Homochiral G-quadruplexes with Ba2+ but not with K+: The cation programs enantiomeric self-recognition [2]

Full text of DOI:10.1021/ja004330v

6738
J. Am. Chem. Soc. 2001, 123, 6738-6739
Homochiral G-Quadruplexes with Ba2+ but Not with
+
K : The Cation Programs Enantiomeric
Self-Recognition
Xiaodong Shi, James C. Fettinger, and Jeffery T. Davis*
Department of Chemistry and Biochemistry
UniVersity of Maryland, College Park, Maryland 20742
ReceiVed December 27, 2000
In biological and synthetic systems, noncovalent interactions
often control formation of assemblies from multiple components,
and the thermodynamically favored structure can vary with
changes in the building blocks, template, or environmental
Figure 1. (A) A side view of the crystal structure of the G-quadruplex
formed from (D)-G 1 and Ba2 picrate. The picrate counterions are deleted
+
1
conditions. Some intriguing examples of this dynamic equilibrium
2
for clarity. (B) Four G-quartets, G
4
4
1-G 4, make up the G-quadruplex.
shifting involve formation of homochiral assemblies from racemic
The two Ba2 cations are indicated, as are the picrate hydrogen bonds
+
ligands.3 Enantiomeric self-recognition of nucleosides is par-
,4
4 4
with the amino N2 HB proton of G 2 and G 3.
5
6
ticularly interesting, since the genetic material is homochiral.
We report that cations of similar size, but of different charge,
promote formation of stereoisomeric assemblies from the same
racemic nucleoside. Specifically, (D,L)-5′-silyl-2′,3′-O-isopro-
pylidene guanosine (G 1) forms homochiral aggregates in the
Scheme 1
2+
presence of Ba picrate but gives heterochiral diastereomers when
+
K is the guest (Scheme 1).
Guanosine derivatives self-associate in the presence of cations
7
to form hydrogen-bonded G-quartets. Individual G-quartets stack
+
to give G
8
-M sandwiches and higher-ordered G-quadruplexes.
+
+
8-10
Besides K and Na , G-quadruplexes also bind divalent cations.
Since octacoordinate K+ (r ) 1.51 Å) and Ba (r ) 1.42 Å)
2+
11
+
have similar ionic radii, we reasoned that comparing the K
and Ba2 complexes formed from G 1 would reveal how the
+
12
cation’s charge affects G-quadruplex structure and dynamics.
While studying ligand exchange, we discovered that Ba2+ picrate
directs enantiomeric self-recognition of (D,L)-G 1 (Scheme 1). In
this case, the divalent cation and the picrate anion cooperate to
enable chiral resolution of (D,L)-G 1 on the supramolecular level.
First, we confirmed that Ba2 picrate templates G-quadruplex
formation. NMR integration showed that (D)-G 1 extracted Ba2
linked by four picrate anions that hydrogen bond to the “inner”
G-quartets (Figure 1). NMR mixing experiments using [(D)-G 1]16
[BaPic ] and the isomorphous [(D)-G 1]16‚2[SrPic ] indicated
that the M G-quadruplexes retain the hexadecamer structure in
CD Cl and that the picrate anions stabilize this hexadecamer in
solution. The only significant difference between the X-ray
‚
2
2
2
2+
+
2
2
+
14
picrate from water into CD
complex with 8 equiv of nucleoside bound to each Ba picrate.
] indicated that 16 units
2
Cl
2
to give a hydrogen-bonded
2+
+
15
structures of the Ba and K G-quadruplexes is the cation
2+
+
occupancy. For the K G-quadruplex, a cation is present between
A crystal structure of [(D)-G 1]16‚2[BaPic
2
each G-quartet, raising the possibility that charge-charge
2+
of G 1 associate around two Ba cations to give a complex with
+
repulsion between adjacent cations might destabilize the K
G-quadruplex relative to the Ba G-quadruplex. For the Ba
four G-quartet layers.13 This lipophilic G-quadruplex is composed
2+
2+
2+
of two coaxially stacked C
Within an octamer, sugar-nucleobase hydrogen bonds connect
the 5′-ribose oxygen of the “inner” G-quartet with the N amino
‚Ba2 octamers are
4 8
-symmetric octamers, [(D)-G 1] ‚Ba .
complex, the divalent cations are sandwiched within individual
octamers, and there is no cation located between the “inner” two
G-quartets.
