Helix control in polymers: Case of peptide nucleic acids (PNAs)

doi:10.4161/adna.20572

Artif DNA PNA XNA. 2012 April 1; 3(2): 31–44.

doi: 10.4161/adna.20572

PMCID: PMC3429529

Helix control in polymers

Case of peptide nucleic acids (PNAs)

Filbert Totsingan,¹^* Vipul Jain,^2
,³ and Mark M. Green²

¹Department of Chemistry; New York University; New York, NY USA

²Herman F. Mark Polymer Research Institute; Polytechnic Institute of New York University; Brooklyn, NY USA

³Dow Electronic Materials; Marlborough, MA USA

^*Correspondence to: Filbert Totsingan; E-mail: ft437/at/nyu.edu

This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Abstract

The helix is a critical conformation exhibited by biological macromolecules and plays a key role in fundamental biological processes. Biological helical polymers exist in a single helical sense arising from the chiral effect of their primary units—for example, DNA and proteins adopt predominantly a right-handed helix conformation in response to the asymmetric conformational propensity of D-sugars and L-amino acids, respectively. In using these homochiral systems, nature blocks our observations of some fascinating aspects of the cooperativity in helical systems, although when useful for a specific purpose, “wrong” enantiomers may be incorporated in specific places. In synthetic helical systems, on the contrary, incorporation of non-racemic chirality is an additional burden, and the findings discussed in this review show that this burden may be considerably alleviated by taking advantage of the amplification of chirality, in which small chiral influences lead to large consequences. Peptide nucleic acid (PNA), which is a non-chiral synthetic DNA mimic, shows a cooperative response to a small chiral effect induced by a chiral amino acid, which is limited, however, due to the highly flexible nature of this oligomeric chimera. The lack of internal stereochemical bias is an important factor which makes PNA an ideal system to understand some cooperative features that are not directly accessible from DNA.

Keywords: helix control, chiral amplification, cooperativity, helical polymers, PNA

Helix Control in Biological Systems (Nucleic Acids and Proteins): Overwhelming Chirality

The helix is a widely encountered conformational state found in biological molecules, peptides, DNA, RNA and viruses as well as in a multitude of synthetic macromolecules. In nature these structures are formed using building blocks of one mirror form with the consequence that the helices formed are of a single mirror-image sense.¹ Most biological polymers adopt helical conformations which are clearly seen in the polynucleotide duplexes and the α-helices formed by peptides and portions of protein structures. The presence of stabilizing soft interactions in such biological systems gives rise to a barrier for inversion of helix handedness,²^-⁴ which is usually not overcome. Many internal and external factors have an effect on the handedness of the helix and have been an interesting topic for scientists who study the origin of chirality and the evolution of biological molecules.⁵

In DNA and RNA (Fig. 1A), one helical sense prevails because each monomer along the chain is forced to maintain the same chirality. One limitation of this chiral constraint is the lack of ability to vary the overall chirality of the polymer and through this, the helical handedness and thus the chiral optical properties. Control of chiral properties would yield helical systems in which the helical sense is a variable.

Figure 1. Schematic structures of DNA, RNA (A) and peptides (B).

In the situation of amino acid-derived biomolecules such as peptides (Fig. 1B), the chiral stereocenter is internal to each of the many monomeric units and therefore is overwhelming in control of helical sense. However, biological systems can occasionally turn to mirror-related amino acids to accomplish specific structural objectives.⁶ The biological synthetic mechanisms at work block the use of “wrong” enantiomer amino acids in the formation of proteins, requiring isomerizing enzymes to introduce these mirror isomers on the completed protein.⁶^-⁸ In vitro, however, methods of synthesis of peptides offer no impediment to the placement of mirror-image-related amino acids. Work in this area has discovered the helical changes, following from enantiomerically mixed monomer units, on the conformational properties of peptides derived from α-helical-forming amino acids.⁹^,¹⁰ Biologically interesting polymers other than peptides from natural amino acids have been synthesized from mixed enantiomers.¹¹^-¹³

Helical Polymers in which Helical Sense is a Variable: Seminal Input from the Italian School

In using homochiral systems, nature blocks our observation of certain interesting aspects of the cooperativity of helical systems, a cooperativity which can lead to large chiral amplification effects. This can act to alleviate the burden of synthesizing enantiomerically pure building blocks for these synthetic systems, and this can be seen most clearly in the simplest version of the nylons, the polyisocyanates, which are stiff helical polymers with a high degree of cooperativity along the polymer chains (Fig. 2).¹⁴ This cooperativity arises from infrequent helical reversals which separate long blocks of opposing helical senses, forcing many units of the chain to take the same helical sense. In this way the chiral bias on each unit of the chain is amplified, with the resulting relative proportions of right- and left-handed segments determined experimentally by measuring the chiral optical properties of the polymers.

