Influence of a GC Base Pair on Excitation Energy Transfer in DNA-Assembled Phenanthrene π‑StacksFlorian Garo and Robert Haner*

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland

*S Supporting Information

ABSTRACT: The effect of a GC base pair on the excitationenergy transfer in a DNA-based, light harvesting assembly ofphenanthrene and pyrene chromophores is described. Afterabsorption of light at 320 nm by the stacked phenanthrenebuilding blocks, the excitation energy is transferred to thepyrene and leads to the formation of a phenanthrene-pyreneexciplex. The fluorescence intensity depends on the number oflight absorbing phenanthrenes, as well as on the type of DNAbase pair flanking the phenanthrene stack. In comparison to anAT base pair, a GC base pair located next to the stackedaromatic residues results in a reduction of fluorescence. Thedegree of quenching is dependent on the length of thephenanthrene stack that separates the GC base pair from the exciplex. Overall, a large number of stacked phenanthrenespositively affects exciplex fluorescence by increasing the quantity of absorbed light and, at the same time, reducing the effect ofquenching by GC base pairs.

■ INTRODUCTION

The use of sunlight as a source of energy is one of the topchallenges in today’s research.1−4 Photosynthetic organisms areusing sunlight in an impressively elegant way to satisfy theirenergy needs.5 In this process, sunlight is collected throughabsorption by chromophores arranged in an antenna complex,transferred to a reaction center and converted to chemicalenergy by charge separation across a bilayer membrane.6−8 Thefirst two steps of the photosynthetic cascade, light harvestingand energy transfer, are essential elements for the effectivenessof the whole process. In plants and purple bacteria, a proteinscaffold places and organizes the antenna chromophores in theproper distance and orientation to ensure efficient lightharvesting and fast energy transfer.9−13 In the chlorosome,the light harvesting antenna complex of green sulfur bacteria,thousands of chromophores are self-assembled, π-stacked andhighly organized without the aid of a protein scaffold.14−17 Thevast number of antenna chromophores and their packing withinthe arrays allows for energy production under very low lightintensities rendering chlorosomes probably the most efficientantenna complexes found in nature. Inspired by nature,scientists are aiming at the development of mimics of thelight harvesting complexes (LHCs). Over the last two decades,different approaches have been pursued in the design ofartificial photosynthetic systems.18−25 The preparation ofsynthetic light harvesting and energy transferring devices istherefore a topic of ongoing interest.26−32

DNA is increasingly used as a scaffold for the placement andassembly of functional components including proteins,chromophores, metal ligands, and nanoparticles.33−38 This

area of chemical research finds applications in the fields ofmolecular diagnostics, electronics, and material sciences.39−46

The DNA-guided assembly of chromophores for theconstruction of arrays with distinct properties, including energytransfer, has gained considerable attraction over the pastdecade.47−57 The use of DNA as a molecular scaffold allows forthe construction of stable and well-defined π-stacks.58−64 Inaddition, the arrangement of non-nucleosidic, polyaromaticchromophores leads to constructs with interesting proper-ties.65−75 We recently reported on the light harvestingproperties of DNA-organized, multichromophoric arrays.76 Inthese arrays, light is absorbed by multiple, π-stackedphenanthrenes (P) and efficiently transferred to an exciplex-forming pyrene (S) unit. The design of the assembly results inPS-exciplex fluorescence at one end of the arene π-stack. Theexcitation energy is transferred and concentrated to a specificlocation of the construct before it is reemitted. This type ofarray is reminiscent of the natural chlorosome and can beviewed as a mimic of one small segment. Thus, it serves as aprototype for the design of synthetic light harvesting systems.The DNA sequences used in the previous study76 excluded

the presence of guanine entirely to minimize fluorescencequenching by charge separation.77−79 In the course of exploringand investigating the light harvesting phenanthrene arrays inmore detail, the question about the effect of a GC base pair onthe energy transport within the π-stack arose. In the hitherto

