolecules have attracted a widespread interest sponges, capping agents for the synthesis of noble metal nano-
for their potential applications in various fields. Linear or particles, and systems for the complexation and cell transfec-
branched polyethyleneimine (PEI) polymers [1-5], as well as tion of genetic material [17-22]. In particular, the complexation
polypropyleneimine (PPI) [6-8] and polyamidoamine and transfection of polynucleotides also have been successfully
(PAMAM) [7-16] dendrimers, have been used as proton accomplished by means of polycationic cyclodextrin or
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calixarene derivatives, obtained by anchoring suitable polyam- considered by targeting their abilities in gene internalization.
monium or imidazolium pendant groups onto the main macro- However, a detailed examination of the relevant stoichiometric
cycle scaffold [23-28]. The latter example is interesting, or thermodynamic aspects is lacking. We were interested in
because of the well-known ability of these macrocycles to form verifying how the presence of the dendrimer-like “bush” of
inclusion complexes with diverse organic guest molecules polyamine pendants at the primary rim, and its protonation
[29-35]. Cyclodextrins (CDs), in particular, constitute appealing status as a function of the pH, might affect the inclusion proper-
systems due to their biocompatibility, which allowed them to be ties of the main CD scaffold. At the same time, we wanted to
approved by the FDA as human friendly products [36]. Thus, clarify the microscopic features and quantitative aspects of the
polycationic CDs might be used in principle as bimodal ligands interaction between AmCDs and polyanions such as poly-
for the simultaneous internalization of a polynucleotide (inter- nucleotides. For these purposes, we investigated by means of
acting with the polycationic branches) and a further bioactive/ polarimetry the behaviour of materials CD1–CD3 (Figure 1a),
drug molecule (included into the host cavity). The critical obtained in a previous work [37], with a set of selected neutral
examination of the available literature suggests that one main and anionic model p-nitroaniline derivatives 1–4 (Figure 1b) at
drawback of this approach is the fact that the syntheses of the different pH values. The materials chosen differ for the length
tailored macrocyclic ligands (as pure chemical species) re- and number of N atoms of the polyamine chains, and for the
ported so far are lengthy and expensive, affording low overall different average number of pendants per CD unit (i.e., 5.7, 6.1
yields. Thus, a cheaper, more straightforward alternative route and 4.5 for CD1, CD2 and CD3, respectively). Moreover, we
would be highly desirable.
tested the potential ability of these materials to interact with
polyanions by studying their behaviour towards sodium algi-
Recently, we have prepared useful polyaminocyclodextrin ma- nate (Alg, Figure 1c) chosen as suitable model compound.
terials (AmCDs) in high overall yields (> 90%) by simply Finally, we performed some preliminary tests in order to assess
reacting a heptakis(6-deoxy-6-halo)-β-CD with an excess of a their interaction with a model plasmid DNA (pUC19) and to
suitable polyamine [37]. The reaction leads to the exhaustive evaluate whether they may influence the internalization of
nucleophilic displacement of the halogen atoms on the starting exogenous DNA in bacterial systems, in particular the Gram-
material [38,39]. However, the products obtained constitute negative model microorganism Escherichia coli.
complex mixtures of various inseparable derivatives, having a
different number of polyamine branches linked to the CD scaf-
fold, that are isolated as partial hydrohalides. In fact, the same
polyamine unit can undergo multiple substitution reactions (a
possible mechanistic scheme is depicted in Supporting Informa-
tion File 1, Figure S1), on the same N atom or on different
N atoms. The characterization of the materials by means of
combined ESIMS, NMR and potentiometric titration tech-
niques, enabled to determine the average number of pendant
arms (<np>) and hydrohalic acid molecules (<nHX>) per AmCD
unit. The acid–base behaviour of these materials can be
modelled as a mixture of independent virtual weak bases. We
already have employed these products as capping agents for the
preparation of silver nanocomposites [37], which in turn have
been tested as catalysts for nitroarene reduction and as antimi-
crobial agents in synergism with classical antibiotics [40,41].
Moreover, the same products have been used for the synthesis
of pH-responsive nanosponges [42].
In view of possible further applications, the present work is
aimed at verifying the abilities of AmCD materials synthesized
by us to act as bimodal supramolecular ligands. To the best of
our knowledge, the possible inclusion of a generic guest/drug
molecule into CD derivatives bearing amine groups have been
Figure 1: Structures of: a) AmCDs CD1–3; b) p-nitroaniline guests
1–4; c) sodium alginate (Alg).