Figure 2. Circular dichroism spectra in hexane solution at room temperature of the homopolymers and copolymers of (R)- and (S)-2,6-dimethylheptyl isocyanates plotted as molar ellipticity against wavelength. Reprinted with permission from reference (more ...)

Questions concerning helical polymers with variable sense were first addressed by Italian researchers in Pisa under the supervision of Piero Pino in the 1960s who began to synthesize stereoregular isotactic vinyl polymers with chiral, non-racemic pendant groups [i.e., from (S)- and (R)-3-methyl-1-pentene] and discovered the absence of a linear relationship between the optical activities of such polymers in solution and the configurational enantiomeric characteristics of the monomer units. This nonlinear relationship was difficult to understand except as arising from the chiral units affecting some aspect of the chain conformation. Although the measurements were made in solution rather than with the crystal, the results pointed to the presence of a helical conformation. A full understanding, however, was prevented by the absence of an accessible chromophore, therefore limiting a direct observation of the chiral optical properties by circular dichroism (CD). Moreover, the magnitudes of the cooperative effects were limited by the flexibility of the polymer since helical reversal states were relatively easily accessible. Such structural defects limited the cooperativity, which is responsible for the nonlinear effects.

To gain further insight into the chiral optical properties of isotactic vinyl polymers, Pino and coworkers in Pisa used the Ziegler-Natta catalysts to produce polymers with high stereoregularity from chiral monomers of 1-alkenes. It was well-known from previous work that increasing isotacticity leads to increased crystallinity and therefore to decreased solubility, so that samples could be fractioned based on their isotacticity by dissolution in increasingly high boiling solvents at high temperatures. All fractions of the optically active polymers produced in this way showed increased optical activity compared with the starting monomer units (Table 1).¹⁵^,¹⁶ However, as isoctaticity increased, as evidenced by decreasing solubility, so did the temperature- dependence of the optical activity.

Table 1. Physical properties of poly-(S)-3-methyl-1-pentene fractions having different stereoregularity

According to the data reported in Table 1, Pino hypothesized that helical conformations can exist above the melting point and in dilute solution. Although such conformations could be experimentally evidenced in the crystals of isotactic vinyl polymers, there had been no experimental means to directly address the question in solution. This issue was taken up by Allegra and coworkers in Milan using force field calculations. They found that helical conformations were important in isolated chains,¹⁷^,¹⁸ therefore strongly supporting Pino’s hypothesis.

If the isotactic polymer chain exists as a series of left-handed and right-handed segments separated by helical reversals, the data in Table 1 can be understood. The bias per unit from the chiral pendant groups casting the left- and right-handed helical senses into a diastereomeric relationship must be multiplied by the number of units with the same helical sense, and the chiral optical properties arise not from the units but rather from the helical conformation. Later study performed by Pino and coworkers suggested the possibility of roughly estimating the population of the proposed helical reversals and even their possible effect on the overall polymer properties.¹⁹ At the time of initial work, direct experimental evidence was sought through observation by CD of the helical chromophore, but this could not be probed because of its inaccessible wavelength. To further seek other avenues to support their hypothesis, Pino and coworkers synthesized an isotactic copolymer of styrene with a large excess of (R)-3,7-dimethyl-1-octene.²⁰ The result of their findings is reported in Figure 3. The large increase in the CD signal of the aromatic chromophore in the copolymer compared with the model compound was suggested as arising from an extended conformation of the polymer, which could only reasonably be helical. The experiment was further extended to isotactic copolymers derived from monomeric units offering conflicting information to the helical sense of the chain. A series of copolymers of enantiomers from three structurally different 1-alkenes [(S)-5-methyl-1-heptene; (S)-4-methyl-1-hexene and (R)-3,7-dimethyl-1-octene] were then synthesized and their optical activities were measured.²¹ The results are reported in Figure 4.

Figure 3. CD spectra at 25°C of the diethyl ether extractable fraction of the styrene-(R)-3,7-dimethyl-1-octene copolymer (A) and of (3S,9S)-3,9-dimethyl-6-phenylundecane (B) in chloroform; De is based on one unit of styrene. Reprinted (more ...)