2
+
group of the “outer” G-quartet. The [(D)-G 1]
8
Although structurally similar, the Ba2 G-quadruplex is
+
+
(
1) (a) Hasenknopf, B.; Lehn, J. M.; Boumediene, N.; Dupont-Gervais, A.;
thermodynamically and kinetically more stable than the K
van Dorsselaer, A.; Kniesel, B.; Fenske, D. J. Am. Chem. Soc. 1997, 119,
G-quadruplex. For example, the picrate anion binds more strongly
1
0956-10962. (b) Calama, M. C.; Timmerman, P.; Reinhoudt, D. N. Angew.
2
+
to the G-quadruplex filled with divalent cations. For the Ba
Chem., Int. Ed. 2000, 39, 755-758. (c) Hof, F.; Nuckolls, C.; Rebek, J., Jr.
J. Am. Chem. Soc. 2000, 122, 4251-4252.
1
system, separate picrate H NMR signals were observed for an
equimolar mixture of [(D)-G 1]16‚2[BaPic ] (δ ) 8.99 ppm) and
free” anion (δ ) 8.71 ppm) in CD Cl (Supporting Information
Figure 4). In contrast, a time-averaged NMR signal (δ ) 8.85
ppm) for a 1:1 mixture of [(D)-G 1]16‚4[Kpic] and solvated picrate
indicated faster anion exchange between the K G-quadruplex
(
2) (a) Lehn, J.-M. Chem. Eur. J. 1999, 5, 2455-2463. (b) Cousins, G. R.
2
L.; Poulsen, S. A.; Sanders, J. K. M. Curr. Opin. Chem. Biol. 2000, 4, 270-
79.
3) (a) Masood, M. A.; Enemark, E. J.; Stack, T. D. P. Angew. Chem., Int.
“
2
2
2
16
(
Ed. 1998, 37, 928-932. (b) Kondo, T.; Oyama, K.; Yoshida, K. Angew. Chem.,
Int. Ed. 2001, 40, 894-897.
+
(
4) (a) Prins, L. J.; Huskens, J.; de Jong, F.; Timmerman, P.; Reinhoudt,
D. N. Nature 1999, 398, 498-502. (b) Prins, L. J.; de Jong, F.; Timmerman,
P.; Reinhoudt, D. N. Nature 2000, 408, 181-184.
(13) Crystal data for [(D)-G 1)]16‚2Ba2+(picrate)
) 8888.18, crystal dimensions 0.515 × 0.255 ×
0.161 mm , tetragonal, space group I4, a ) 30.780 Å, b ) 30.780 Å, c )
4 2 3 6
‚(H O)11‚(CH CN) : C352.76
(
5) Shi, X. D.; Fettinger, J. C.; Cai, M.; Davis, J. T. Angew. Chem., Int.
2 104 r
H562 Ba N O119Si16; M
3
Ed. 2000, 39, 3124-3127.
3
(
6) Feringa, B. L.; van Delden, R. A. Angew. Chem., Int. Ed. 1999, 38,
418-3438.
7) Guschlbauer, W.; Chantot, J. F.; Thiele, D. J. Biomol. Struct. Dynam.
25.831(5) Å, R ) 90°, â ) 90°, γ ) 90°, V ) 24 472(6) Å , Z ) 2, D )
x
3
-1
3
1.206 mg/m , u(Mo KR) ) 0.283 mm . Data were collected on a Bruker
(
SMART 1000 CCD diffractometer at 193(2) K. Structure determination was
1
9
1
990, 8, 491-511.
done by direct methods using the program XS. Refinement, using the XL
20 2 2
(
(
(
8) Chen, F. M. Biochemistry 1992, 31, 3769-3776.
9) Smirnov, I.; Shafer, R. H. J. Mol. Biol. 2000, 296, 1-5.