studied only occasionally [41,43-48]. Moreover, the interaction
of polycationic CDs with polynucleotides has been mainly
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Results and Discussion
large as ca. 0.5, 0.33 and 0.25 for CD1, CD2 and CD3, respec-
Polarimetric behavior of AmCDs
tively (Figure 3). Thus, keeping into account the number of
A preliminary investigation of the polarimetric behaviour of basic N atoms of the relevant polyamine branches (i.e., 2 for
free AmCDs was a prerequisite before addressing their com- A1, 3 for A2 and 4 for A3), it is immediately apparent that these
plexation abilities by means of polarimetry. Thus, the relevant maxima correspond to the situation in which on average one H+
molar optical rotations Θ were measured at different pH values, has been attached to each polyamine unit. The latter observa-
in order to study the possible effect of the progressive proton- tion is interesting, because it has been reported that in the case
ation of the polyamine groups and the results are depicted in of mono-[6-(3-dimethylamino)propylamino]-6-deoxy-β-cyclo-
Figure 2 (the complete data set is collected in the Supporting dextrin the first protonation step occurs on the farthest N atom
Information File 1, Table S2). Noticeably, Θ values were deter- with respect to the CD cavity [48]. Thus, it is reasonable to
mined in the absence of any buffering or supporting electrolyte, expect that the same applies also to the polyamine branches of
simply by adjusting the pH with small amounts of added conc. our AmCDs, in such a way to minimize Coulomb repulsion be-
HCl or NaOH. As we can easily notice, on varying the pH value tween cationic tail groups. Considering that the polarimetric
of the solvent medium, and consequently the charge status of response of CDs depends on both their intrinsic chirality and on
the AmCDs, the Θ values show a peculiar M-shaped trend. their conformational dynamism, the behaviour observed indi-
Starting from ca. pH 12, at which the products are almost cates that our AmCDs experience their most extensive confor-
uncharged, Θ initially increases, then decreases, then again rises mational rearrangements as the first protonation step at each
up to a maximum value, and finally undergoes a regular de- polyamine branch occurs. This suggests the presence of strong
crease up to pH 5 and beyond. This behaviour is more pro- intrachain interactions before protonation.
nounced for CD1 than for the other two products.
Binding abilities of AmCDs towards
Noticeably, reporting Θ vs the protonation fraction χH+ (i.e., the p-nitroaniline derivatives 1–4
fraction of N atoms present on average in the product which p-Nitroanilines constitute a good class of probe molecules for
have undergone protonation at the given pH conditions, see testing the microscopic behaviour of cyclodextrins [43,49-53].
Supporting Information File 1 for mathematical details), the Moreover, polarimetry is a technique of choice for these
absolute maxima of the three curves occur for χH+ values as systems, having been proven particularly valuable for its versa-
Figure 2: Trends of the molar optical rotation Θ of AmCDs CD1–3 vs pH.
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Figure 3: Trends of the molar optical rotation Θ of AmCDs vs χH+.
tility and informative nature [51-53]. The complete polari- As a preliminary observation, the trends of polarimetric data
metric data relevant to the inclusion of guests 1–4 into AmCDs (i.e., optical activities of the samples i vs concentration of the
are collected in Supporting Information File 1 (Tables S3–S5), guest, see Experimental) show the possible occurrence of two
namely the values of the binding constants (K) and both the different behaviours (Figure 4).
absolute (ΔΘ) and the normalized (RΘ) differential molar
optical rotations as a function of the pH value and the possible
presence of a buffer as supporting electrolyte. For the sake of
clarity, ΔΘ is the difference between the molar optical rotations
of the complex and the host, respectively, whereas RΘ is
defined as RΘ = 100·ΔΘ/Θ (here Θ is considered at the given
pH conditions). It is important to stress here that ΔΘ values for
the different systems studied are not directly comparable, owing
to the intrinsic differences in the absolute molar optical rota-
tions Θ of the different hosts, and for the same host at different
pH values. Thus, homogeneous comparisons can be rather
carried out on the relative variations accounted for by the
normalized parameter RΘ [43]. It is also worth recalling here
that ΔΘ and RΘ values for p-nitroanilines are affected by an in-
duced circular dichroism effect due to the interaction between
the dipole moments of the polarized chromophore guest moiety
and of the cyclodextrin cavity. Therefore, these parameters
provide an estimation of the time-averaged tilt angle between
the nitroaniline C2 symmetry axis and the ideal axis of the host,
Figure 4: Polarimetric data trends for the inclusion of 4 in CD1 at
different pH values.
and serve as a good probe of the overall conformational rigidity
of the complex.
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With the neutral guest 1 at any pH and with the anionic guests On the grounds of these results, the behaviour of CD2 and CD3
2–4 at the highest pH values, data trends account for the exclu- was investigated with anions 2 and 4 only. The results obtained
sive formation of a 1:1 host–guest inclusion complex. By appear quite peculiar. In fact, monoanion 2 does not present the
contrast, with guests 2–4 at the lowest pH values, i.e., when- same simple monotonic trend for K observed with CD1; by
ever an anionic guest meets a host bearing a significant positive contrast, for dianion 4 the expected regular increase of K values
charge, deviations in data trends occur on increasing the analyti- on decreasing the pH is observed. These findings indicate that,
cal concentration of the guest. These deviations indicate the for- on increasing the extension of the polyamine pendant bush, the
mation of higher-order aggregates (see below). As long as the outcome of favourable Coulomb effects decreases, probably due
behaviour of host CD1 is concerned, we observed that K values to a consequent decrease in the charge density of the bush itself.