Figure 4. Molar rotator power ( An external file that holds a picture, illustration, etc.
Object name is adna-3-31-e1.jpg

), referred to one monomeric unit, in hydrocarbon solution for the unfractionated methanol-insoluble polymers obtained from samples having different optical purity (P_i) of (S)-5-methyl-1-heptene (A), (S)-4-methyl-1-hexene (more ...)

Alternative studies to confirm the helical hypothesis were also performed by the Italian researchers by synthesizing copolymers of enantiomerically pure units randomly dispersed among achiral units and by measuring the optical activity using mixtures of homopolymers as a control. A linear response of the optical activity to the proportion of the chiral units was observed only in the mixture of homopolymers. In the copolymer of the chiral and achiral units, 50% of the chiral unit was enough to yield the full optical activity.²²

However, in the seminal works performed in Italy, cooperative effects were limited by the flexible nature of vinyl polymers. Clearly, these chiral, nonlinear relationships could be further amplified using helical polymers with a lower probability of helical reversals, that is, stiff polymers. This is the subject of the next section.

Helix Control in Stiff Helical Polymers

Dynamic helical systems: e.g., polyisocyanates and poly(phenylacetylene) derivatives

As in the isotactic vinyl polymers discussed above, other helical polymers such as polyisocyanates, which are synthesized from achiral units, allow equal populations of both helical senses, which are separated by helical reversals. Such reversals are likely to cause a change in the direction of the polymer chain, that is, an effect on the persistence length of the chain. What is the critical chain length that allows these changes to occur? Focusing on this question and others concerning the chiral amplification in polyisocyanates, which are archetypical stiff helical polymer, Green and coworkers first synthesized and measured the optical activities of homopolymers of 1- and 2-deuterio-n-hexyl isocyanates (Fig. 5).¹⁴^,¹⁶

Figure 5. CD and UV spectra of poly(1-deuterio-n-hexyl isocyanate) (α) and poly(2-deuterio-n-hexyl isocyanate) (β). Also shown are the structures and changes in optical activities from the monomers into these polymers. Reprinted (more ...)

Poly(n-hexyl isocyanate) has no preference for one helical sense and the concept of introducing a single stereospecific deuterium substituent in the side chain of every unit arose from the desire to cast the mirror helical states into a diastereomeric relationship without changing the torsional characteristics of the backbone.²³ The poly(1-deuterio-n-hexyl isocyanate) and poly(2-deuterio-n-hexyl isocyanate) exhibited large [α]_D values of opposite sign compared with the precursor monomer (see Fig. 5; -444° vs. +0.65° and +302° vs. -0.43°, respectively). Therefore the optical activity of the polymer could not be arising only from the deuterated stereocenter. Figure 5 shows a large CD signal for the helical chromophore of the two polymers, which is direct evidence proving an excess of one helical sense in these polymers and demonstrating a large chiral amplification. The per unit bias favoring one helical sense arising from deuterium substitution must be very small, while the CD intensities are consistent with a large excess of the preferred helical sense.

In chains of a stiff helical polymer that are short enough there can be expected no disruption of handedness, no helical reversal. In such chains the helical sense excess, as measured by the CD intensity, should track with chain length, that is, with degree of polymerization. As the chain length increases, the helical reversal energy allows the possibility of reversals and the CD intensity should level off and become independent of degree of polymerization, but should decrease greatly with increasing temperatures.²⁴^,²⁵ These expectations are precisely observed, and in combination with theoretical calculations²⁴ have led to determination of the helical reversal energy in the range of 4,000 cal/mole, which at ambient temperature corresponds to one reversal approximately every 800 units along the chain. Knowledge of this energy solved a problem of understanding the source of the limit to the persistence length in the nylon-1 which had perplexed physicists interested in these problems.²⁶

Amplification of the minute chiral information per monomeric unit, as shown in Figure 5, demonstrates the power of cooperativity in these helical polymers which can be expressed in a different way as reported in Figure 6.²⁷ In this case, incorporation of few chiral units which have preference for one helical sense in a polymer with a large number of achiral monomers (e.g., one chiral unit among many hundred achiral units) causes the entire polymer to adopt one helical sense so that additional chiral units have no significant effect on the CD intensity. This is termed the “sergeant and soldiers experiment.”²⁵

Figure 6. Molar ellipticity at 254 nm of achiral/chiral copolymer as function of the fraction of the chiral units (r). Reprinted with permission from reference ²⁷.