Received: June 7, 2012Revised: September 18, 2012

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studied systems containing only AT base pairs, the PS-exciplexacted as the major “energy collecting center”. The presence of aGC base pair at the opposite end of the π-stack will quenchsome of the excitation energy. The degree of quenching can bedirectly measured by a reduction of the exciplex fluorescence.Here, we describe the effect of a GC base pair on the excitationenergy transfer in a DNA-based light harvesting antennacomposed of phenanthrene and pyrene chromophores.Sixteen different oligomers (1−16) were synthesized (Figure

1 and Table 1) and are grouped into four sets of hybrids for this

study. Phenanthrene (P, blue disks) and pyrene (S, green disk)units constitute the central segment (core) of the system, asillustrated in Figure 1. The core of each hybrid includesdifferent numbers of P units. An S unit, which is placedopposite an abasic site analogue (orange disk, φ) to eliminatethe possibility of positional isomers, was located at one end ofthe π-stack. The resulting hybrids contain, thus, one S unit andzero, two, four, or eight P units. The two outer segments (graycylinders) of the hybrids are exclusively composed of AT basepairs, except for one base pair next to the π-stack (red and gray

square plates, R and Y), which may also be a GC base pair.Guanine, which has the lowest oxidation potential of the fourcanonical DNA nucleobases,80−82 acts as a fluorescencequencher. In the four different sets, S and G are either indirect contact (control set) or separated by an intermediatephenanthrene stack (sets 1, 2, and 3).

■ EXPERIMENTAL PROCEDURES

Synthesis. Syntheses of the pyrene (S) and phenanthrene(P) phosphoramidite building blocks were carried out aspreviously described.83−85 The abasic site analogue (φ, GlenResearch) and the natural nucleoside phosphoramidite buildingblocks were purchased from SAFC Proligo. Oligonucleotides1−16 were synthesized on an Applied Biosystems 394-DNA/RNA synthesizer (“trityl-off” mode) using standard phosphor-amidite chemistry on a 1 μmol synthesis scale. The holdingtime in the coupling step was set at two minutes for the artificialbuilding blocks. The oligonucleotides were cleaved from thesolid support and deprotected by treatment with 30%ammonium hydroxide solution (55 °C, 2 h) and purified byreverse-phase HPLC (LiChrospher 100 RP-18 5 μm column;eluents: acetonitrile and 0.1 M triethylammonium acetate at pH7.0). The oligonucleotides were characterized on a ShimadzuLCMS-2010EV (Waters XTerra MS C-18 3.5 μm column;eluents: acetonitrile and 50 mM ammonium formate) andquantified by absorbance measurement at 260 nm (phenan-threne P: ε260 = 26 900 L mol−1 cm−1, pyrene S: ε260 = 8600 Lmol−1 cm−1).

Spectroscopy. All experiments were carried out at a 2 μMoligonucleotide concentration (each strand), 100 mM sodiumchloride, and 10 mM sodium phosphate buffer at pH 7.0.Absorbance and thermal denaturation experiments were carriedout on a Varian Cary-100 Bio-UV/vis spectrophotometer(optical path length 10 mm). Melting temperature (Tm) valueswere determined from the first derivative of the second coolingramp of a cooling−heating−cooling cycle in the temperaturerange 10−90 °C using a temperature gradient of 0.5 °C/min.Fluorescence data were collected on a Varian Cary Eclipsefluorescence spectrophotometer [2.5 nm ex./em. slit width;detector sensitivity: 750 V (fluorescence), 700 V (excitation);15 °C probe temperature]. DNA hybrids: a solution of a 1:1mixture of the two complementary oligomers was heated to 90°C and allowed to cool to room temperature. Fluorescencespectra were recorded after an equilibration time of 15 min.

Figure 1. Schematic representation of the DNA-assembled chromophoric systems studied in this paper. Phenanthrene units (P, blue discs) and onepyrene unit (S, green discs) built the core segment. The influence of the DNA base pair (Y and R, red and gray square plates) next to the coresegment was investigated. Gray cylinders on both sides of the core segment represent the DNA sequences composed entirely of AT base pairs. Theused artificial building blocks are displayed on the right side.