for the neutral guest 1 and the anionic guest 3 regularly de- In all cases, non-monotonic RΘ trends are found. Again, the
crease on decreasing the pH, i.e., on increasing the average presence of a buffering electrolyte tends to disfavour the inclu-
charge on the host, whereas the opposite is observed with sion process and significantly affects both Θ and RΘ values, al-
anions 2 and 4. In all cases, however, a regular increase of though general trends cannot be clearly envisaged. Such an
RΘ values generally occurs, with few exceptions. Finally, the effect of the electrolyte on RΘ values is particularly interesting,
presence of a buffer electrolyte decreases K values and causes because it suggests the occurrence of a significant interaction
significant variations of the RΘ values. According to literature between the cationic polyamine pendant chains and the counter-
[51-53], the regular increase of RΘ observed on decreasing the anions of the buffer, probably by either ion pairing or forma-
pH, indicates a concomitant decrease of the average tilt of the tion of multiple hydrogen bonds. Consequently, the mobility of
guest with respect to the ideal host axis. This, in turn, suggests the chains and, in turn, the conformational dynamics of the en-
that the polarized guest molecule penetrates more and more tire CD scaffold, are significantly affected. The latter considera-
deeply into the CD cavity on increasing the overall positive tion may also justify the possible formation of higher order
charge, owing to the occurrence of stronger dipolar interactions. host–guest aggregates with anionic guests mentioned previ-
Therefore, the inclusion complex becomes stiffer and stiffer, ously. In fact, due to molecular size, modelling considerations
with a consequent unfavourable effect on the complex forma- rule out the accommodation of more than one guest unit into the
tion entropy [43,50]. A further unfavourable contribution may host cavity. Thus, we may reasonably hypothesize the occur-
also come from the increasingly difficult desolvation of the rence of a loose ion-pairing external association between the
charged host. These combined effects cause the observed de- cationic pendant groups of the host and the anionic guest
crease of K values for the neutral guest 1. By contrast, for the (Figure 5).
anionic guests 2 and 4 the same effects are largely counterbal-
anced by the concomitant occurrence of very favourable Binding abilities of AmCDs towards Alg
Coulomb interactions. However, the case of guest 3 is Further assessment of a possible out-of-cavity interaction for
intriguing, because its trend of K values neatly mismatches AmCDs was achieved by studying their interaction with sodi-
those for the other anions. This surprising finding can be ex- um alginate (Alg). This is an easily available and stable block
plained considering that the ancillary chain of 3 is unable to copolymer, constituted by β-D-mannuronate and β-L-
give multiple hydrogen bonding with the host cavity, due to the guluronate units linked by 1→4 glycosidic bridges. Therefore, it
methyl group placed on the amino N atom. According to litera- seemed an ideal candidate as model polyanion, in order to study
ture, this peculiar structural feature is able to enhance largely the stoichiometric and thermodynamic features of possible com-
the outcome of entropy-unfavourable stiffening effects [50,52]. plexation with AmCDs. In particular, for our purposes the main
Figure 5: Possible association of AmCDs with guests 2–4.
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points under examination were: i) the stoichiometry of the At high pH values, we found that the optical activity observed
possible complex formed and ii) the intimate mechanism of the was merely the sum of the independent contributions from
interaction.
AmCD and Alg. In particular, it undergoes a nearly linear de-
crease, owing to the fact that Alg is laevorotatory (we
Series of working samples (see Experimental) were prepared at determined for Alg an equivalent optical activity as large as
given pH values by mixing variable amounts of a concentrated −26.3 ± 0.4 deg dm−1 N−1). This provides a convincing proof
solution of the polyanion (25 mN) with fixed aliquots of a solu- that the uncharged AmCD does not interact with the polyanion.
tion (1.5 mM) of each AmCD. From a qualitative viewpoint, we On the other hand, for the samples prepared at lower pH values
observed three different behaviours, depending on the case. At the optical activities of the supernatant liquor after centrifuga-
high pH values, i.e., in the presence of the almost uncharged tion decrease accounting for the progressive subtraction of the
AmCD, the prepared samples resulted clear, irrespective of the AmCD from the solution. Indicating with nr the average molar
amount of polyanion added. On reducing the pH, clear solu- ratio between the AmCD and the monomer units of alginate in
tions were formed only at the lowest Alg concentrations, where- the precipitate formed, we derived analytically (see Supporting
as an intense turbidity developed on increasing the amount of Information File 1 for mathematical details) the expression for
Alg beyond a limit value. On further reducing the pH down to the relationship between the optical activity of the samples and
4.6, i.e., as the AmCD approaches its highest protonation status, the amount of polyanion added (Equation 1):
the addition of Alg in any amount always caused the formation
of precipitates. The latter observation suggests that in this case
the added Alg is almost completely precipitated from the solu-
(1)
tion by the polycationic AmCD. This implies that a larger and
larger amount of AmCD is subtracted from the solution at the
same time. Noticeably, because the pKa value reported for
alginic acid is far below 4.0 [54], we can rule out that Alg is
neutralized up to a significant extent under our experimental where the index i applies to the generic i-th sample of the series,
conditions. We verified that Alg alone does not form precipi- α is a suitable intercept value, vi and V0 are the volumes of the
tates under the pH conditions used. Working samples were sub- Alg and AmCD mother solutions mixed in the sample, respec-
jected to polarimetric analysis after centrifugation and typical tively, c0Alg and c0CD the relevant concentrations. Trends of the
trends are depicted in Figure 6.