Another experiment measuring the cooperativity of a helical polymer is possible, in which enantiomeric chiral units with propensities favoring opposite helical senses compete in controlling the handedness of the polymer (Fig. 7).²⁸^-³⁰ Unlike the “sergeant and soldiers experiment,” or the deuterium substituted experiment discussed above¸ the helical reversal probability is dependent not solely on the helical reversal energy but also on the nature of the competition between the enantiomeric units. As shown in the experiment below (Fig. 7), a small enantiomeric excess can control the entire polymer chain, which may be compared with the “majority rule” situation in a democracy.²⁵^,²⁹^,³⁰

Figure 7. Optical activity of (R)/(S) copolymer as function of fraction of (S)-enantiomer [p = S/(R+S)]. Reprinted with permission from reference ²⁸. Also shown is the structure of (R)/(S) copolymer.

Following the initial work on the polyisocyanates discussed above, chiral amplification phenomena have been found in other covalent polymers also in supramolecular helical systems involving non-covalent assemblies of molecular components.³¹^-⁴⁰ For example, poly(phenylacetylene) derivatives bearing achiral functional side groups have been synthesized. The polymers possess a stereoregular cis-transoidal structure. Excess single-handed helicity of the main chain can be induced for the polymers by the interaction with chiral molecules.⁴¹^-⁴³ In early studies performed by Yashima et al.,⁴¹ the concept of memory of macromolecular helicity in poly[(4-carboxyphenyl)acethylene] (Fig. 8) was reported. This highly dynamic helical polymer possesses a large number of helical units separated by helical reversals and has therefore no preference for one helical sense. However, interaction of the polymer carboxyl group with optically actives amines causes induction of macromolecular helicity, therefore resulting in optical activity (Fig. 8). Apparently, the highly cooperative interactions in the pendant groups give rise to a large excess of one helical sense arising from complexation with the chiral guests, which considerably alters the population of left- and right-handed helices of the polymer. The complex of the polymer with optically active amines shows a characteristic CD signal which depends on the configuration of the chiral amine (Fig. 8B). Remarkably, the induced macromolecular helicity remains even after substitution of the chiral inducers by achiral ones (Fig. 8).

Figure 8. Schematic representation (A) of induced macromolecular helicity the memory of macromolecular helicity in (poly[(4-carboxyphenyl)acethylene]; poly-1) and CD changes at 374 nm (B) in the presence of amines. Reprinted with permission from (more ...)

The CD absorptions in the example discussed above are not based on the chiral amine but on the excess helicity of the main chain of polymer as clearly understood from the wavelength range. These results have been interpreted to mean that poly[(4-carboxyphenyl)acetylene] originally having a rather irregular twist of the adjacent double bonds around a single bond may be transformed into the helical conformation with an excess screw sense by the interaction with the chiral amines (Fig. 9). Poly(phenylacetylene) derivatives having a chiral side chain have also been reported to show interesting helical effects that depend on side chain chirality⁴⁴ as have polysilanes.³⁵^,⁴⁵

Figure 9. Helix control in poly(phenylacetylene) derivatives through interactions with chiral amines.

Non-dynamic helical systems: poly(trityl methacrylate) and related polymers

Vinyl polymers without the capacity to undergo helical reversals can be prepared from methacrylates with a bulky side group (e.g., trityl) by isotactic anionic or radical polymerization.⁴⁶^,⁴⁷ This type of polymer (Fig. 10) was first anionically asymmetrically synthesized from trityl methacrylate using a complex of n-butyl lithium.⁴⁸

Figure 10. Structure of poly(trityl methacrylate):poly(TrMA).

Asymmetric anionic polymerization is performed using a complex of an organolithium with a chiral ligand (ligand control) or using a chiral organolithium initiator (initiator control) (Fig. 11).⁴⁸^,⁴⁹ Selection of the helix-sense occurs on the basis of the chirality of the ligand or the initiator.

Figure 11. Helix control in asymmetric anionic polymerization by a chiral ligand (A) or a chiral organolithium initiator (B). Reprinted with permission from reference ⁴⁹.

