Duplex foldamers from assembly induced folding

Article abstract of DOI:10.1021/ja0361897

Oligoamide strands 1, 2, and 3, consisting of 4-H-bond units, were originally designed to form noncovalent polymers based on the expectation that they would adopt an extended conformation. Instead of assembling into the expected supramolecular polymer thr

Full text of DOI:10.1021/ja0361897

Published on Web 07/23/2003
Duplex Foldamers from Assembly Induced Folding
Xiaowu Yang,† Suzana Martinovic,‡ Richard D. Smith,‡ and Bing Gong*,†
Department of Chemistry, UniVersity at Buffalo, The State UniVersity of New York, Buffalo, New York 14260, and
EnVironmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory,
Richland, Washington 99352
Received May 16, 2003; E-mail: bgong@chem.buffalo.edu
The association of biomacromolecules is often accompanied by
conformational changes. In many cases, an otherwise poorly defined
structure folds into a well-defined conformation upon associating
with another molecule. Such an assembly coupled folding process
is best exemplified by the formation of double-stranded DNA: The
zippering of two flexible single strands leads to the formation of a
well-defined, double helical structure. Association-induced folding
is also found in DNA-binding1,2 and protein-protein3,4 interactions.
To control intermolecular associations, various strategies have been
described. Most of these strategies are based on the design of
molecular modules carrying linear arrays of hydrogen bond donors
(D) and acceptors (A).5-8 The design of modules for directing
molecular association has focused on the preorganization or
rigidification of the corresponding molecular components.9-15 On
the other hand, the development of unnatural folding oligomers,
or foldamers, with well-defined secondary structures, has focused
on constructing backbones that undergo specific intramolecular
interactions.16-18 Few unnatural systems that combine specific
intermolecular association with subsequent formation of folded
structures are known.19,20 In this paper, we would like to report
oligoamide strands that not only sequence-specifically associate
(self-assemble) into H-bonded duplexes but also adopt folded
conformations in the final assembled architectures.
Single strand 2, formed by linking two 4-H-bonding DDAD units
in a head-to-head way, was originally designed to associate with
single strand 1, consisting of two AADA units linked in a head-
molecules of 3 adopted an extended conformation and thus
to-head fashion. If strands 1 and 2 adopted extended conformations,
associated in a staggered fashion as required by its ADAD units,
they would only partially overlap with each other due to their
the strength of its intermolecular H-bonds would be similar to those
unsymmetrical 4-H-bonding units, leading to the formation of
of the 4-H-bonded self-dimer 3′‚3′.
noncovalent copolymers. On the other hand, strand 2′, if it adopted
Further 1D 1H NMR experiments confirmed that the inter-
an extended conformation, would be completely complementary
molecular H-bonding interactions between 1 and 2 and among the
to an extended strand 1, leading to the formation of an 8-H-bonded,
molecules of 3 were very strong. At 1 mM, the aniline NH signals
extended duplex. Similar to the design of 1 and 2, linking two self-
of the 1:1 mixture of 1 and 2 and those of 3 showed insignificant
complementary ADAD units in a head-to-head fashion leads to
shifts with increasing percentage (up to 20%) of DMSO-d6 in
oligoamide strand 3. Extended strand 3 would self-associate into
CDCl3. Diluting a sample of 1 and 2 (1:1), or that of 3 in a mixed
homopolymeric aggregates.
solvent containing 10% DMSO-d6 (down to 10 µM) ,in CDCl3 did
Examining a 1:1 mixture of 1 and 2 by one-dimensional (1D)
not lead to any apparent change in the chemical shifts of the aniline
1H NMR (CDCl3, 500 MHz) indicated that these two strands indeed
NH signals that are involved in intermolecular H-bonding. The
associated via H-bonds.21 The signal of proton g appeared at 9.66
stabilities of the H-bonds of 1 and 2, and those of 3, are in sharp
ppm in the spectrum of single strand 1 (1 mM, 23 °C in CDCl3).
contrast to those of the corresponding 4-H-bonded (i.e., DDAD/
In contrast, proton g moved to 10.03 ppm in the spectrum of the
AADA and DADA/ADAD) duplexes,13,22 whose association con-
1:1 mixture of 1 and 2 (1 mM, 23 °C in CDCl3). When the 1D 1H
stants were previously shown to be in the 104 M-1 range in
NMR spectrum of 3 was compared to that of 3′ whose ADAD array
chloroform and could be easily determined by NMR dilution
was shown to dimerize into a self-complementary, 4-H-bonded
experiments.
duplex,13 the signal of proton a of 3 appeared at 10.59 ppm, while
1
The appearance of the 1D H NMR spectra of the 1:1 mixture
that of proton a of 3′ appeared at 9.89 ppm. These results suggest
of 1 and 2, and 3 was not consistent with the formation of polymeric
that the molecules of 3 associated through much stronger H-bonding
aggregates: several sets of well-resolved, sharp signals were
interactions than those of 3′. This was not expected because if the
observed.21 Furthermore, in CDCl3, the signal of the methylene
protons L1 and L2, which appeared at 3.54 ppm as a singlet in the
spectrum of single strand 1, split into two peaks (3.11 and 4.55
† University at Buffalo, The State University of New York.
‡ Pacific Northwest National Laboratory.
9
9932
J. AM. CHEM. SOC. 2003, 125, 9932-9933
10.1021/ja0361897 CCC: $25.00 © 2003 American Chemical Society