Table 1. Oligomers 1−16 and Melting Temperature (Tm)Values of the Hybrids

no. hybridTm

a

[°C]

controlset

1 5′-TAA TAA ATT S TTA AAT AAT 27.02 3′-ATT ATT TAA φ AAT TTA TTA3 5′-TAA TAA ATC S TTA AAT AAT 31.04 3′-ATT ATT TAG φ AAT TTA TTA

set 1 5 5′-TAA TAA ATT P S TTA AAT AAT 34.56 3′-ATT ATT TAA Pφ AAT TTA TTA7 5′-TAA TAA ATC P S TTA AAT AAT 40.08 3′-ATT ATT TAG Pφ AAT TTA TTA

set 2 9 5′-TAA TAA ATT P P S TTA AAT AAT 36.510 3′-ATT ATT TAA P Pφ AAT TTA TTA11 5′-TAA TAA ATC P P S TTA AAT AAT 41.512 3′-ATT ATT TAG P Pφ AAT TTA TTA

set 3 13 5′-TAA TAA ATT P P P P S TTA AAT AAT 37.014 3′-ATT ATT TAA P P P Pφ AAT TTA TTA15 5′-TAA TAA ATC P P P P S TTA AAT AAT 41.016 3′-ATT ATT TAG P P P Pφ AAT TTA TTA

aConditions: oligomer concentration 2 μM (each strand), 100 mMsodium chloride, and 10 mM sodium phosphate buffer at pH 7.0; Tmvalues ±1 °C.

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■ RESULTS

The melting temperature (Tm) values of the hybrids obtainedby thermal denaturation experiments varied between 27.0 and41.5 °C (Table 1 and SI). The relatively low Tm values in thecontrol set (1*2 and 3*4) are due to the high AT content aswell as to the abasic site analogue φ, which is only partlycompensated by the presence of the intercalating Sresidue.85−87 A growing number of interstrand stacking residuesin sets 1, 2, and 3 lead to an increase in hybrid stability. In allfour sets, the presence of a GC base pair next to the coresegment had a stabilizing effect. To ensure duplex stability forall hybrids, all UV/vis and fluorescence experiments wereperformed at 15 °C.Figure 2 shows the UV/vis absorption profiles of selected

single strands and all hybrids. The spectra can be divided intotwo regions: below 300 nm, where the DNA nucleobasesabsorb and above 300 nm, where only P and S absorb. The longwavelength absorbance bands of P (λmax ∼320 nm) and S (λmax∼360 nm) are well separated to allow selective excitation ofeither type of building block (P: λex = 320 nm; S: λex = 365nm).The oligomers of the control set were next investigated by

fluorescence spectroscopy. The emission spectra of singlestrands 1 and 3, possessing one S but no P units, are given inFigure 3. The fluorescence intensities of single strand 1 with a5′-T next to S (Figure 3a, black line) and of single strand 3 witha C in this position (Figure 3b, black line) were compared. Thecurves of 1 and 3 with maximum intensity around 400 nm(pyrene monomer emission) show no significant differences inshape and intensity after excitation of S at 355 nm. Thus, thetwo different nucleobases, T or C, do not lead to significantchanges in the emission behavior of S. The fluorescenceemission spectrum of hybrid 1*2 showed an emission spectrum(Figure 3a, red line) that was nearly identical in emissionintensity and curve shape as that of single strand 1 alone. Incontrast, the intensity changed significantly upon hybridformation between 3 and 4 (Figure 3b, red line). Thefluorescence at 400 nm of 3*4 was strongly quenchedcompared to 3 alone. No pyrene-guanine exciplex emissionwas detected.88,89

Oligomers of sets 1, 2, or 3 that contain both types ofchromophores (P and S) can be excited separately at either ofthese units (see above, Figure 2). Excitation of P at 320 nm insingle strands having one S and one, two, or four P units in thesame sequence results in a broad emission with a maximum ataround 450 nm (strands 5, 7, 9, 11, 13, and 15, Figure 4a andb, black lines). This band has been previously assigned tophenanthrene/pyrene-exciplex fluorescence.90,91 As in thecontrol set, no significant differences in the emission behaviorwas observed if a C or T pyrimidine nucleobase was adjacent tothe phenanthrenes. Intensities and shapes of the emissioncurves of all mentioned single strands were essentially identical.Excitation of single strands containing only P units (strands 6,8, 10, 12, 14, and 16, Figure 4a,b, blue lines) at 320 nm showedrelatively weak fluorescence with maximum intensities between380 and 410 nm depending on the number of P units. Thepresence of G in the 3′-position of P (Figure 4b, strands 8, 12,

Figure 2. UV/vis absorption profiles of (a) selected single strands (5 black, 6 gray, 9 blue, 10 light blue, 13 red, 14 orange) and (b) hybrids (1*2black, 3*4 gray, 5*6 light blue, 7*8 blue, 9*10 red, 11*12 orange, 13*14 green, and 15*16 light green).