Although a chiral side group was necessary in inducing a helical conformation with an excess helical sense in solution for stereoregular vinyl polymers, the synthesis of helical poly(trityl methacrylate) is achieved from the achiral (prochiral) vinyl monomer with the chiral information arising from the initiator. A nearly completely isotactic configuration and a single-handed helical conformation of the main chain, which is stabilized by steric repulsion of the bulky side groups, is obtained, which shows high optical activity based on the conformation.⁴⁸ The helical conformation is lost when the trityl group is removed from the polymer chain. Thus, the poly (methacrylate) derived from the poly(trityl methacrylate) after removal of the trityl group shows only a small optical activity based on the configurational chirality of the stereocenters in the vicinity of the chain ends.⁵⁰ Helical copolymers of trityl methacrylate with other monomers have also been synthesized and their chiral optical properties have been studied.⁵¹

Other poly(trityl methacrylate) derivatives have parallel characteristics. For example, monomers having the pyridyl group in the side chain,⁵²^-⁵⁴ were polymerized and were designed with the idea that the ester linkage should be more stable to methanolysis than that of poly(trityl methacrylate). Helix control in these polymers was achieved via anionic polymerization as for trityl methacrylate (Fig. 11)⁴⁹ and also by radical polymerization using chiral entities as chain transfer agents or initiators (Fig. 12).⁴⁹ In radical polymerization of bulky methacrylate derivatives, the helix control is governed by the chirality of the monomer itself or an additive.

Figure 12. Helix control in radical polymerization using optically active thiols as initiator or chain transfer agent. Reprinted with permission from reference ⁴⁹.

Figure 13 shows the relationship between enantiomeric excess (ee) of the monomer and the optical activity of the derived polymer obtained by radical polymerization of phenyl-2-pyridyl-o-tolylmethyl methacrylate.⁵⁵ A nonlinear dependence indicates that the optical activity of the polymer is not based only on the side chain chirality. Furthermore, the chirality of a one-handed helical part induced by the major enantiomer (in excess) units can overcome the opposing chiral induction by the minor enantiomer units. In other words, once a one-handed helical radical comes under the influence of the major enantiomer, an entering minor enantiomer becomes a part of the one-handed helix whose direction may be unfavorable to the chiral nature of the minor enantiomer, that is, the majority rule.²⁹^,³⁰

Figure 13. Optical activity of the polymer derived from radical polymerization of phenyl-2-pyridyl-o-tolylmethyl methacrylate as function of enantiomeric excess of the monomer. Reprinted with permission from reference ⁵⁵. Also shown is the structure (more ...)

Helix Control in Peptide Nucleic Acids (PNAs)

Helix induction in single-stranded PNAs: helical preorganization

Peptide nucleic acids (PNAs)⁵⁶ are DNA analogs in which the sugar-phosphate backbone has been replaced by an N-(2-aminoethyl) glycine unit covalently linked to the nucleobase (Fig. 14).

Figure 14. Chemical structures of achiral and acyclic chiral PNAs.

Using the original N-(2-aminoethylglycine) unit as starting point, several modifications have been introduced into the backbone⁵⁷^,⁵⁸ based on the “preorganization” concept, i.e., the ability to adopt a conformation which is more suitable for DNA binding. In particular, incorporation of a stereocenter at the γ-position results in stabilization of PNA-DNA duplex by ~3°C per chiral unit. The basis of this enhanced stabilization can be understood from structural data. Superposition of PNA strands from a crystal structure of γ-PNA:DNA duplex with methyl group at the γ-position,⁵⁹ to the solution structure of a single-stranded (CT) γ-PNA dimer⁶⁰ shows structural similarities of the γ-PNA strands to one another in backbone conformation, nucleobase orientation and carboxymethylene bridge projection (Fig. 15). In both the single-strand and the duplex forms, the (S) methyl group at the γ-position is in a trans configuration with the carboxymethylene bridge, which, in turn, is in trans with the backbone carbonyl oxygen within the same unit. The striking similarities between the two structures, in both the unbound and the bound states, suggest that the molecular interactions that direct the folding of the γ-PNA:DNA duplex also direct the folding of the individual γ-PNA single strands.

Figure 15. Comparison of PNA strands from crystal structures of γ-PNA:DNA (cyan)⁵⁹ and chiral box α-PNA:DNA (green)⁶¹ with the NMR structure of single-stranded (CT) γ-PNA dimer (blue).⁶⁰ Reprinted with permission from reference (more ...)