10) Kotch, F. W., Fettinger, J. C.; Davis, J. T. Org. Lett. 2000, 2, 3277-
program, was done to convergence on F with R(F) ) 9.94% and wR(F ) )
22.03% for all 15 958 independent reflections.
(14) Shi, X. D.; Fettinger, J. C.; Davis, J. T. Angew. Chem., Int. Ed. 2001.
In press.
3
280.
(
(
11) Shannon, R. D. Acta Crystallogr., Sect. A 1976, 32, 751-767.
12) Tohl, J.; Eimer W. Biophys Chem. 1997, 67, 177-186.
(15) Forman, S. L.; Fettinger, J. C.;Pieraccini, S.; Gottarelli, G.; Davis, J.
T. J. Am. Chem. Soc. 2000, 122, 4060-4067.
1
0.1021/ja004330v CCC: $20.00 © 2001 American Chemical Society
Published on Web 06/13/2001

Communications to the Editor
J. Am. Chem. Soc., Vol. 123, No. 27, 2001 6739
1
Figure 2. A series of H NMR spectra (CD
2
Cl
2
at room temperature)
+
2+
showing the H8 region for the K G-quadruplex and the Ba G-qua-
druplex during enantiomeric mixing experiments. Due to the “head-to-
4
tail” stacking of two G -quartets an enantiomerically pure G-quadruplex
has two signals for each proton in G 1. Panel 1: (A) enantiomerically
pure [(D)-G 1]16‚4[Kpic]; (B) an equimolar mixture of [(D)-G 1]16‚4[Kpic]
1
Figure 3. A series of
2 2
H NMR spectra in CD Cl showing the H8 region
+
during dynamic equilibration. (A) [(D)-G 1] ‚4K
16
4
(pic) . (B) after
(
2 mM) and [(L)-G 1]16‚4[Kpic] (2 mM) 1 day after mixing; (C) 2 days
extraction of K picrate from water by (D,L)-G 1. (C) after stirring the
+
after mixing; (D) 5 days after mixing; (E) a control experiment generated
by extracting K picrate from water into CD
2
mixture of [(D)-G 1]16‚2Ba (pic)
(
mixing; (E′) a control experiment generated by extracting Ba picrate
from water into CD Cl using (D,L)-G 1.
solution from (B) overnight with a water solution of Ba2+picrate; (D)
+
2+
2
2
Cl
2
using (D,L)-G 1. Panel
after extraction of Ba picrate from water into CD Cl using (D,L)-G 1.
2
2
: (A′) enantiomerically pure [(D)-G 1]16‚2Ba +(pic)
; (B′) an equimolar
4
2
+
2+
4
(2 mM) and [(L)-G 1]16‚2Ba (pic)
4
+
2 2
showed that stirring a CD Cl solution of the heterochiral K
2 mM) 1 day after mixing; (C′) 3 days after mixing; (D′) 9 days after
2+
G-quadruplexes with water containing Ba picrate established
2+
an equilibrium favoring the homochiral Ba2 G-quadruplexes
+
2
2
(Figure 3).
Simply switching from a monovalent to a divalent cation
changed the expression of stereochemical information embedded
and the unbound state. Picrate is held tighter to the Ba2+
+
G-quadruplex than to the K G-quadruplex, probably due to the
in (D,L)-G 1. Barium picrate directs significant enantiomeric self-
2+
greater charge density of Ba .
+
recognition of (D,L)-G 1, while K picrate leads to heterochiral
NMR mixing experiments illustrated the difference between
2+
G-quadruplexes. With Ba picrate as template, there is efficient
Ba2 picrate and K picrate in promoting enantiomeric self-
+
+
stereocontrol within and between individual G-quartets, resulting
recognition of (D,L)-G 1 in CD
2
Cl
2
. First, we grew separate
2+
+
in a homochiral hexadecamer. Since Ba and K are similar in
size, the cation’s charge density is the major factor controlling
n+
n+
crystals of [(D)-G 1]16‚M picrate and [(L)-G 1]16‚M picrate
+
2+
for the K and Ba complexes. We then monitored the dynamic
17
enantiomeric self-association of (D,L)-G 1. By strengthening
1
equilibration of stereoisomers by H NMR spectroscopy.