Figure 3. Fluorescence emission spectra of single strands and hybridsfrom the control set after excitation at 355 nm (black lines = singlestrands, red lines = hybrids) with (a) an AT base pair next to the coresegment (1*2) and (b) a GC base pair in the same position (3*4).

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and 16) resulted in significant fluorescence quenchingcompared to adenine (A) in the same position (Figure 4a,strands 6, 10, and 14).Hybrid 5*6 showed a higher exciplex emission intensity at

450 nm than the single strand 5 alone (Figure 4a, n = 1, red lineversus black line). Hybrid 7*8, on the other hand, had a lessintense emission curve than single strand 7 alone (Figure 4b, n= 1, green line versus black line). This is in agreement with thecontrol set where addition of a G in the hybrid next to thechromophore resulted in strong quenching of the S monomerfluorescence. The presence of G also resulted in the quenchingof exciplex fluorescence in hybrid 7*8 compared to hybrid 5*6.The hybrids in set 2 behaved in analogy to those in set 1.

Hybrid 9*10 with an AT base pair next to the core segmentshowed stronger fluorescence at 450 nm compared to hybrid11*12 with a GC base pair at this site. As expected, excitationof hybrid 13*14 at 320 nm in set 3 resulted in the highestexciplex fluorescence emission intensity at 450 nm. This hybridcontains the largest number of P residues and no GC base pairnext to the chromophore segment. Again, in the GC-containinghybrid 15*16, the emission was quenched in comparison to13*14. In contrast to the observations made with sets 1 and 2,however, the emission intensity of 15*16 was higher than thatof single strand 15.As mentioned above, selective excitation of S at 365 nm is

possible in all hybrids. In this case, the resulting emission curvesof hybrids 5*6, 9*10, and 13*14 showed equal exciplexfluorescence intensities at 450 nm (Figure 4c, red lines). One Sunit is present in all these hybrids, and the varying number of Punits has no influence on the PS-exciplex emission intensities.Furthermore, no significant variation in the maximum emissionwavelength was observed compared to excitation at 320 nm.On the other hand, emission intensities of hybrids 7*8, 11*12,

and 15*16, which have the GC base pair next to thechromophore stack, were different (Figure 4c, green lines)from those of hybrids with an AT base pair in this position.Hybrid 7*8 had the least intense exciplex emission and wasconsiderably quenched compared to 5*6. This quenching effectby GC was less pronounced in set 2; in set 3, hybrid 15*16showed almost the same emission intensity as hybrid 13*14.Thus, the quenching effect was gradually reduced with anincreasing number of P units located in the stack between thesite of excitation (pyrene, S) and the GC base pair.An overview on the emission intensities of the various

hybrids is given in Table 2 and the values are displayed

graphically in Figure 5. The chart is grouped into emissionintensities observed after excitation at 320 nm (excitation of P,blue and black bars) or 365 nm (excitation of S, red and greenbars). Black and green bars represent hybrids with an AT basepair next to the core segment (5*6, 9*10, and 13*14; n = 1, 2,and 4), whereas red and blue bars stand for hybrids with GC

Figure 4. Fluorescence spectra of single strands and hybrids containing a variable number (2n) of phenanthrenes in each strand. (a) Excitation at320 nm of hybrids 5*6 (n = 1), 9*10 (n = 2), and 13*14 (n = 4). Single strands with only P units (6, 10, 14) are shown in blue, single strands withP and S units (5, 9, 13) in black and DNA hybrids in red. (b) Excitation at 320 nm of hybrid 7*8 (n = 1), 11*12 (n = 2), and 15*16 (n = 4). Singlestrands with only P units (8, 12, 16) are shown in blue, single strands with P and S units (7, 11, 15) in black, and DNA hybrids in green. (c)Excitation of all hybrids at 365 nm. Hybrids with AT next to the core segment (5*6, 9*10, and 13*14) are shown in red, hybrids with GC next tothe core (7*8, 11*12, and 15*16) are shown in green.