To elucidate whether conformational preorganization of γ-PNA occurs as a result of base stacking or is intrinsic to the individual building blocks, a series of γ-modified Boc-protected PNA monomers containing amino acids with increasing side-chains [glycine (unmodified), l-alanine, l-valine and l-isoleucine] (Fig. 16A) was investigated.⁵⁹ Solution structures obtained by ¹H NMR revealed that glycine and alanine monomers do not have a preferred helical conformation, while valine and isoleucine monomers show ³J-coupling constants consistent with a right-handed conformation (Fig. 16B), presumably due to the large isopropyl and sec-butyl side-chain of valine and isoleucine, respectively, which cause restricted rotation around the C2-C3 bond. The fact that the alanine monomers do not exhibit a preferred conformation as individual units but that they do when covalently linked together into an oligomer suggests that base stacking between adjacent units play an essential role in determining the helical sense as well as in stabilizing the helical conformation.

Figure 16. (A) Structures of Boc-protected unmodified and γ-modified PNA thymine monomers (R, amino acid side-chain). (B) Newman projection showing the preferred conformation around the C2-C3 bond for (S)-isoleucine. ¹H NMR splitting patterns (more ...)

Standard single stranded PNA is not chiral and tends to fold into complex globular structures,⁶² probably due to the conformational collapse of the hydrophobic nucleobases. However, insertion of a stereocenter either at the α- or at the γ-position (Fig. 14) can preorganize the PNA strand,⁵⁹^,⁶⁰^,⁶³ by shifting the preference toward a left- or right-handed helical conformation, according to the configuration of the stereocenter. For example, a γ-backbone modification by L-amino acids such as l-isoleucine⁵⁹ or l-serine⁶⁰ can transform the randomly folded peptide nucleic acid into a conformationally preorganized right-handed helix, as reported by Ly and coworkers. Figure 17 compares the CD spectra of a series of PNAs with increasing number of γ-modified monomers with that of the corresponding achiral PNA, the latter, of course, unable to exhibit a CD band in the nucleobase absorption region (220–300 nm) even if there were base stacking (P1, Fig. 17). However, γ-PNAs (P2-P5, Fig. 17) exhibit CD signals with biphasic exciton coupling patterns characteristic of right-handed helices.⁶⁴ The CD signal of γ-PNAs gradually decreases with increasing temperatures and becomes similar to that of achiral PNA at high temperatures. Furthermore, upon cooling, the CD signal returns to the original spectral pattern indicating that the observed exciton coupling occurs as a result of molecular preorganization rather than an intermolecular interaction. The results of this study⁶⁰ were interpreted as showing that the determining factor for helical induction in γ-PNAs appears to be sterically driven and stabilized by base stacking [for stereochemical model obtained from a monomer in the crystal structure, showing the effect of substituents derived from D- or L-amino acids either on the C2 (α) or on the C5 (γ) carbon of the monomers see ref. ⁵⁷].

Figure 17. CD spectra of single-stranded achiral PNA (P1) and l-serine γ-PNAs (P2-P5). Reprinted with permission from reference ⁶⁰.

Conformational preorganized single-stranded PNAs have also been reported by Sforza and coworkers.⁶³ They reported that modification at the α-position induces in single-stranded PNA a helical conformation which exhibits a CD profile similar to that of a PNA-PNA double-helix (see Fig. 18), although the CD signals of the α-PNAs reported were weak compared with those of γ-PNAs studied by Ly et al. A direct comparison between α- and γ-PNA is seen in Figure 19, which shows that γ-position has a larger chiral effect than the α-position (P6 vs P7, Fig. 19). Interestingly, the fact that the CD shape and intensity in the nucleobase absorption region is not dependent on the number of the chiral units (P7 vs. P8, Fig. 19), suggests that a single chiral unit may be sufficient to preorganize the entire oligomer into a single favored helical conformation, therefore following the “sergeant and soldiers” concept developed by Green and coworkers to explain the chiral amplification in polyisocyanates.¹⁶^,²⁵

Figure 18. CD spectra of single-stranded α-(L/D)-Lys-PNAs and the corresponding PNA:PNA duplexes with the complementary achiral PNA strand. Reprinted with permission from reference ⁶³.

Figure 19. CD spectra of single-stranded l-serine α-PNA (P6) and l-serine γ-PNAs (P7 and P8). Reprinted with permission from reference ⁶⁰.

