Herein we describe a novel Ir system that is able to promote the reduction of pyrimidine bases from a distance without the presence of an external quencher. Instead, DNA-mediated ET is triggered by DNA-mediated HT. Thus, photoactivation of these Ir assemblies results in both a forward and a reverse pattern for charge migration, which we term ping-pong electron transfer through DNA (Scheme 1)

Augustyn

Bandyopadhyay

Boal

Boon

Carell

Chang

Clever

Conwell

Cook

Dohno

Drummond

Elias

Ghosh

Giese

Gorodetsky

Hall

Kawai

Kelley

Kitamura

Lewis

Manetto

Merino

Musa

Nakatani

Nunez

O'Neill

Ossipov

Porath

Seidel

Shao

Steenken

Stemp

Takada

Valis

Wang

Yang

PubMed

Crossref

Ping-Pong Electron Transfer through DNA

Elias, Benjamin

Genereux, Joseph C

Barton, Jacqueline K

DIAL UCLouvain

Ping-pong electron transfer through DNA.

Genereux, Joseph C.

Barton, Jacqueline K.

Caltech Authors - Main

Ping-Pong Electron Transfer through DNA**
Benjamin Elias [Prof.],
Chimie Organique et Médicinale, Université catholique de Louvain (Belgium)
Joseph C. Genereux, and
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
91125 (USA)
Jacqueline K. Barton*
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
91125 (USA)
DNA charge transport (CT) chemistry has been characterized in detail[1] owing to its utility
in the construction of DNA-based sensors and nanoscale devices.[2–4] Interestingly, recent
evidence also points to the application of this chemistry within the cell in the context of DNA
damage and repair.[5] Both DNA hole transport (HT) and electron transport (ET) have been
explored using spectroscopy,[6] biochemical assays,[7] and DNA electrochemistry.[8] In
reporting on DNA-mediated HT, N2-cyclopropylguanine and N6-cyclopropyladenine (CPA)
have been useful hole traps owing to their low oxidation potentials and their fast rates of ring
opening (10−11 s) upon one-electron oxidation (Scheme 1).[9] Similarly, owing to their redox
potentials,[10] the pyrimidines N4-cyclopropylcytosine (CPC)[11] and 5-bromouridine (BrU),
[12] have been sensitive probes for DNA-mediated ET.
Recently, direct comparisons of HT with ET were carried out using a charge injector strongly
coupled to the base stack and able to oxidize or reduce bases from a distance within the same
DNA assembly.[13,14] Taking advantage of the powerful photochemistry of IrIII
biscyclometalated complexes, we have shown that the [Ir(ppy)2(dppz′)]1+, functionalized
through a modified dipyrido[3,2-a:2′,3′-c]phenazine (dppz′; ppy=2-phenylpyridine; Scheme
1), can serve both as a photooxidant and reductant of distal DNA bases.[13,15] Strikingly, we
found that DNA HT and ET have similar characteristics; both show a remarkably shallow
distance dependence in their reactions as well as an equal sensitivity to perturbations in stacking
of the intervening DNA bridge.
Significantly, although the excited state of the IrIII complex is sufficiently potent to oxidize
guanine or adenine,[15] efficient electron injection into DNA required the use of the flash-
quench technique.[16] Indeed, the excited state of the IrIII complex is not sufficiently long-
lived (τ<10 ns) in water to photoreduce BrU from a distance in substantial yield.[13] When
sodium ascorbate is used as an external reducing agent, however, photolysis of the tethered
IrIII complex generates a long-lived ground-state reductant, which is in turn able to induce
significant BrU decomposition from a distance.
Herein we describe a novel Ir system that is able to promote the reduction of pyrimidine bases
from a distance without the presence of an external quencher. Instead, DNA-mediated ET is
triggered by DNA-mediated HT. Thus, photoactivation of these Ir assemblies results in both
**This work was supported by the NIH (GM49216).
© 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
*Fax: (+1)6265774976, E-mail: jkbarton@caltech.edu.
NIH Public Access
Author Manuscript
Angew Chem Int Ed Engl. Author manuscript; available in PMC 2009 September 22.
Published in final edited form as:
Angew Chem Int Ed Engl. 2008 ; 47(47): 9067–9070. doi:10.1002/anie.200803556.
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a forward and a reverse pattern for charge migration, which we term “ping-pong” electron
transfer through DNA (Scheme 1).
We have designed Ir–DNA conjugates containing two modified bases embedded in an AT