Table 2. Fluorescence Intensities (Ifl, auca) of

Phenanthrene/Pyrene-Containing Hybrids

λex = 320 nm λex = 365 nm

hybridIfl

[auc]ΔIfl[auc]

relative[%] Ifl [auc]

ΔIfl[auc]

relative[%]

5*6 20 877 8371 100 13 504 4276 1007*8 12 506 60 9228 689*10 30 612 8350 100 13 375 2024 10011*12 22 262 73 11 351 8513*14 49 038 9614 100 13 699 889 10015*16 39 424 80 12 810 94

aArea under the emission curve.

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next to the core segment (7*8, 11*12, and 15*16).Fluorescence intensities [Ifl, given as area under the curve(auc) values] after excitation at 320 nm were reduced by thepresence of a GC base pair in each set by approximately thesame fraction compared to the corresponding hybrids with anAT base pair (black vs blue bars, see also SI). The differences inintensity (ΔIfl values) were relatively constant, i.e., to a largepart independent of the number of P units present in thechromophore stack. A look at the relative intensities, however,reveals that the quenching effect of the GC base pair afterexcitation at 320 nm becomes less important when the numberof P units increases. Hybrid 7*8 shows an exciplex fluorescencewhich is quenched by 40% compared to hybrid 5*6, whileemission of hybrid 15*16 is only quenched by 20% comparedto 13*14. Fluorescence intensities after excitation at 365 nm (Sunit) reveal a clear length dependence (green bars versus redbars): the more P residues present, the less important thequenching effect of the GC base pair on the PS-exciplexfluorescence becomes. A doubling of the number of P unitsbetween each set results in a reduction of the quenching effect

(ΔIfl) by approximately a factor of 2. In all hybrids that arelacking the GC base pair, the fluorescence intensity is equalafter excitation at 365 nm (green bars). Thus, it can beconcluded that a GC base pair reduces exciplex fluorescence byconstant (absolute) value if excitation occurs at 320 nm(phenanthrenes), but after excitation at 365 nm (pyrene), thequenching effect is gradually diminished by increasing numbersof phenanthrenes.Excitation spectra between 230 and 420 nm of all hybrids are

shown in Figure 6a (λem = 450 nm, maximum intensity of thePS-exciplex). To better visualize the quenching effect of the GCbase pair, the spectra are normalized at 365 nm, the maximumof pyrene excitation (Figure 6b). The obtained values are alsosummarized in Table 3. The intensity at 320 nm (phenan-threne) increases steadily with increasing number of P units,whereas the values at 365 nm are relatively constant. Withineach set, the hybrid containing the GC base pair shows a lessintense excitation band at 320 nm compared to the hybrid withthe AT base in this position. The difference between the values(ΔIF) within one set is almost constant at 320 nm (Table 3)

Figure 5. Dependence of the fluorescence intensity (area under curve, auc) of different hybrids on the number of P units, the DNA sequence, andthe excitation wavelength. Excitation (λex): 320 nm (blue and black bars) or 365 nm (red and green bars). Black and green bars: hybrids with an ATbase pair adjacent to the arene segment. Blue and red bars: hybrids with a GC base pair adjacent to arene segment.

Figure 6. Excitation spectra of different hybrids observed at 450 nm: (a) uncorrected and (b) normalized at 365 nm (5*6 black, 7*8 gray, 9*10 blue,11*12 light blue, 13*14 red, and 15*16 orange).

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but decreases at 365 nm when the length of the phenanthrenestack is extended. Normalization to the 365 nm band revealsthat the 320 nm band is reduced by a relatively constantfraction (∼12−14%).

