Available online at www.sciencedirect.com
ScienceDirect Nanomaterials and nanoclusters based on DNA modulation Yan Fu, Xian Wang, Jinli Zhang and Wei Li Besides the inherent chirality, DNA is enriched by nitrogen and oxygen functional groups that are preferential to coordinate with transition metal ions, and its self-assembled structures, including the G-quadruplex, the i-motif, and the conventional Watson–Crick duplex, etc., can be adjusted via different base pairings. Recently biotemplating on the basis of DNA selfassembly has been considered as an attractive method to construct switchable nanomaterials, to direct crystal growth and to design enantioselective selectors/catalysts. This review briefly covers the recent progress relevant to DNA modulated nano/subnano materials. The long-term goal of this area of research is to explore novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/ subnano clusters and enantioselective recognition platforms respectively, through DNA-based modulation. Addresses Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People’s Republic of China Corresponding authors: Li, Wei ([email protected])
Current Opinion in Biotechnology 2014, 28:33–38 This review comes from a themed issue on Nanobiotechnology Edited by Jonathan S Dordick and Kelvin H Lee
0958-1669/$ – see front matter, # 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.copbio.2013.10.014
Introduction DNA can self-assemble into polymorphic supramolecular structures including the G-quadruplex, the i-motif, and the duplex and so on [1,2], via the conventional Watson– Crick base pairings but also reverse Watson–Crick, Hoogsteen, reverse Hoogsteen pairings in the presence of certain cations [3], or small-molecule ligands [4], or under cellular mimicking conditions (illustrated in Figure 1) [5]. On the basis of plenty of thermodynamic and kinetic studies on the structural transition [6–8,9], recently DNA self-assembly has been extensively explored as promising scaffolds, not only to design responsive nanostructures [10,11], but to direct controllable assembly of proteins, nanoparticles, or membrane channels [12,13,14]. This review will focus on the recent progress of nanomaterials and nanoclusters with distinct physicochemical properties modulated by structural interconversions of polymorphic DNA, in association with the metal-nucleic acid interactions, and inherent chirality of DNA. www.sciencedirect.com
Switchable nanomachines tuned via polymorphic DNA structures Polymorphic DNA structures such as i-motif and Gquadruplex, have been used to control functional nanomaterials that can respond to chemical stimulus on the time scales of minutes, based on the conformational switch. Numerous adaptive DNA-based nanomachines have been developed that can reversibly switch conformations, acting as walkers, steppers and intracellular detection systems [15,16]. Chemical stimulus involving protons, metal ions, etc., are inputted to activate DNA nanomachines based on the structural transition among polymorphic DNA. Meanwhile, signal such as color, fluorescence or chemiluminescence, can be generated from the complexation of G-quadruplex with catalytic hemin or luminescent dye, to output switching states (Figure 2a). Triggered by fuel/antifuel strands, DNA ‘walkers’ assembled on nucleic acid scaffolds were activated in solution or on surfaces including electrodes or CdSe/ZnS quantum dots (Figure 2b). The DNA machines led to the switchable formation or dissociation of the hemin/G-quadruplex on the scaffolds, which enabled fluorescence resonance energy transfer, electrochemical, chemiluminescence resonance energy transfer, and photoelectrochemical transduction of the switchable states [17]. Notably, the coexistence of a G-quadruplex and an i-motif in a single oligonucleotide was reported to be operated as a NOTIF logic gate stimulated by pH and cation, on the basis of fluorescent enhancement of crystal violet that selectively bound to the G-rich loop [18]. In addition polymorphic DNA can be utilized to modify surfaces/interfaces of inorganic materials, as well as to fabricate smart release systems and electrodes. A reversible photon-fueled controlled release vehicle was fabricated using photo-irradiated pH-jump system mediated by conformational switch of i-motif