molar ratio nr obtained as a function of the AmCD, the pH and
the possible presence of a buffer electrolyte, are reported in
Table 1 and depicted in Figure 7.
It is interesting to notice that in general the nr values never coin-
cide with the average charge (<nH+>) on the AmCD. Thus, the
precipitate must embed ions from the solution. Noticeably, CD1
shows lower nr values in the presence of a buffer, indicating
that the amount of inorganic anions retained by the precipitate
increases on increasing the content of salts in solution. On in-
creasing their protonation status, the AmCDs appear less effec-
tive as precipitating agents on a relative scale, because nr values
are significantly larger than <nH+> at high pH values, whereas
the opposite occurs at low pH. A comparison between the three
different AmCDs suggests that CD2 is the most effective
ligand, showing the largest nr values at any pH.
For the sake of completeness, we also attempted to evaluate by
means of DLS measurements the size of possible AmCD–Alg
aggregates. Unfortunately, very poor results were obtained. At
pH 6.5, the clear supernatant liquor of the prepared samples
after 24 h standing, showed the presence of no object larger
than 2 nm (which corresponds, more or less, to the hydrody-
namic diameter of a single AmCD unit). The same attempt
Figure 6: Polarimetric data trends for the CD1–Alg interaction (with
buffer).
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Table 1: nr Values for the AmCD–Alg interaction.
CD1
CD1 (with buffer)
pH
<nH+>a
nr
pH
<nH+>a
nr
11.2
8.4
7.3
6.5
4.6
0.1
4.8
0
11.4b
8.4c
6.5d
5.3e
0.1
4.8
0
4.3 ± 0.3
5.0 ± 0.2
6.5 ± 0.4
6.8 ± 0.5
3.5 ± 0.3
5.0 ± 0.4
9.4 ± 0.6
6.5
8.1
8.1
10.7
11.2
CD2
CD3
pH
<nH+>a
nr
pH
<nH+>a
nr
10.0
9.0
7.8
7.0
6.1
3.5
6.0
5.9 ± 0.2
8.0 ± 0.3
9.8
9.0
8.1
7.1
5.9
4.2
6.4
5.0 ± 0.1
7.2 ± 0.3
8.2 ± 0.2
8.5 ± 0.4
9.9 ± 0.5
8.8
10.4 ± 0.3
11.5 ± 0.9
13.2 ± 0.8
9.2
11.4
13.9
11.5
14.5
aCalculated according to analytical data in Supporting Information File 1. bNa2HPO4/Na3PO4 buffer (I = 0.1 M). cB(OH)3/NaB(OH)4 buffer (I = 0.1 M).
dNaH2PO4/Na2HPO4 buffer. eCH3COOH/CH3COONa buffer (I = 0.1 M).
made at pH 8.4 revealed the presence of a very small popula- substantial charge compensation in the aggregates between the
tion of objects having an average diameter of 450 ± 150 nm. polyanion Alg, the polycationic AmCD and the buffer ions.
However, their concentration was so low that the relevant diffu-
sion signal was very poor in quality. Therefore, the result found In order to rationalize these results, it is worth preliminarily
must be considered only merely indicative. However, this recalling here that binding between AmCD and Alg does not
apparent failure is informative, because it indicates that the involve the host cavity, but implies a different mechanism, i.e.,
AmCD–Alg aggregates possess a very low ζ-potential, due to external electrostatic and hydrogen bond interactions. There-
fore, it is not comparable with the interaction with p-nitro-
anilines. Moreover, it must be considered that the three AmCDs
differ for both the average number of pendant groups (<nP>)
and N atoms on each CD unit. It can be reasonably hypothe-
sized that the polyamine bush of CD2 should experience a
larger flexibility and conformational freedom as compared to
CD3 or CD1 (see Supporting Information File 1 for further
discussion of the point). Therefore, CD2 turns out to be the best
ligand towards Alg because it is able to achieve the best fitting
upon the polyanion chain. We have also mentioned that proton-
ation of the AmCD occurs first on the farthest N atoms with
respect to the CD scaffold. Therefore, at relatively high pH
values, charged groups on each AmCD unit benefit from a
larger conformational freedom, in such a way that the ligand
can interact with the polyanion in the most effective way. By
contrast, at lower pH values, further positive charges on the
AmCD must be allocated in the relatively narrow space around
the primary cyclodextrin rim. Therefore, the increase in charge
cannot much effectively improve the binding ability of the
Figure 7: nr Values for the AmCD–Alg interaction as a function of
<nH+>.
ligand, expressed in terms of number of anionic monomers per
polycation unit.