■ DISCUSSIONThe present system constitutes a light harvesting assembly ofphenanthrene (P) and pyrene (S) chromophores. The arenesare arranged in a π-stacked assembly within a double-strandedDNA framework. The P building blocks absorb light at 320 nm.On excitation, a PS-exciplex is formed which results in intensiveexciplex fluorescence around 450 nm. A linear increase ofexciplex fluorescence after excitation at 320 nm of hybrids 5*6,9*10, and 13*14 with an AT base pair next to the arenesegment (Figure 5, black bars) is attributed to efficientexcitation energy transfer from P-units to the PS-exciplex.This energy transfer becomes also apparent when thefluorescence emission curves of hybrid 5*6, 9*10, and 13*14are compared to the emission curves of the single strands alone.The fluorescence curve resulting from a hybrid is notcorresponding to the sum of the two spectra of the singlestrands (see also SI, Figures S14−S16). The hybrid exhibitsincreased fluorescence intensity and a more pronounced signal(Figure 4a, red versus black and blue lines) than the singlestrands. No significant S or P monomer emission was detectedin the emission spectra of hybrids containing phenanthrenesindicating that loss of excitation energy due to inefficienttransfer to the exciplex is minimal. Formation of P excimers to aminor degree cannot be completely ruled out based on theemission spectra of single strands 10, 12, 14, and 16.92−95 Evenif these kinds of excimers were formed after excitation, they are,obviously, not affecting the overall efficiency of the excitationenergy transfer process, which is best illustrated by a linear

increase of exciplex emission upon increasing the number of Punits (see also SI, Figure S17).The picture changes when a GC base pair is introduced into

the DNA-part, directly adjacent to the chromophore stack(hybrids 7*8, 11*12, and 15*16). The introduction of this GCbase pair results in the presence of a second “trap” for theexcitation energy. Fluorescence quenching by the formation ofcharge-separated states between excited chromophores andguanine is a well-known and extensively studied mecha-nism.81,96,97 This effect is clearly present, as shown, e.g., bythe control set (1*2 and 3*4) exhibiting a strong reduction of Sfluorescence by the GC base pair (Figure 3). This quenchingeffect is also present, albeit to a lesser extent, when bothchromophores, S and P, are present in the hybrid. Thus, hybrid7*8 shows reduced exciplex fluorescence compared to 5*6(Figure 4b, green lines). The emission spectrum of hybrid 7*8is not superimposable with the sum of the spectra reported forsingle strands 7 and 8 alone (see SI, Figure S14). Despite thisquenching effect, also GC-containing hybrids (7*8, 11*12, and15*16) reveal an increase of the exciplex emission intensitywith a growing number of P units. After irradiation at 320 nm,the absolute amount of fluorescence quenching compared tohybrids lacking the GC base pair is rather constant, irrespectiveof the number of involved P units (see also Figure 5, black barsversus blue bars). This is best illustrated by a fairly constantΔIfl-value over the three sets after excitation at 320 nm (seeTable 2). Analysis of the excitation spectra recorded at themaximum emission wavelength of the exciplex (λem = 450 nm)confirms this observation. Hybrids containing a GC base pairshowed a signal of lower intensity at 320 nm compared tohybrids lacking the GC base pair. The P-excitation band wasreduced by a rather constant amount. Thus, less excitationenergy from the P-units leads to exciplex emission in thepresence of a GC base pair, and a relatively constant (absolute)fraction of excitation energy is absorbed by guanine from the P-stack irrespective of the number of P units. Consequently, lessexcitation energy is transferred to the S unit resulting in areduction of exciplex fluorescence. It can be concluded thatlonger P-arrays partly “compensate” the energy trapping effectof the GC base pair. The relative quenching effect is gettingsmaller as the length of the P-stack increases (Table 2). Evenwhen quenching by a GC base pair was observed, it isimportant to note that in all cases studied the main direction ofenergy transfer in the P-stack remained toward the PS-exciplex,i.e., the quenching effect never exceeded 40%.