DNA, where malachite green carbinol base (MGCB) was immobilized on pore walls of mesoporous silica nanoparticles (MSN) as the reversible light-induced hydroxide ion emitter and imotif DNA was grafted on the surface of MSN as the cap material (Figure 2c). The release profile of Ru(bipy)32+ was strongly dependent on the unfolding of i-motif DNA due to the MGCB-mediated pH increase of solution in the presence of UV light, and the entrapped guest molecules could be delivered in small portions by turning the UV light on and off alternately [19]. A novel NIR and pH dual-responsive dynamic DNA system was constructed for controlled catch and release of cells, based on the NIR-induced dsDNA dissociation, and the pH-stimulated switching of i-motif [20]. Current Opinion in Biotechnology 2014, 28:33–38
34 Nanobiotechnology
Figure 1
(a)
(b)
N N H N H
H
N
H N
N
H N O H
H
N
N
N H
N
O
N H
O
+ N H
N
N H
O
N
N N
H N
N
H
H N
H
H
N O
M+
O
N
N
N
H
N
i-motif G-quadruplex (c)
to lf ta
H N
H
H
H
H
O
N
N
N
pl
O H
N
N O
N
Triplex
W at
so
N
H
du
N
ic k
O
N
ex
T×A·T
Cr
N
O
n-
N
N
N N
en
N
O
H
m
O
ro n
H
H
N
En vi
N+
N
ac
H
H N
rs
C+×G·C
Current Opinion in Biotechnology
Representative polymorphic DNA structures: (a) G-quadruplex (PDB id: 143D) and G-tetrad composed of four guanine bases through Hoogsteen base pairs; (b) i-motif (PDB id: 1EL2) and hemiprotonated C:C+ pairs; (c) parallel triplex (PDB id: 1BWG) and T AT and C+ GC pairs; Thermodynamic equilibrium between Watson-Crick duplex and these structures can be regulated by environmental factors such as cation, proton, small ligand, protein, hydration, etc.
Nanomaterials/clusters stabilized via the coordination of nucleotides Polymorphic DNAs are distinguished from other capping agents in the synthesis of metallic nanomaterials because they not only present nitrogen and oxygen functional groups that coordinate with metal, but also assemble to supramolecular structures via unique base pairings to provide spatial constraints. In the field of bioinorganic chemistry, according to different binding models of metal–nucleic acids, three kinds of metal ions can be classified as the phosphate binding group (Na+, K+, Mg2+, etc.), the nucleobase and phosphate binding group (Ni2+, Zn2+, Cu2+, etc.), and the exclusive nucleobase binding group (Ag+, Pt2+, Hg2+, etc.). At neutral pH, it is suggested that the binding stability for nucleobase complexes with transition metals decreases in the order: N7/O6(G) > N3(C) > N7(A) > N1(A) > N3(A,G) [21]. Therefore, DNA and their components have been widely used as biotemplates to control the crystal growth of Current Opinion in Biotechnology 2014, 28:33–38
semiconductor nanomaterials [22]. Functional groups such as carbonyl and amine/nitrogen moieties on the nucleobases primarily coordinate cations on the nanocrystal for surface passivation, and the overhanging phosphate backbones prevent irreversible aggregation of nanoparticles. Physicochemical properties including fluorescence emission as well as particle size, were dependent upon the surface reactivities of DNA templates with growing nanocrystals, for example, PbS capped by poly A without carbonyl groups, exhibited very dim emission properties compared to those formed with other sequences including poly GT, poly T, and poly C. Moreover, the backbone twist or the secondary structure formation was also detected for the capping DNA, for example, TBA and AS1411 strands can fold into G-quadruplex on the PbS surface [23]. The interactions between DNA sequences and surfaces of metal nanocrystals were shown to be highly www.sciencedirect.com
Nanomaterials and nanoclusters based on DNA modulation Fu et al. 35
Figure 2
(a)
3′
(II)
(I)
3′
3′
H2O2
Substrate
+
Chemiluminescence
5′
G-quadruplex Random coil
Mn+
Hemin
3′ 5′ 3′
5′
5′
Mn+
H2O
+
H+ 5′
i-motif
G-quadruplex
+ Duplex H
(III)
hν
3′
Oxidized Substrate
hν ’
3′
5′ 3′
Output
+
Input
Dye
Random coil
i-motif 5′
(b) (I)
Color Fluorescence
5′
(c) (II)
hν
T
E FR
Hemin
Acceptor Electrode
Donor
hν ’ Electrode
e-
e-
Luminol Hemin
QD
UV light
H2O Current
Fluorescence (III)
Release
H2O2
H2O2
CR
ET
hν
Dark H2O MGCB
Ru(bipy)32+
Photocurrent (d)
G-quadruplex
Outside-growth
i-motif
duplex
Inside-growth Current Opinion in Biotechnology