Helix induction in double-stranded PNAs

The PNA:PNA duplex is expected to form a mixture of equally populated right-handed and left-handed helices.⁶⁵ Driven by questions of induction and amplification of chirality in these non-natural DNA-like molecules, Nielsen and coworkers investigated the influence of a C-terminal amino acid on the helical sense of PNA:PNA duplexes.⁶⁶ Attachment of a lysine to the C-terminal base of one of the two PNA strands leads to a preferential helical sense for the PNA:PNA double helix (Fig. 20) and helices induced by L- and d-lysine were found to be exactly of opposite helical sense as expected and as shown by the CD spectra in the nucleobase absorption region (Fig. 21).⁶⁶ In this experiment, the initial stereochemical bias is propagated through the PNA:PNA duplex by cooperative interactions throughout the helical conformation, with a propagation of chirality via the “sergeant and soldiers” type.¹⁷^,²⁶

Figure 20. Helical sense preference induced in PNA:PNA duplex by a C-terminal chiral amino acid. D- and L-amino acid attached to the C-terminus of one PNA strand induce helices with opposite helical sense.

Figure 21. CD spectra of PNA:PNA duplexes with L- and d-lysine linked to the C-terminus of one PNA strand: H-AGTGATCTAC-(L/D-Lys)-NH₂ and H-GTAGATCAGT-(L/D-Lys)-NH₂. Reprinted with permission from reference ⁶⁶.

Choice of the proper base sequence was also found to be fundamental in inducing the preferred helicity in the PNA:PNA duplex, stabilized by the C-terminal amino acid. It was found that the base closest to the terminal amino acid must be either a guanine or a cytosine to give a well-defined CD pattern, indicative of the preferred helical sense. Substitution of lysine with other amino acids gave the same CD spectral pattern, demonstrating that the intrinsic chirality of the amino acid is not of major importance in affecting the coupling between the transition moments of the nucleobases as a result of their helical stacking.

The effect of a terminal l-lysine in a series of PNA:PNA duplexes with increasing chain lengths led to the conclusion that the chiral influence of lysine extends only as far as the tenth base pair, at which point a loss of stereochemical bias was supposed to occur, leading to constant CD signals on a per monomer unit basis.⁶⁶ This result was interpreted as suggesting a limit of the cooperative properties of PNA:PNA duplexes: after 10 base pairs the chiral bias of base stacking interactions is attenuated to such an extent as allowing a reversal of the double-helical sense.

To further understand the problem of chiral amplification in PNA:PNA duplexes, we extended the studies of the effect of terminal amino acids on the PNA double-helix by varying the appending various amino acids and using longer oligomers⁶⁷ than previously investigated by Nielsen and coworkers.⁶⁶ Circular dichroism, UV melting, NMR as well as temperature-dependence of CD signals showed that the terminal amino acid has an influence not only on the helical sense of the double helix, but also on the conformational properties of the double helix. The terminal amino acid affects the duplex structure distal to its point of attachment as a result of an extended range of conformational states in solution with a population which depends on both the amino acid and the oligomer length of the duplex. A simple model illustrating this fact for a terminal l-lysine is reported in Figure 22.

Figure 22. Schematic representation of multiple conformational states model. Only two states are shown for simplicity. The terminal l-lysine can stabilize one of the two handedness and one of the two states by interacting with the adjacent base (more ...)

The optical activities as function of the terminal amino acids and the chain lengths are shown in Figure 23 for two different solvents (water and glycerol/water). The length dependence of the optical activity from different amino acids in particular showed complex behavior, consistent with a structural model in which an ensemble of PNA duplex conformations differ as a function of the terminal amino acid, suggesting that the PNA duplex itself is intrinsically conformationally heterogeneous, in contrast to the solid state where a unique helical conformation is the situation as observed by X-ray crystallography.⁶⁸ Attachment of an amino acid may stabilize and restrict this manifold to a smaller set, but the system remains multistate in nature. These results support and extend conclusions gained from a crystallographic study of partially self-complementary PNA showing that several types of H-bonding schemes can occur in PNA duplex.⁶⁹

Figure 23. Optical activities of PNA:PNA duplexes in water (A) and in glycerol/water (9:1) mixture (B), as function of the terminal amino acid and the oligomer chain length. Reprinted with permission from reference ⁶⁷.