tract,[17] a CPA for hole injection, and either a BrU or a CPC as an electron trap (Scheme 2).
For synthetic reasons, we required three different strands, one short strand (5-mer) covalently
tethered to the IrIII complex, one strand (13-mer) containing a CPA-modified base, and one
complementary strand (18-mer) containing either a BrU or CPC. It should be noted that 1) the
presence of a nick in the phosphate backbone of the DNA helix does not affect the CT process,
[18] 2) the intercalative dppz′ unit stabilizes the short Ir strand in the duplex,[19] and 3) the
irreversible ring-opening of CPA precludes back ET.
Figure 1 shows the decomposition percentage of CPA and BrU obtained after 30 min irradiation
of the DNA assemblies at 365 nm as a function of the CPA position (see the Experimental
Section). Clearly, both modified bases undergo a decomposition reaction upon photolysis. No
decomposition of BrU is observed without both CPA and tethered IrIII complex in the assembly.
Moreover, the extent of BrU decomposition varies with the position of CPA. We therefore see
that the BrU decomposition is correlated with CPA ring-opening. We ascribe this correlation to
the ping-pong reaction, where the highly oxidizing IrIII excited state[13,15] is reductively
quenched in an intraduplex reaction by the distal CPA (migration of a “ping” electron); the
ground-state Ir reductant, formed by the intraduplex flash-quench scheme, is identical to the
one generated using an external quencher[13] and is capable of reducing BrU by ET through
the DNA stack (migration of a “pong” electron).
We have further tested the ping-pong reaction using CPC as a reductive probe, and here
substantial yields of decomposition of the modified base are observed.[11,15] While CPC can
be either photoreduced or photooxidized by the IrIII complex, it has been shown that this
modified base is reductively ring-opened by excited Ir when embedded in a thymine stack.
[15] Figure 2 shows the decomposition percentages of CPA and CPC as a function of CPA
position in Ir–DNA conjugates, which contain CPA within an A tract and CPC on the
complementary strand. Here, a higher relative yield is obtained for the decomposition of the
reductive probe compared to that of BrU. In fact, the CPC decomposition is stoichiometric
with CPA decomposition. Importantly, in the absence of CPA, little CPC decomposition is
obtained; the presence of CPA is required for significant CPC yields of decomposition. Also,
no decomposition is observed without the presence of tethered IrIII complex. Furthermore, no
change in CPC decomposition is found in assemblies where CPC is base-paired to an inosine
(Figure 2); if decomposition of CPC were to occur through photooxidation, an enhancement in
yield would be evident without the competitive oxidative guanine sink.[20] Thus CPC ring-
opening here results from reduction by DNA-mediated ET and not from a photooxidation
process. The ping-pong reaction is, then, highly efficient. Figure 2 shows also the
decomposition yields for CPC in the absence of CPA, both without (gray bars) and with (white
bars) an external reductive quencher (sodium ascorbate) known to reductively quench the
IrIII excited state.[13] The ground-state reduced metallic species, generated through CPA
oxidation, can effectively reduce the distal CPC, indeed comparably to an external reductive
quencher.
The sensitivity of DNA CT to DNA structure and dynamics is illustrated also for the ping-pong
reaction through variations in the DNA sequence. Despite equal overall energetics, the
decomposition efficiency in these assemblies is seen to depend upon the position of the redox
trap in the double helix. For instance, exchanging the CPA and CPC and the AT tract from one
strand to the other significantly affects the overall yield, especially for reduction (Figure 3).
This result is consistent with sequence variations seen earlier for DNA-mediated ET, and more
generally for CT in DNA with variations in the intervening base stack.[13,21]
Elias et al. Page 2
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Thus, for the first time, DNA-mediated HT and ET have been triggered consecutively within
the same DNA duplex by irradiation of a unique charge injector. The ping-pong reaction likely
involves hole migration primarily through the purine strand with electron migration facilitated
by stacked pyrimidines. Critically, the analogous parameters govern both HT and ET through