C O M M U N I C A T I O N S
dimer 3‚3, and [3 + Cl]- (m/z ) 1335.6), corresponding to single
strand 3, were the two major ions detected.
In summary, we have designed and discovered molecular
duplexes whose formation is characterized by the combination of
sequence-specific self-assembly and folding of the component
strands. Our evidence indicates that an initial assembly process is
followed by the folding of the component strands, which leads to
the final folded, dimeric species. Such assembly induced folding
systems are reminiscent of biomacromolecules such as duplex DNA
and DNA-recognizing proteins. The assembled and folded structures
are stabilized by both H-bonding and aromatic stacking interactions.
The modular nature of this system allows the convenient design of
longer oligomers which should assemble and fold into duplex
foldamers with multiple stacks of H-bonded units. Similar to the
stacking of Watson-Crick base pairs in duplex DNA, the stacking
of the H-bonded units in our duplex foldamers not only provides
additional stabilization to the assembled structure but also shields
the H-bonds away from solvent molecules. On the basis of this
novel assembling and folding motif, sequence-specifically formed
duplex foldamers that are stable in competitive media such as
aqueous solution should become available.
Figure 1. Illustration of duplex foldamers (A) 1‚2 and (B) 3‚3.
1
ppm) in the spectrum of the 1:1 mixture of 1 and 2. The 1D H
NMR spectrum of 3 demonstrated similar features: in CDCl3, the
methylene protons L1 and L2 split into two signals at 2.50 and
2.81 ppm, respectively; in DMSO-d6, on the other hand, methylene
protons L1 and L2 appeared as one signal (a triplet at 2.36 ppm).
These results suggest that the rotational freedom of the trimethylene
linker of 1 or 3 was restricted when 1 and 2, or the molecules of
3, associates through intermolecular H-bonds. The best explanation
for these observations is that, instead of being extended, strands 1
and 2, and 3, adopt folded conformations when associated into their
corresponding H-bonded assemblies.
Cross-strand NOEs from 2D NMR (NOESY) studies indicate
that the 1:1 mixture of 1 and 2, and the self-complementary 3,
sequence-specifically associate through their 4-H-bonding units.21
Acknowledgment. We thank the donors of the Petroleum
Research Fund, administered by the ACS, for support of this
research (37200-AC4). NASA, NIH, and ONR are acknowledged
for partial funding.
1
This and the above results, combined with the facts that the H
NMR spectra of 1 and 2, and that of 3, contained the same number
of aniline NH signals as the corresponding 4-H-bonded duplexes,
suggested that the two 4-H-bonding units in 1, 2, or 3 were
indistinguishable in their H-bonded assemblies. These 4-H-bonded
units acted cooperatively, leading to enhanced intermolecular
H-bonding strengths between 1 and 2 and between the molecules
of 3. In other words, a molecule of 1 mostly likely associates with
another molecule of 2 through two 4-H-bonded units, leading to
the formation of an 8-H-bonded heterodimer 1‚2. Similarly, single
strand 3 very likely self-dimerizes into a homodimer 3‚3.
Examining the H-bonding sequences of 1 and 2 leads to only
one possibility for the formation of an 8-H-bonded dimer: 1 and
2 can only adopt the folded (stacked) conformations as shown in
Figure 1A. On the basis of the same analysis, the molecules of 3
can associate into a homodimer only by adopting the similar folded
conformation (Figure 1B). This model of self-assembling foldamers
is fully consistent with the above experimental results.