Table 3. Intensities (IF) in Excitation Spectra of theDifferent Hybrids (λem = 450 nm; see Figure 6)

excitation spectra ratio

hybrid# of Punits

IF(320 nm) ΔIF

IF(365 nm) ΔIF (320/365) [%]

5*6 2 138 54 90 28 1.51 1007*8 2 84 62 1.36 88.59*10 4 196 45 87 11 2.25 10011*12 4 151 76 1.95 87.013*14 8 324 60 90 6 3.61 10015*16 8 264 84 3.16 86.3

Figure 7. Amber-minimized model100 of hybrid 15*16. The pyrene unit (S) is shown in green, phenanthrene units (P) in blue, and guanine (G) inbrown. Excitation at 320 nm (step 1) is followed by excitation energy transfer (step 2) from P units to the PS-exciplex, which results in fluorescenceat 450 nm (step 3). The presence of a GC base pair next to the core segment leads to a partial quenching of the excitation energy. The degree ofquenching depends inversely on the number of phenanthrenes in the stack.

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After selective excitation of the S unit at 365 nm, exciplexfluorescence is constant and not dependent on the number of Presidues (Figure 5, green bars), as long as a GC base pair nextto the arene core segment is avoided. Introduction of a GCbase pair, however, again reduces exciplex fluorescence intensityalso after S excitation. The effect correlates again inversely withthe number of intervening P units (Figure 5, red bars). Whereasthe quenching effect was significant (∼32%, Table 2) in set 1(only two P units), only a marginal reduction (∼6%) wasobserved in set 3 (eight P units). Thus, exciplex fluorescencequenching by guanine after excitation of the S unit is significantwith two and four intervening P units but becomes negligible ifeight P units are present in the stack. The findings aresummarized and illustrated in Figure 7. A stack of up to eight Punits acts as light absorbing unit. Excitation leads to formationof a PS-exciplex with an emission maximum at 450 nm.Fluorescence intensity increases with the number of phenan-threnes. A guanine located at the end of the P-stack leads to apartial quenching of exciplex fluorescence. The degree ofquenching is dependent on the length of the phenanthrenestack that separates the GC base pair from the exciplex. Overall,a large number of stacked phenanthrenes positively affectsexciplex fluorescence by increasing the quantity of absorbedlight and, at the same time, reducing the effect of quenching byGC base pairs.

■ CONCLUSIONS

The effect of a GC base pair on the excitation energy transfer ina DNA-embedded, light harvesting assembly of phenanthrene(P) and pyrene (S) chromophores is described. Afterabsorption of light at 320 nm by the stacked P building blocks,the excitation energy is transferred to S and results in theformation of a fluorescent PS-exciplex (Figure 7). Thefluorescence intensity is dependent on the number of lightabsorbing P units, as well as on the nature of the DNA base pairnext to the P-stack. Several double-stranded hybrids werestudied that contained P-stacks of zero, two, four, and eightunits. Excitation of the hybrids at 320 nm (excitation of Punits) results in a steady increase of exciplex fluorescence withincreasing length of the P-stack. On the other hand, it wasfound that a GC base pair adjacent to the P-stack results insignificant fluorescence quenching in comparison to an AT basepair at this location. The reduction of fluorescence intensity(ΔIfl) was rather constant in all sets of hybrids. In relativeterms, however, the quenching effect by this GC base correlatesinversely with the number of P units separating it from theexciplex. The stacked P units have, thus, a length-dependent,insulating effect98,99 that prevents quenching of the exciplex bythe GC base pair. The PS-exciplex can also be generated byexcitation of the S unit. As expected, the degree of exciplexfluorescence is not influenced by the number of P units in thehybrids composed of AT base pairs only. If, however, a GCbase pair is present, exciplex fluorescence is quenched also inthis case. Again, a longer P-stack counteracts the quenchingeffect and becomes negligible in the hybrid containing a total ofeight P units. The π-stacked arrays of aromatic hydrocarbonsdescribed here represent a valuable model system to practicallyand theoretically study light harvesting and energy transfereffects and may find relevance in the design and construction ofrelated systems with other kinds of chromophores.

■ ASSOCIATED CONTENT*S Supporting InformationAnalytical data for modified oligomers, Tm value curves, UV/visand fluorescence spectra. This material is available free ofcharge via the Internet at http://pubs.acs.org.

■ AUTHOR INFORMATIONCorresponding Author*E-mail: robert.haener@ioc.unibe.ch.NotesThe authors declare no competing financial interest.

■ ACKNOWLEDGMENTSFinancial support by the Swiss National Science Foundation(grant 200020-132581) is gratefully acknowledged.

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