the DNA base-pair stack.
Experimental Section
All DNA oligonucleotides were synthesized using standard phosphoramidite chemistry.
Strands containing a CPA or CPC were synthesized by placing an O6-phenylinosine or 4-
thiouridine at the target CPA or CPC site, respectively. After 16 h incubation at 60°C in 6M
aqueous cyclopropylamine leading to simultaneous substitution reaction, cleavage from the
solid support, and deprotection, the strands were purified using reversed-phase HPLC and
characterized by MALDI mass spectrometry. [Ir(ppy)2(dppz)′]+ was synthesized and
covalently tethered to DNA oligonucleotides according to previously described methods.[13,
15] Ir–DNA conjugates were prepared by combining equimolar amounts (1:1:1) of the desired
DNA single strands. After annealing (solution was heated to 90°C for 5 min, then slowly cooled
down to 15°C over a period of 3 h), all of the resulting duplexes showed melting temperatures
above ambient temperature.
Aliquots (30 µL) of the Ir–DNA conjugates (10 µM in 50 mM TrisHCl, pH 7.0) were irradiated
for 30 min at 365 nm (Hg/Xe lamp, 1000W, with monochromator). Subsequent cleavage into
deoxynucleosides upon digestion with phosphodiesterase I and alkaline phosphatase was
carried out and the results analyzed by HPLC. The percentage of base decomposition, that is,
the amount of decomposed CPA, CPC, or BrU, was determined by subtracting the ratio of the
area under the peak of the undecomposed base in an irradiated sample over that in a non-
irradiated sample from unity, with adenine or inosine as an internal HPLC standard. Irradiation
experiments were repeated three times and the results averaged.
References
1. a) Carell T, Behrens C, Gierlich J. Org. Biomol. Chem 2003;1:2221. [PubMed: 12945689]O’Neill,
MA.; Barton, JK. Charge Transfer in DNA: From Mechanism to Application. Wagenknecht, HA.,
editor. New York: Wiley; 2005. p. 27 c) Conwell EM. Proc. Natl. Acad. Sci. USA 2005;102:8795.
[PubMed: 15956188] d) Giese B. Top. Curr. Chem 2004;236:27.
2. a) Bandyopadhyay A, Ray AK, Sharma AK, Khondaker SI. Nanotechnology 2006;17:227. b) Porath
D, Cuniberti G, Di Felice R. Top. Curr. Chem 2004;237:183. c) Clever GH, Kaul C, Carell T. Angew.
Chem 2007;119:6340.Angew. Chem. Int. Ed 2007;46:6226. d) Guo X, Gorodetsky AA, Hone J, Barton
JK, Nuckolls C. Nat. Nanotechnol 2008;3:163. [PubMed: 18654489]
3. a) Drummond TG, Hill MG, Barton JK. Nat. Biotechnol 2003;21:1192. [PubMed: 14520405] b) Yang
Y, Wang Z, Yang M, Li J, Zheng F, Shen G, Yu R. Anal. Chim. Acta 2007;584:268. [PubMed:
17386614] c) Wang X, Ozkan CS. Nano Lett 2008;8:308.
4. a) Boon EM, Ceres DM, Hill MG, Drummond TD, Barton JK. Nat. Biotechnol 2000;18:1096.
[PubMed: 11017050] b) Boon EM, Salas JW, Barton JK. Nat. Biotechnol 2002;20:282. [PubMed:
11875430] c) Boal AK, Barton JK. Bioconjugate Chem 2005;16:312.
5. Merino EJ, Boal AK, Barton JK. Curr. Opin. Chem. Biol 2008;12:229. [PubMed: 18314014]
6. a) Wan C, Fiebig T, Kelley SO, Treadway CR, Barton JK, Zewail AH. Proc. Natl. Acad. Sci. USA
1999;96:6014. [PubMed: 10339533] b) Takada T, Kawai K, Cai X, Sigimoto A, Fujitsuka M, Majima
T. J. Am. Chem. Soc 2004;126:1125. [PubMed: 14746481] c) Lewis FD, Zhu H, Daublain P, Cohen
B, Wasielewski MR. Angew. Chem 2006;118:8150.Angew. Chem. Int. Ed 2006;45:7982.
7. a) Hall DB, Holmlin RE, Barton JK. Nature 1996;382:731. [PubMed: 8751447] b) Ghosh A, Joy A,
Schuster GB, Douki T, Cadet J. Org. Biomol. Chem 2008;6:916. [PubMed: 18292885] c) Nakatani
K, Saito I. Top. Curr. Chem 2004;236:163. d) Nunez ME, Hall DB, Barton JK. Chem. Biol 1999;6:85.
[PubMed: 10021416]
Elias et al. Page 3
Angew Chem Int Ed Engl. Author manuscript; available in PMC 2009 September 22.
N
IH
-PA Author M
anuscript
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IH
-PA Author M
anuscript
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IH
-PA Author M
anuscript
8. a) Gorodetsky AA, Barton JK. Langmuir 2006;22:7917. [PubMed: 16922584] b) Kelley SO, Hill MG,
Barton JK. Angew. Chem 1999;111:991.Angew. Chem. Int. Ed 1999;38:941. c) Drummond TG, Hill
MG, Barton JK. J. Am. Chem. Soc 2004;126:15010. [PubMed: 15547981]
9. a) Nakatani K, Dohno C, Saito I. J. Am. Chem. Soc 2001;123:9681. [PubMed: 11572693] b) Musa
OM, Horner JH, Shahin H, Newcomb M. J. Am. Chem. Soc 1996;118:3862. c) O’Neill MA, Dohno
C, Barton JK. J. Am. Chem. Soc 2004;126:1316. [PubMed: 14759170] d) Dohno C, Ogawa A,