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Binding abilities of AmCDs towards pUC19
Table 2: Minimum N/P ratios for complete binding of different forms of
and biological assays
nucleic acids.
Our AmCDs also were tested for their abilities to bind plasmid
DNA. For this, each AmCD was mixed with pDNA at various
N/P ratios (average number of nitrogen atoms on the cyclo-
dextrin core/number of phosphate groups of pDNA) and the
complexation efficiency was evaluated by electrophoretic
mobility shift assays (EMSA). When electrophoresis is applied
to pDNA, different forms may be detected, i.e., the circular,
linear and supercoiled topoisomers (Figure 8; in some prepara-
tions of pDNA, even after RNAse treatment, RNA can be
Nucleic acid form
CD1
CD2
CD3
supercoiled pDNA
linear pDNA
RNA
16.5
38.5
16.5
49.5
38.5
27.5
49.5
27.5
16.5
present). Two sets of experiments were carried out: the first one Differences in the apparent binding abilities of AmCDs towards
(Figure 8a) with the same N/P ratios for each AmCD, and the pDNA may depend upon several factors affecting their mutual
second one with more appropriate N/P ratios (Figure 8b).
interaction, i.e., the state of charge, average number and length
of polyamine arms of AmCDs, and the intrinsic flexibility of
The results obtained indicate that CD1 has the best binding abil- the polynucleotide polyanion as well. Indeed, the best perfor-
ities towards pDNA with respect to CD2 and CD3 (pDNA lacks mances of CD1 with the supercoiled pDNA appear in disagree-
migration in the gel due to AmCD binding). In fact, CD1 bound ment with the results obtained with Alg. It is worth noting that,
the supercoiled conformation of pDNA almost completely at under the pH conditions used (i.e., pH 7.5), CD1 has a lower
N/P 16.5 and the linear one at 38.5. Both, CD2 and CD3 bound average charge (ca. 6.2) as compared to CD2 and CD3 (ca. 10.4
the supercoiled conformation of pDNA almost completely at both). Different binding efficiencies towards pDNA can be
N/P 49.5, the linear one at 38.5 and 27.5, respectively. The lack easily explained considering that, due to its peculiar conforma-
of RNA migration occurred at N/P 16.5, 27.5 and 16.5 for CD1, tion, the closer disposition of the negatively charged phosphate
CD2 and CD3, respectively. The minimum N/P ratios for com- groups enables an optimization of the electrostatic interactions
plete binding are summarized in Table 2.
with the cationic AmCD. It is also reasonable to assume that the
Figure 8: Electrophoretic mobility shift assays of pDNA in the presence of AmCDs at different N/P ratios, as indicated. I and II indicate the linear and
supercoiled conformation of the pDNA, respectively. Binding is shown by the disappearance of one of the three bands: a) N/P ratios were between 0
(pUC19 only) and 27.5 for each AmCD; b) N/P ratios up to 38.5, 60.6 and 49.5 were used.
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presence of the polycation may induce significant conforma- Taking into account the results obtained by EMSA, the transfor-
tional changes in the fairly flexible pDNA polyanion, at the cost mation assays were performed using the following N/P ratios:
of inducing a certain amount of strain. Of course, these changes 38.5 for CD1 or 49.5 for CD2 and CD3. As reference, the same
can hardly occur for the much stiffer Alg structure [55]. There- amount of free pDNA was used. Surprisingly, our experiments
fore, CD1 may overall appear more effective towards pDNA revealed that all the AmCDs showed an adverse effect on the
because, due to its smaller charge, binding involves a larger transformation efficiency reducing the number of bacterial
amount of polycation units, each inducing a relatively small colonies significantly. As a matter of fact, the transformation
strain along the polyanion chain. By contrast, the most charged efficiency, considered as the number of colony forming units/µg
CD2 or CD3 units cause larger strain, overall destabilizing the of pDNA used (CFU), which was obtained after transformation
interaction. For the sake of completeness, the AmCD–nucleic of E. coli cells was as large as 1.3·105 by using only the pDNA.
acid complexes were subjected to the heparin challenge test in By contrast, the CFU value dramatically decreased to approxi-
order to assess their stability. Heparin is a highly negatively mately 5·102, 2·102 and 1.4·104 when the complexes of pDNA
charged sulfated polysaccharide, which is used as a competitor with CD1, CD2 and CD3, respectively, were used. This result
polyanion. The results obtained (see Supporting Information suggested that the AmCDs may interact with cell membranes,
File 1, Figure S2) show that dissociation occurred at a heparin e.g., by electrostatic interaction, or neutralize the anionic nature
concentration of 400 µg/mL for CD1 and 500 µg/mL for CD2 of pDNA, making the addition of calcium chloride in the prepa-
and CD3. This indicates that the binding between DNA and ration of competent cells pointless.