Helix control in PNA:PNA duplexes bearing one or more chiral units within the oligomer chain have also been investigated.⁶³^,⁷⁰^-⁷² Early studies performed by Sforza and coworkers⁶³ showed that incorporation into the PNA strand of one chiral unit of either L- or d-lysine-based PNA monomer modified at the α-position (α-PNAs) induces in the PNA:PNA duplex a preferred helical sense. In this case, the exciton coupling patterns in the nucleobase absorption region were opposite when comparing αD-Lys-PNA:PNA and αL-Lys-PNA:PNA duplexes (Fig. 18).⁶³ As shown in Figure 18, the CD spectra of the PNA:PNA duplexes exhibit a higher intensity, but were quite similar in shape to the spectra of single-stranded PNAs suggesting that the preferred handedness was already induced in the single strand, and that this preference was enhanced in the duplex, therefore supporting the concept of “preorganization” in single-stranded PNAs discussed above. Interestingly, the shape and intensity of the PNA:PNA duplexes containing three lysine monomers distributed along the chain was similar to those of the PNA:PNA duplexes bearing only one lysine monomer in the middle of the strand (Table 2), suggesting that one chiral unit was enough to induce the helical sense preference, consistent with the “sergeant and soldiers” concept.¹⁷^,²⁶

Table 2. Molar ellipticity at 256 nm of PNA:PNA duplexes bearing one or three α-substituted chiral units, reprinted with permission from reference ⁶³

Replacement of lysine with other amino acids was also studied and the optical activities at 256 nm of various PNA duplexes are shown in Table 2. The helical sense preference of the PNA:PNA duplex with three α-L-Asp-based monomer units distributed along the chain was identical to that of the duplex with three α-L-Lys-based monomer units, and the helical sense preference of the PNA:PNA duplex with three α-D-Glu-based monomer units was identical to that of the duplex with three α-L-Lys-based monomer units. Since two groups of opposite charges showed the same helical sense, it can be deduced that the interaction involved is not a specific ion-dipole interaction or H-bonding, but rather a solvation effect of the polar groups, which are likely to be shifted away from the PNA backbone because of water solvation. The induced conformational changes are transmitted to the nearest base, thus modifying the stacking interactions and affecting the helical preference.

The effect of substitution in either the 5-position (γ) or both the 2- (α) and 5-position on the helical sense preference of PNA:PNA duplexes has also been reported.⁷⁰Figure 24 shows the CD spectra of PNA:PNA duplexes bearing one chiral (L/D)-lysine-based monomers at either the 2-position, 5-position or both.

Figure 24. CD spectra of PNA:PNA duplexes bearing a chiral lysine-based monomer with one or two stereogenic centers at 2- (α) or 5- (γ) position. Reprinted with permission from reference ⁷⁰.

In the 2-position (α), the D-configuration favors right-handed helices, while the L-configuration favors left-handed helices, which is consistent with the results reported in Figure 18 (see the discussion above). Quite interestingly, the opposite is true if the stereogenic center is placed in the 5-position (γ): the D-enantiomer favors left-handed helices, while the L-enantiomer favors right-handed helices. When two stereogenic centers were simultaneously present, two different situations arose: (1) (2L,5D) as well as (2D,5L) leads to “chiral accordance” since both stereocenters induce the same preferential handedness; (2) (2L,5L) and also (2D,5D) give rise to a “chiral conflict,”⁷³ by inducing opposite helical handedness. The helical sense of the derived PNA:PNA duplexes was similar to that of the duplexes with only the 5-substitution demonstrating that the 5-position appears to be prevalent in inducing the preferred helical conformation and overwhelms the effect of the chiral induction exerted by the stereogenic center at the 2-position.

This behavior may be rationalized according to the following considerations. The preferential helical senses are hypothesized to arise from the attempt to minimize the intra-strand steric clashes due to the amino acid side chains.⁷⁰^,⁷² When a PNA with a “chiral conflict” adopts a helical conformation that is either right-handed or left-handed, this helical arrangement should be sterically unfavorable for one of its two “conflicting” amino acid side chains; therefore, one or more bonds must rotate in order to minimize the clashes, eventually inducing a modification in the preferred PNA conformation. Interestingly, based on the chiral conflict concept encountered in the polyisocyanates, temperature could play an interesting chiral optical role in these chirally conflicted PNA-PNA duplexes.⁷³

Acknowledgments

The present review is being written in honor of Prof Rosangela Marchelli for her leading contributions in the field of DNA recognition by peptide nucleic acids (PNAs).

Footnotes

Previously published online: www.landesbioscience.com/journals/artificialdna/article/20572

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