Covalent hemin-DNA adducts for generating a novel class of artificial heme enzymes

Article abstract of DOI:10.1002/anie.200462567

(Chemical Equation Presented) Well-defined conjugates between DNA and heme enzymes are accessible by the reconstitution of apo-enzymes with covalent hemin-DNA adducts (see picture). This concept allows access to novel redox catalysts with programmable binding properties that may be applied as biocatalysts, sensors, and biomaterials.

Full text of DOI:10.1002/anie.200462567

Angewandte
Chemie
advantage of the distinct functionalities of DNA–protein
conjugates, one must face the challenge of developing
synthetic strategies that permit control over both the stoi-
chiometry and regioselectivity of DNA–protein coupling
reactions.
Herein we report a novel approach toward well-defined
and highly functional conjugates between DNA oligomers
and enzymes that contain the hemin (iron protoporphyrin IX
complex) prosthetic group. In the first step, covalent DNA–
hemin adducts (hemD1 and hemD2; Scheme 1a) were syn-
thesized on solid phase. After cleavage from the solid phase
and purification, the hemD adducts were used to reconstitute
apo-myoglobin (apo-Mb: myoglobin without its hemin pros-
thetic group).[3] Reconstitution of apo-Mb with hemD1 and
hemD2 produced enzymatically active myoglobin that con-
tained one or two DNA oligomers (MbD1 and MbD2,
respectively; Scheme 1b) coupled to the enzyme in close
proximity to the active site. To show that the DNA oligomers
can be used as molecular handles for selective DNA-directed
assembly, the MbD conjugates were hybridized to comple-
mentary capture oligomers immobilized on a solid support
(Scheme 1c). Subsequent analysis of the enzymatic peroxi-
dase activity revealed that the MbD conjugates are far more
active than native myoglobin (Mb).
The oxygen storage protein Mb, which contains a non-
covalently bound heme moiety, has been studied intensively
over the past 30 years as a model system to investigate the
functional role of the heme iron center,[4,5] long-range
electron-transfer processes,[6] and the effects of metal
exchanges or modifications of the heme side chains on the
properties of the protein.[7,8] Although artificial Mbs have
been prepared by site-directed mutagenesis,[9] the relative
ease of heme removal and subsequent reconstitution of apo-
Mb with functional porphyrin derivatives makes this system
convenient for the design and study of artificial heme
enzymes.[6] As an example, Hayashi and co-workers have
shown that heme chemically modified with anionic groups at
its propionate chains imparts Mb with enhanced peroxidase
activity toward cationic substrates.[10]
Artificial Mb was chosen as an initial model system to
investigate our concept of DNA conjugation (summarized in
Scheme 1), as there is already a large body of knowledge
about this protein. To this end, a 5’-alkylamino-modified 12-
mer oligonucleotide (5’-amino-TCTCAACTCGTA) was syn-
thesized with conventional phosphoramidite chemistry.
Hemin was activated with O-(benzotriazol-1-yl)-N,N,N’,N’-
tetramethyluronium hexafluorophosphate (HBTU) and N,N-
diisopropylethylamine (DiPEA) in DMF/CH3CN, and the
resulting solution was injected into a DNA synthesizer to
carry out the coupling reaction with the 5’-amino group of the
oligomer. Following incubation for 30 min and deprotection
under mild conditions (tert-butylamine, MeOH, H2O), the
oligonucleotide was purified with reversed-phase HPLC.[11]
The two major products formed were identified by
MALDI MS as hemin coupled with either one or two DNA
oligomers (hemD1 and hemD2, respectively; Scheme 1a).
Both hemD1 and hemD2 were used in the reconstitution of
apo-Mb to yield the conjugates MbD1 and MbD2, respectively
(Scheme 1b). Chromatographic analysis of the reconstitution
DNA–Enzyme Conjugates
Covalent Hemin–DNA Adducts for Generating a
Novel Class of Artificial Heme Enzymes**
Ljiljana Fruk and Christof M. Niemeyer*
An important goal of nanobiotechnology is the generation of
novel biomaterials with precise control at the nanometer
scale.[1] DNA oligomers play an important role as structure-
directing agents in the bottom-up fabrication of nanostruc-
tured functional devices, owing to their tremendous molec-
ular recognition capabilities. The generation of semisynthetic
DNA–protein conjugates makes it possible to combine the
unique properties of DNA with the almost unlimited variety
of functional components of proteins, which have evolved
naturally to perform highly specific catalytic turnovers,
energy conversions, or translocations.[2] However, to take
[*] Dr. L. Fruk, Prof. Dr. C. M. Niemeyer
Fachbereich Chemie
Biologisch-Chemische Mikrostrukturtechnik
Universitꢀt Dortmund
Otto-Hahn Strasse 6, 44227 Dortmund (Germany)
Fax: (+49)231-755-7082
E-mail: christof.niemeyer@uni-dortmund.de
[**] This work was supported by the Deutsche Forschungsgemeinschaft,
the Alexander von Humboldt Foundation (research fellowship for
L.F.), and the Fonds der Chemischen Industrie. We thank Joachim
Mꢁller for experimental assistance with peroxidase enzyme assays
and Dr. Jens Mꢁller for the provision of the DNA synthesizer.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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DOI: 10.1002/anie.200462567
ꢀ 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
2603