AmCDs is quite strong in comparison to similar systems
[28,56,57].
Conclusion
The binding abilities of AmCDs as bimodal supramolecular
Finally, the effect of the three AmCDs on transformation of ligands were successfully tested towards neutral and anionic
E. coli competent cells was investigated. Cyclodextrins have p-nitroaniline derivatives, sodium alginate and the pUC19
been already reported to change the transformation efficiency of plasmid DNA, chosen as suitable models. First, regarding the
different E. coli strains, although not in a standardized manner. inclusion of small-sized guests into the CD scaffold cavity, we
Different cyclodextrin derivatives can cause from a 10-fold verified that the process is largely affected by the protonation
decrement up to a four-fold increment in the number of trans- status of the host, as a function of the pH, and by the possible
formants compared to control experiments [58]. It is worth presence of buffering electrolytes. The main factors ruling the
mentioning here that bacteria have different ways to interact binding efficiency are Coulomb interactions, medium effects
with extracellular DNA. In some cases they can naturally inter- and conformational restraints, with a subtle interplay deter-
nalize and integrate exogenous DNA (natural competence) and mining the occurrence of non-linear data trends in some cases.
this can result in the acquisition of new genetic traits (e.g., anti- Therefore, the behavior observed and the relevant rationaliza-
biotic resistance genes) and the emergence of multidrug resis- tion proposed by us, appear perfectly consistent with the
tant strains [59]. In addition, extracellular DNA has been shown previous literature on the topic [50]. Second, our materials are
to be important for biofilm establishment and maintenance by able to form stable aggregates with polyanions such as alginate
pathogenic bacteria, such as Pseudomonas aeruginosa and or pDNA. In these cases, of course, binding implies an outer-
Staphylococcus aureus [60-62]. Some other bacteria, such as sphere interaction of the polyanion with the polyamine cationic
E. coli, can undergo a transient period of competence after a “bush”, so it cannot be compared with the interaction with
pretreatment with calcium chloride followed by a short heat or p-nitroanilines. As long as Alg is concerned, analysis of the
electric shock. The addition of CaCl2 promotes the binding of composition of the aggregates, as accounted for by nr values,
pDNA to the outer membrane of Gram-negative bacteria. The enabled us to evidence i) the effect of inorganic electrolytes,
Ca2+ ions both attract the negatively charged DNA backbone which ensure charge counterbalance, resulting in low ζ-poten-
and neutralize the negative charges at the cell surface, thus tial and precipitation and ii) the effect of the structure of the
avoiding electrostatic repulsion between the cell and the phos- polyamine branches, in term of both their pH-dependent overall
phate DNA groups. For other bacteria, these methods do not charge and their conformational freedom. Third, the interac-
work well, so they hardly accept exogenous DNA and gene tions of AmCDs with pDNA, studied by means of EMSA and
manipulation is hampered [63-65]. The latter cases represent a transformation of E. coli Ca-competent cells assays, revealed a
bottleneck in bacterial genetic manipulation and microbial very strong binding, which ultimately hampers the desired cel-
biotechnology, since the procedures to get recombinant bacteri- lular uptake.
al strains are cost and time-consuming. Thus, an increased
transformation efficiency for difficult-to-manipulate strains can As a further remark, we can outline that the latter apparently
be very useful.
negative result is quite intriguing indeed, because we may
2759

Beilstein J. Org. Chem. 2017, 13, 2751–2763.
envisage a possible use of our materials as scavengers of extra- was dissolved in dry DMSO (10 mL), then, 4-nitrofluoroben-
cellular DNA (eDNA). As a matter of fact, recent studies have zene (1.41 g, 10 mmol) and anhydrous Na2CO3 (1.06 g,
shown that eDNA is important for biofilm establishment and 10 mmol) were added. The reaction mixture was kept at 70 °C
maintenance by pathogenic bacteria, such as P. aeruginosa and under stirring for 18 hours. Afterwards, the resulting slurry was
S. aureus [60-62]. In addition, eDNA with its negative charge dissolved in water (200 mL) and the solution was extracted
can sequester cationic antibiotics contributing to antibiotic twice with ethyl acetate (ca. 70 mL each). Then, the aqueous
resistance; thus, removing eDNA from the biofilm matrix can phase was acidified with HCl (6 M) up to pH 2, and the desired
weaken the biofilm and can raise its susceptibility to antibiotics. product was extracted thrice with ethyl acetate (100 mL each).