cation-dipole interactions, G-quartet hydrogen bonds, and G-qua-
druplex-picrate interactions the divalent cation may provide the
enthalpic stabilization needed to overcome the unfavorable entropy
associated with enantiomeric self-recognition. In this system,
bridging picrate anions play a supporting role in the enantiomeric
self-association of G 1 by enhancing stereochemical communica-
+
The racemic mixture of [(D)-G 1]16‚4K picrate and [(L)-G 1]16
‚
+
4
2 2
K picrate slowly equilibrates in CD Cl (Figure 2-Panel 1) to
give a new set of NMR signals, distinct from those for the
enantiomeric G-quadruplexes. These new NMR signals indicate
formation of heterochiral diastereomers of lower symmetry. The
1
diasteromeric mixture was not statistical, as the simple H NMR
2+
18
8
tion between the two G -Ba octamers. Finally, since only (D)-
spectrum in Figure 2D indicates a bias toward a few of the many
nucleosides are found in DNA and RNA it is tempting to suggest
that enantiomeric self-association of nucleosides might be relevant
+
possible heterochiral diastereomers for a [(D,L)-G 1]16‚4K
hexadecamer. In these mixing experiments, we made sure that
the system reached equilibrium. Thus, the NMR spectrum 5 days
after enantiomer mixing (Figure 2D) was similar to that of a
6
to biomolecular homochirality. Certainly, we have shown that
homochiral self-association of nucleosides can occur under the
appropriate conditions.
control experiment (Figure 2E) obtained by using racemic (D,L)-G
+
Acknowledgment. We thank Mary Rosenberg for her help with the
synthesis of (L)-G 1. We thank the Department of Energy for financial
support. J.D. thanks the Dreyfus Foundation for a Teacher-Scholar Award.
1
to extract K picrate from water into CD
2
Cl
2
.
In contrast, significant enantiomeric recognition occurred when
2+
the templating cation was the divalent Ba (Figure 2-Panel 2).
The NMR spectrum in Figure 2E′ indicates that the homochiral
Supporting Information Available: Crystallographic tables, final
pair, [(D)-G 1]16‚2Ba2 and [(L)-G 1]16‚2Ba , account for at least
+
2+
coordinates and thermal parameters, selected bond lengths and angles,
1
and selected H NMR spectra (PDF). X-ray crystallographic files (CIF).
9
0% of the diastereomers observed at equilibrium. Furthermore,
CD spectra of mixtures of [(D)-G 1]16‚2Ba2 and [(L)-G 1]16
+
This material is available free of charge at http://pubs.acs.org.
‚
2+
JA004330V
2Ba in CH
2
Cl
2
showed a linear relationship between the chi-
roptical activity at 262 nm and the enantiomeric composition of
the solution, consistent with homochiral self-sorting (Supporting
(
17) The divalent cation is essential for homochiral G-quadruplexes. We
2+
observed similar enantiomeric self-association of G 1 with Sr picrate and
2
+
4a
Pb picrate.
Information, Figure 5). Most importantly, treatment of the
(
18) While the G-quadruplex is stabilized by picrate, relative to a less
+
2+
diasteromeric K G-quadruplexes with Ba illustrated the
reversible nature of these nucleoside assemblies. NMR data
coordinating anion like thiocyanate (ref 14), mixing experiments with [(D)-G
1)]16‚2Ba (SCN)
enantiomeric self-association of G 1.
(19) Sheldrick, G. M. Acta Crystallogr., Sect. A 1990, 46, 467-473.
(20) Sheldrick, G. M. Shelxl-93, Program for the Refinement of Crystal
Structures; University of G o¨ ttingen: Germany, 1993.
2
+
2+
4
4
and [(L)-G 1)]16‚2Ba (SCN) also showed significant
(
16) The solvated picrate anion was generated in CD
2
Cl
2
by encapsulating
2+
+
the Ba or K cations with [2.2.2]-cryptand: Lehn, J.-M., J. P. Sauvage, J.
P. J. Am. Chem. Soc. 1975, 97, 6700-6707.