Communications
compared with that of native Mb.[12] To attain
maximal assay sensitivity, Amplex UltraRed
(Molecular Probes) was chosen as substrate,
which, in the presence of H2O2, is converted
into a fluorescent dye by peroxidase activ-
ity.[13] Figure 2a shows the increase in fluo-
rescence from the enzymatic transformation
of Amplex UltraRed by either native Mb,
MbD1, or MbD2 (5 pmol in each case). It is
evident that the activities of MbD1 and
MbD2 are significantly higher than that of
native Mb. Interestingly, MbD2 shows an
even higher activity than MbD1 despite the
greater potential for steric hindrance of the
MbD2 active site by the two bulky DNA
moieties nearby. Although the reasons
behind its enhanced activity remain unclear,
MbD2 was detectable in quantities as small
as 0.1 pmol, whereas detection of native Mb
reached a limit at 2 pmol. Further studies of
the peroxidase activity, including investiga-
tions of other substrates, are currently under-
way.
To demonstrate that the DNA oligomers
can indeed be used as recognition sites for
selective binding to complementary oligonu-
cleotides, we performed DNA-directed im-
mobilization assays of MbD1 and MbD2 on
solid phase (Scheme 1c). We have previously
demonstrated that the DNA-directed immo-
bilization of proteins proceeds with high
efficiency and allows reversible, site-selec-
tive functionalization of solid substrates with
proteins or other chemical functionalities.[14]
Peroxidase activity was measured after
MbD1 and MbD2 were immobilized to strep-
tavidin-coated microplate wells functional-
ized with complementary biotinylated cap-
Scheme 1. Schematic representation of the synthesis and assembly of DNA–heme-enzyme conju-
gates; a) solid-phase synthesis of covalent DNA–hemin adducts hemD1 and hemD2, which contain
one or two DNA oligomers, respectively; b) reconstitution of apo-Mb with hemin–DNA adducts
leads to the formation of DNA–Mb conjugates MbD1 and MbD2; c) DNA-directed immobilization of
the DNA–Mb conjugates. CPG=controlled pore glass; HOBt=1-hydroxybenzotriazole.
ture
oligomers
(5’biotin-TACGAGTT-
GAGA; Figure 2b). Again, the MbD2 con-
jugates showed a significantly higher activity
than MbD1. Moreover, in control assays
carried out in plate wells containing non-
by anion-exchange FPLC revealed that the uptake of hemD2
was significantly slower than that of hemD1 (36 and 24 h,
respectively), which may be attributed to the greater steric
bulk of hemD2 which limits its diffusion into the heme-
binding pocket of apo-Mb. Representative chromatograms of
hemD purification (Figure 1) demonstrate the significant
difference between the retention times of apo-Mb and the
respective hemD and MbD conjugates, which enables fast and
efficient purification. UV/Vis spectra of both MbD1 and
MbD2 show an absorption maximum at 408 nm (sharp Soret
band) and weak bands at 502, 543, and 632 nm (Q bands),
which are in agreement with literature values for native Mb,
as well as a broadened peak at 276 nm that arises from
absorbance by proteins and DNA.[11]
complementary capture oligomers, no enzymatic activity was
detected. This indicates that the immobilization occurs
exclusively by specific Watson–Crick base pairs formed
between the Mb-bound DNA moieties and the capture
sequences.
We have shown that novel artificial myoglobin proteins
can be generated by reconstitution of apo-Mb with covalent
DNA–hemin conjugates. Although we could clearly analyze
the composition and chromatographic properties of these
novel DNA–Mb conjugates, the elucidation of their particular
catalytic properties reported herein has only just begun. Our
future work will therefore focus not only on the peroxidase
activity, but on characterizing the redox and electron-transfer
properties of these conjugates as well.[17] Moreover, the highly
specific binding properties of the DNA moiety will be studied
in more detail by assembly of the DNA–Mb conjugates both
To further characterize the semisynthetic MbD conju-
gates, the peroxidase activities of MbD1 and MbD2 were
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Chemie
Figure 2. a) Peroxidase activity of 5 pmol native Mb (a), MbD1
Figure 1. FPLC chromatograms of the reconstitution of apo-Mb with
a) hemD1 and with b) hemD2; the dotted and solid lines indicate the
absorbance measured at 280 and 405 nm, respectively.
(g), and MbD2 (c) measured in solution with Amplex UltraRed
as the substrate. A control reaction (d) was carried out in the
absence of peroxidase. b) Peroxidase activity of MbD1 (a) and
MbD2 (c) bound to microplate surfaces through DNA-directed