Nakatani K, Saito I. J. Am. Chem. Soc 2003;125:10154. [PubMed: 12926921]
10. a) Steenken S, Telo JP, Novais LP, Candeias LP. J. Am. Chem. Soc 1992;114:4701. b) Seidel CAM,
Schultz A, Sauer MHM. J. Phys. Chem 1996;100:5541.
11. a) Lu W, Vicic DA, Barton JK. Inorg. Chem 2005;44:7970. [PubMed: 16241147] b) Shao F, O’Neill
MA, Barton JK. Proc. Natl. Acad. Sci. USA 2004;101:17914. [PubMed: 15604138]
12. a) Manetto A, Breeger S, Chatgilialoglu C, Carell T. Angew. Chem 2006;118:325.Angew. Chem.
Int. Ed 2006;45:318. b) Cook GP, Greenberg MM. J. Am. Chem. Soc 1996;118:10025. c) Ito T,
Rokita SE. J. Am. Chem. Soc 2003;125:11480. [PubMed: 13129334]
13. Elias B, Shao F, Barton JK. J. Am. Chem. Soc 2008;130:1152. [PubMed: 18183988]
14. Valis L, Wang Q, Raytchev M, Buchvarov I, Wagenknecht HA, Fiebig T. Proc. Natl. Acad. Sci. USA
2006;103:10192. [PubMed: 16801552]
15. a) Shao F, Elias B, Lu W, Barton JK. Inorg. Chem 2007;46:10187. [PubMed: 17973372] b) Shao F,
Barton JK. J. Am. Chem. Soc 2007;129:14733. [PubMed: 17985895]
16. a) Chang IJ, Gray HB, Winkler JR. J. Am. Chem. Soc 1991;113:7056. b) Stemp EDA, Arkin MR,
Barton JK. J. Am. Chem. Soc 1997;119:2921.
17. The A tract was chosen because of its resistance to inherent charge trapping. See a)Kawai K, Osakada
Y, Fujitsuka M, Majima T. J. Phys. Chem. B 2007;111:2322. [PubMed: 17291027] b)Augustyn KE,
Genereux JC, Barton JK. Angew. Chem 2007;119:5833. Angew. Chem. Int. Ed 2007;46:5731.
18. Liu T, Barton JK. J. Am. Chem. Soc 2005;127:10160. [PubMed: 16028914]
19. Duplexes show higher melting temperature in the Ir band (365 nm) than in the DNA band (260 nm)
by 9–10°C. This indicates that the complex prevents the two end strands from separating. This
observation is characteristic of a DNA complex containing an intercalated planar ligand and has
already been observed in other systems. See a)Kitamura Y, Ihara T, Okada K, Tsujimura Y, Shirasaka
Y, Tazaki M, Jyo A. Chem. Commun 2005:4523. b)Ossipov D, Pradeepkumar PI, Holmer M,
Chattopadhyaya J. J. Am. Chem. Soc 2001;123:3551. [PubMed: 11472126]
20. Inosine is structurally similar to guanosine but has a higher oxidation potential. Therefore, if CPC is
oxidized, a higher extent of decomposition is expected when CPC is base-paired to inosine rather
than to guanosine, as less competition for hole formation is expected. No decomposition enhancement
with inosine versus guanine indicates that a different process other than hole formation must be
involved. See Refs. [11] and [13] for further discussion.
21. Shao F, Augustyn KE, Barton JK. J. Am. Chem. Soc 2005;127:17445. [PubMed: 16332096]
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Figure 1.
Decomposition percentage for CPA (red) in position 7, 9, 11, or 13 from Ir attachment
and BrU (blue) in position 5 from Ir after 30 min irradiation (365 nm).
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Figure 2.
Decomposition percentage for CPA (red) in position 9, 11, or 13 from Ir attachment and CPC
(blue) in position 7 from Ir after 30 min irradiation (365 nm). The CPC is base-paired either to
a guanine (left) or to an inosine (right). In both cases, the gray and white bars show the
decomposition percentage for CPC without the presence of CPA, with (white) or without (gray)
an external reductive quencher (sodium ascorbate, 200 mM).
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Figure 3.
Decomposition percentage for CPA (red) in position 9, 11, or 13 from Ir attachment and CPC
(blue) in position 7 from Ir after 30 min irradiation (365 nm). Both the AT tract and the CPA
and CPC have been flipped compared to sequences presented in Figure 2.
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Scheme 1.
Representation of the ping-pong reaction generated through photoactivation of an Ir–DNA
assembly along with modified base traps for hole (CPA) and electron (BrU and CPC) transport.
Upon excitation, the excited IrIII complex irreversibly oxidizes a CPA base from a distance.
The subsequent reduced metallic species is, in turn, able to reduce distal BrU or CPC bases.
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Scheme 2.
The assembly of three modified DNA single strands annealed to generate the Ir–DNA duplex
for the ping-pong reaction.
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English

Ping-Pong Electron Transfer through DNA

Abstract

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