The fact that these cyclodextrin derivatives might be loaded The organic extracts were dried over Na2SO4 and distilled in
with an antibiotic allows speculating that a possible vacuo (Rotavapor) to afford the crude product, which was dis-
antibiotic–CD complex could target the pathogen and in the solved in a methanolic solution of sodium methoxide (2 M,
meanwhile to bind and sequester extracellular DNA, inhibiting 10 mL). Diethyl ether (80 mL) was then added to precipitate the
its role in vivo. Finally, a particular mention is deserved to the pure product, which was finally filtered off. Yield 60% (1.79 g).
fact that, once again, simple polarimetry proves to be a versa- IR (nujol) ν (cm−1): 1597, 1516, 1339; 1H NMR (300 MHz,
tile and powerful tool for the study of supramolecular interac- D2O) δ (ppm) 3.95 (s, 4H, -CH2-), 6.47 and 8.03 (2d,
tions, even in situations where quite complex systems are J = 9.5 Hz, 2H + 2H, p-NO2-C6H4-N<); Anal. calcd for
involved.
C10H8N2O6Na2: C, 40.28; H, 2.70; N, 9.40; Na, 15.42; found:
C, 40.24; H, 2.73; N, 9.39; Na, 15.43.
Experimental
Materials
Polarimetry
All the reagents needed were used as purchased (Sigma, Polarimetric determinations were performed on a JASCO
Aldrich), without further purification. The sodium alginate sam- P-1010 polarimeter. In order to obtain molar optical rotations Θ
ple used (Sigma, lot 077K1583, extracted from Macrocystis of AmCDs at different pH values, 1.5 mM mother solutions of
pyrifera), presented an average content of mannuronic and the materials in double-distilled water were prepared. Then a
guluronic units of 61% and 39%, respectively, and a molecular small volume of either standard HCl (1 M) or NaOH (1 M) was
weight in the range 70–100 kDa. The AmCDs CD1–CD3 [37] added to aliquots (3 mL each) of the solutions, in order to adjust
were prepared by solvent-free aminolysis at 60 °C for 48 h of the pH to the desired value. From the observed optical rotations
the heptakis(6-deoxy-6-iodo)-β-CD with a 140-fold mole-to- of the samples (corrected for the small dilution effect), the rele-
mole excess of the proper linear polyamine, i.e., 3-(N,N- vant Θ values were easily calculated. Measurements of the
dimethylamino)propylamine (A1) for CD1, bis(3-amino- binding constants for guests 1–4 were accomplished according
propyl)methylamine (A2) for CD2 and bis-1,2-[(3-amino- to the general procedure described elsewhere [51,53]. In brief,
propyl)amino]ethane (A3) for CD3. The products were isolated 1.5 mM stock solutions of the hosts were prepared by
and purified by repeated precipitations from ethanol/diethyl dissolving the proper amount of substance either in pure water
ether. The characterization was carried out by means of poten- followed by adjusting the pH at the desired value by adding
tiometric acid–base titration, which confirmed that the ioniza- small amounts of HCl (1 M) or NaOH (1 M), or in an aqueous
tion behaviour of the AmCDs can be modelled as a mixture of buffer solution at the desired pH value (the buffers used are
four independent virtual weak bases. The results obtained were specified in the footnote of Tables S3–S5, in Supporting Infor-
in full agreement with the values reported in the cited reference mation File 1). Then, sets of sample solutions were prepared by
(relevant discussion and mathematical details are reported in mixing variable amounts (up to 150 μL) of a concentrated guest
Supporting Information File 1). The p-nitroanilines 1–3 [50] solution (usually ca. 0.25 M) to fixed volumes (3 mL) of the
were prepared by nucleophilic aromatic displacement reaction host solution. In each case, the actual pH value of the solutions
between 4-nitrofluorobenzene and a slight excess (ca. 10%) of was checked with a pH-meter. Polarimetric data were subjected
the proper amine in DMSO at 70 °C for 4 hours in the presence to regression analysis by means of the proper equation derived
of Na2CO3 (1 equiv). The same procedure was adapted for the analytically [51,53]. Good fitting provides convincing evidence
synthesis of guest 4.
that only 1:1 host–guest complexes are present in the samples.
Otherwise, deviations from the expected trend give evidence of
N-(4-Nitrophenyl)iminodiacetic acid disodium salt (4) the formation of higher order aggregates.
Iminodiacetic acid (1.33 g, 10 mmol) was treated with an
equimolar amount of sodium methoxide, obtained by dissolving In order to study the interaction between AmCDs and Alg, a
metallic sodium (0.46 g, 20 mmol) in dry methanol (20 mL), stock alginate solution 25 mN was first prepared as follows.
and the mixture was distilled in vacuo (Rotavapor). The residue The proper amount of substance (99.5 mg) was dissolved in
2760

Beilstein J. Org. Chem. 2017, 13, 2751–2763.
warm water and after cooling to rt the volume was adjusted to pUC19 DNA as reference. At the end of the electrophoresis, the
20 mL. Finally, the solution was filtered through a 0.45 μ Milli- gels were visualized under UV light using a Bio-Rad Trans illu-
pore® filter. For the sake of clarity, the concentration minator. The illuminated gels were photographed by using a
(normality) was calculated according to the formula weight of Polaroid camera.