immobilization. Control reactions with noncomplementary capture
oligomers (g and d) indicate the specificity of surface-capture
events.
at the micrometer and nanometer length scales. Whereas the
arrangements in the micrometer range should be useful for
the generation of enzyme microarrays, the nanoscale assem-
bly holds great potential for the fabrication of multifunctional
protein constructs for applications in materials research[15]
and life sciences.[2,16]
Notably, Mb served as a representative model system in
this study for the seminal demonstration of our concept of
generating well-defined DNA–heme-enzyme conjugates
through the reconstitution of apo-enzymes with covalent
hemin–DNA adducts. This method should transfer well to
other heme enzymes, and we therefore anticipate that this
approach will open the door to a large variety of novel redox
catalysts. Through the programmable binding properties
made possible by the specificity of DNA hybridization, such
semisynthetic DNA–protein conjugates may be useful in a
broad range of applications, from biocatalysts, sensors and
transducer elements, to building blocks for micro- and
nanostructured devices.
Keywords: DNA · enzymes · heme proteins · immobilization ·
.
self-assembly
[1] C. M. Niemeyer, C. A. Mirkin, Nanobiotechnology: Concepts,
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[2] C. M. Niemeyer, Trends Biotechnol. 2002, 20, 395 – 401.
[3] The reconstitution of apo-enzymes, in particular glucose oxidase
with chemically modified flavin adenine dinucleotide (FAD)
cofactors, has been used to generate artificial enzyme conjugates
and to immobilize such enzymes to electrode surfaces. For
examples, see: a) A. Riklin, E. Katz, I. Willner, A. Stocker, A. F.
Buckmann, Nature 1995, 376, 672 – 675; b) M. Zayats, E. Katz, I.
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Received: November 10, 2004
Published online: March 18, 2005
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Please note: Minor changes have been made to this manuscript since
its publication in Angewandte Chemie Early View. The Editor.
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Communications
[6] a) T. Hayashi, Y. Hisaeda, Acc. Chem. Res. 2002, 35, 35 – 43; b) T.
3,7-dihydroxyphenoxazine; Molecular Probes) in the presence
of H2O2 at a stoichiometric ratio of 1:1 to produce a brightly
fluorescent and strongly absorbing reaction product. The
chemical structure and reaction path of Amplex Red are
shown in the Supporting Information (Figure S4).
Hayashi, H. Dejima, T. Matsuo, H. Sato, D. Murata, Y. Hisaeda,
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[11] UV/Vis data for hemD1, hemD2, MbD1, and MbD2 as well as
MALDI MS spectra and details on the solid-phase coupling of
DNA with hemin, the reconstitution of apo-Mb, and the enzyme
activity assays are available in the Supporting Information.
[12] It is known that Mb reacts with H2O2 to form ferryl species that
correspond to compound II of usual peroxidases.[10] Therefore,
Mb has the potential to catalyze the oxidation of various
substrates in the presence of H2O2. Notably, the peroxidase
activity of Mb is much lower than that of other peroxidases such
as horseradish peroxidase.
[14] a) C. M. Niemeyer, T. Sano, C. L. Smith, C. R. Cantor, Nucleic
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R. Seidel, R. Wacker, H. Schroeder, O. Seitz, M. Engelhard, R.
Goody, C. M. Niemeyer, Chem. Commun. 2003, 822 – 823; e) U.
Feldkamp, R. Wacker, W. Banzhaf, C. M. Niemeyer, ChemPhys-
Chem 2004, 5, 367 – 372; f) R. Wacker, C. M. Niemeyer, Chem-
BioChem 2004, 5, 453 – 459; g) R. Wacker, H. Schroeder, C. M.
Niemeyer, Anal. Biochem. 2004, 330, 281 – 287; h) F. Kukolka,
C. M. Niemeyer, Org. Biomol. Chem. 2004, 2, 2203 – 2206.
[15] C. M. Niemeyer, W. Bꢀrger, J. Peplies, Angew. Chem. 1998, 110,
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[16] C. M. Niemeyer, J. Koehler, C. Wuerdemann, ChemBioChem
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[17] Previous work on electron transfer reactions occurring in a
composite material prepared from myoglobin containing
double-stranded DNA-modified hemin in poly(ethylene oxide)
oligomers was carried out without characterization of the DNA-
protein conjugate: K. Muneyasu, N. Y. Kawahara, H. Ohno,
Solid State Ionics 1998, 113 – 115, 167 – 171.
[13] The structure of Amplex UltraRed (Invitrogen A36006) is
proprietary and undisclosed. However, according to information
supplied by the manufacturer, the nonfluorescent Amplex
UltraRed reacts similarly to Amplex Red reagent (10-acetyl-
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