Supporting Information Available: Synthetic procedures, NMR
spectra, VPO experiments, MS spectra, and other details (PDF). This
material is available free of charge via the Internet at http://pubs.acs.org.
References
(1) Nagadoi, A.; Morikawa, S.; Nakamura, H.; Enari, M.; Kobayashi, K.;
Yamamoto, H.; Sampei, G.; Mizobuchi, K.; Schumacher, Ma.; Brennan,
R. G.; Nishimura. Structure 1995, 3, 1217.
(2) Weis, W. A. Biochemistry 1990, 29, 8020.
(3) Fasshauer, D.; Bruns, D.; Shen, B.; Jahn, R.; Brunger, A. T. J. Biol. Chem.
1997, 272, 4582.
(4) Wahlberg, E.; Lendel, C.; Helgstrand, M.; Allard, P.; Dincbas-Renqvist,
V.; Hedqvist, A.; Berglund, H.; Nygren, P. A.; Hard, T. Proc. Natl. Acad.
Sci. U.S.A. 2003, 100, 3185.
(5) Zimmerman, S. C.; Corbin, P. S. Struct. Bonding 2000, 96, 63.
(6) Gong, B. Synlett 2001, 582.
(7) Archer, E. A.; Gong, H. G.; Krische, M. J. Tetrahedron 2001, 57, 1139.
(8) Sijbesma, R. P.; Meijer, E. W. Chem. Commun. 2003, 5.
(9) Corbin, P. S.; Zimmerman, S. C. J. Am. Chem. Soc. 1998, 120, 9710.
The formation of these folded duplexes has a strict sequence
requirement: a single strand such as 2′ whose two 4-H-bonded
units are linked in a “wrong” way should not form an 8-H-bonded,
folded duplex with 1. Indeed, the 1D 1H NMR spectrum of the 1:1
mixture of strands 1 and 2′ was not consistent with a discrete
(10) Beijer, F. H.; Kooijman, H.; Spek, A. L.; Sijbesma, R. P.; Meijer, E. W.
Angew. Chem., Int. Ed. 1998, 37, 75.
(11) Sessler, J. L.; Wang, R. J. Org. Chem. 1998, 63, 4079.
(12) Folmer, B. J. B.; Sijbesma, R. P.; Kooijman, H.; Spek, A. L.; Meijer, E.
W. J. Am. Chem. Soc. 1999, 121, 9001.
(13) Gong, B.; Yan, Y. F.; Zeng, H. Q.; Skrzypczak-Jankunn, E.; Kim, Y.
1
species: poorly defined, broad H NMR signals, which prevent
W.; Zhu, J.; Ickes, H. J. Am. Chem. Soc. 1999, 121, 5607.
further 2D NMR studies, were observed.21 Thus, linking the same
4-H-bonded units in different ways can result in different molecular
strands that assemble into completely different architectures.
To confirm the dimeric nature of the aggregates formed by 1
and 2, and by 3, vapor pressure osmometry (VPO) measurements21
were carried out (room temp in CHCl3). Using polystyrene as
molecular weight standards and at the concentration range of 15-
50 mM, apparent molecular weights of 2862 ( 6% corresponding
to a heterodimer 1‚2 and 2590 ( 5% corresponding to homodimer
3‚3 were obtained.
The formation of discrete dimers by 1 and 2, and by 3, was
further confirmed by mass spectrometry.21 The ESI spectrum
showed that for the 1:1 mixture of 1 and 2, the doubly charged [1
+ 2 + 2Cl]2- (m/z ) 1454.3) is the most abundant ion detected.
For 3, [3 + 3 + Cl]- (m/z ) 2636.3), corresponding to the self-
(14) Zeng, H. Q.; Miller, R. S.; Flowers, R. A.; Gong, B. J. Am. Chem. Soc.
2000, 122, 2635.
(15) Zeng, H. Q.; Ickes, H.; Flowers, R. A.; Gong, B. J. Org. Chem. 2001, 66,
3574.
(16) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173.
(17) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem.
ReV. 2001, 101, 3893.
(18) Gong, B. Chem.-Eur. J. 2001, 7, 4336.
(19) Zimmerman reported complexation-induced unfolding of heterocyclic
oligoureas: Corbin, P. S.; Zimmerman, S. C.; Thiessen, P. A.; Hawryluk,
N. A.; Murray, T. J. J. Am. Chem. Soc. 2000, 122, 10475.
(20) Dervan described aromatic oligoamides that fold into hairpin structures
upon binding to a DNA minor groove: Dervan, P. B. Bioorg. Med. Chem.
2001, 9, 2215 and references therein.
(21) See Supporting Information for details.
(22) Zeng, H. Q.; Yang, X. W.; Flowers, R. A.; Gong, B. J. Am. Chem. Soc.
2002, 124, 2903.
JA0361897
9
J. AM. CHEM. SOC. VOL. 125, NO. 33, 2003 9933