the monomer unit (C6H7O6Na). Then, sets of samples were pre-
pared by mixing fixed aliquots (3 mL each) of stock AmCD Heparin competitive displacement assays were carried out as
solutions at the proper pH value with increasing micro-amounts follows: AmCD–pDNA complexes at selected N/P ratios
of Alg solution. Each sample was vigorously shaken, allowed to (N/P = 40 for CD1, N/P = 50 for CD2 and CD3) were first pre-
settle overnight and then centrifuged at 5000 rpm for 15 min. pared as described earlier, and were subsequently added with
The supernatant liquors were carefully pipetted and the rele- increasing concentrations of heparin sodium salt solution from
vant optical activities were measured. Data were finally subject- porcine intestinal mucosa. The mixtures were incubated at room
ed to regression analysis according to Equation 1 (the relevant temperature for 30 min. Afterwards, the solution was analysed
mathematical details are reported in Supporting Information by 0.8% agarose gel electrophoresis to examine the released
File 1).
pDNA from complexes.
Dynamic light scattering
Calcium competent E. coli cells were prepared as follows:
DLS measurements to evaluate the possible dimensions of E. coli cells were grown in LB medium at 37 °C up to an OD650
AmCD–Alg aggregates were performed with a Malvern Instru- of 0.6. The cells were collected by centrifugation, resuspended
ments Zetasizer NANO-ZS apparatus. The intensity of the in a 70 mM CaCl2 solution and incubated on ice for 1 hour.
diffused light was evaluated at 173°; autocorrelation functions Then, the cells were collected by centrifugation, treated with
were analysed by means of the cumulants method using the freezing solution (70 mM CaCl2/10% glycerol (w/v)), aliquoted
Sasfit 0.94.4 software package. Samples were prepared in and finally stored at −80 °C. Transformation of calcium compe-
aqueous buffer at either pH 6.5 or pH 8.4, by mixing the proper tent E. coli cells was performed by heat shock treatment using
amounts of Alg with each AmCD in such a way to have concen- 20 µL of different mixtures AmCD/pDNA at selected N/P ratios
trations as large as 0.25 mN for Alg and 1.5 mM for the AmCD. (N/P = 40 for CD1, N/P = 50 for CD2 and CD3), as well as
The turbid mixtures obtained were allowed to settle for 24 h and with free pDNA. The cells were incubated on ice for 30 min, for
then, the apparently clear supernatant liquors were carefully 45 min at 42 °C and again on ice for 2 min. Then, 500 µL of LB
pipetted and analysed.
medium were added to each mixture and cells were incubated at
37 °C for 1 hour. Aliquots of 50 µL of each transformation were
put on a Petri disc containing LB agar medium supplemented
Biological assays
E. coli strain DH10B and the plasmid pUC19 (pDNA) were with 100 µg/mL of ampicillin to select E. coli cells containing
used in this study. E. coli was grown at 37 °C in Luria broth the plasmid. Bacterial growth was allowed overnight at 37 °C.
(LB) or terrific broth (TB) liquid medium. When necessary, The experiment was performed in triplicate. The number of
solid medium was obtained by adding agar to the liquid medi- vital bacteria was considered as the colony forming units (CFU)
um. Standard genetic techniques with E. coli and in vitro DNA obtained in presence of AmCD–pDNA complexes or free
manipulations were performed as described previously [66,67]. pDNA.
The pUC19 (ca. 2700 bp, conferring ampicillin resistance to
E. coli) was extracted by alkaline lysis method [64]. Elec-
Supporting Information
trophoretic mobility shift assays (EMSA) of the pDNA were
performed as described elsewhere [68]. For EMSA experi-
Supporting information features a mechanistic scheme for
ments, constant amounts (200 ng) of pDNA were incubated for
the synthesis of AmCDs and discussion of their synthesis
30 minutes at room temperature in a final volume of 20 µL of
and characterization; analytical and polarimetric data for
binding buffer 1× (12.5 mM Tris HCl pH 7.5, 10% glycerol,
AmCDs; mathematical details about polarimetric
62.5 mM KCl, 0.75 mM DTT), using different N/P ratios (aver-
determination of binding constants and about Equation 1
age number of nitrogen atoms on the cyclodextrin core/number
and heparin challenge tests.
of phosphate groups of pDNA). The pH value of the reaction
Supporting Information File 1
Further experimental information.
medium was kept at 7.5 using TE buffer as the solvent [59]. Ten
µL of each binding reaction sample (mixed with bromophenol
blue dye at a 1:1 ratio) was loaded on a 0.8% agarose gel con-
taining ethidium bromide in TBE 0.5× (5.4 g Tris Base, 2.75 g
boric acid, 2 mL of EDTA, 0.5 M, pH 8) pH 7.5 along with the
[http://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-13-271-S1.pdf]
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Beilstein J. Org. Chem. 2017, 13, 2751–2763.
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Acknowledgements
Prof. G. Lazzara and Dr. F. Parisi (Dept. of Physics and Chem-
istry, University of Palermo) are gratefully acknowledged for
DLS measurements and useful discussion.
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ORCID® iDs
Paolo Lo Meo - https://orcid.org/0000-0001-5089-0556
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