Principles on the construction of DNA-based nanomachines or nanomaterials. (a) (I) Stimuli-triggered interconversions among duplex, G-quadruplex, i-motif, etc.; (II) G-quadruplex combines with the catalytic cofactor hemin and exhibits peroxidase activity in the presence of different substrates, resulting in a change in color, fluorescence or chemiluminescence; (III) G-quadruplex also can selectively bind to different luminescent dyes, resulting in an enhanced fluorescence. (b) Different approaches on generating readout signals for a ‘DNA walker’, of which the core is the G-quadruplex formation/dissociation, (I) FRET between a pair of donor and acceptor, (II) hemin/G-quadruplex-generated current, (III) hemin/G-quadruplex-generated chemiluminescence, and subsequent CRET-generated photocurrent. (c) Photon-fueled release of guest molecules from the pores of mesoporous silica nanoparticles capped with i-motif. (d) Illustration of Ag clusters encapsulated in polymorphic DNA. www.sciencedirect.com
Current Opinion in Biotechnology 2014, 28:33–38
36 Nanobiotechnology
sequence-dependent, for example, the purines adsorbed on the gold surface more strongly than the pyrimidines, in the order of G > A > C > T. Therefore, oligonucleotides have been successfully used to control the morphologies of metal nanomaterials during seedmediated growth [24]. A new DNA-encoding scheme for controlling the synthesis of gold nanomaterials was discovered through governing the morphological controls by different DNA molecules as well as their combinations. A variety of novel shapes involving flat nanohexagons, round rough plates, round flat plates and six-pointed nanostars, can be obtained through the controllable growth on the surface of gold nanoprisms by poly G, poly A, poly C and poly T, respectively [25]. Metal clusters consisting of a few to several hundred metal atoms, have received increasing interests due to their unique physical, electrical, and optical properties, promising for use in catalysis, imaging, and sensing. In recent years, DNA oligonucleotides have been recognized as efficient templates to embed Ag [26], Au [27], Cu [28] clusters, of which fluorescent properties have been proven to be modulated by the sequence composition as well as the DNA conformation [29]. It is illustrated that fluorescent stabilities of Ag clusters, with the cluster size of Ag3–Ag6, were associated with the binding affinities between DNA templates and Ag+ [30,31]. On the basis of DFT calculations, it is indicated that Ag atoms tend to aggregate inside the encapsulated spaces of i-motif or duplex, and the formed Ag clusters were positively charged with high fluorescent spectral features; whereas Ag atoms were preferential to aggregate outside of the G-tetrad, resulting in the formation of Ag nanoparticles without fluorescence (Figure 2d) [32]. In addition, polymorphic DNA has also been used as a unique spatial constraint to stabilize highly active nano/ subnano catalysts. Since the interval between two neighboring CH+C pairings of i-motif was very close to the Pd– Pd bond distance (2.8 A˚) in bulk metal, i-motif-encapsuled Pd8–Pd9 clusters were designed consisting of metallic atoms as well as positively charged Pd ligated by N3 of cytosines. This subnano catalyst facilitated the activation of nitryl group of 4-nitrophenol with a relative rate constant of 2034 min1 (mM Pd)1, higher than other Pd nanocatalysts synthesized with other templates of peptides, proteins, polymers or dendrimers with the relative rate constant ranged from 5 to 1221 min1 mM1 in literatures [33].
DNA-based enantioselective recognition and its applications Supramolecular chirality is intrinsic to natural DNA, therefore, DNA exhibit stereoselective response for chiral molecules. Owing to the intriguing feature of structural polymorphism, DNA molecules are promising for Current Opinion in Biotechnology 2014, 28:33–38
exploration of new methodologies on enantiomeric resolution. DNA-based chiral catalysts, which are selfassembled from DNA and a metal complex with a specific ligand through covalent anchoring strategies, exhibit high stereoselectivity and rate enhancement in asymmetric carbon–carbon or carbon–heteroatom bond-forming reactions, such as Diels–Alder (D–A), Friedel–Craft (F–C) alkylations, and Michael addition [34]. In asymmetric intramolecular F–C reactions, the relationships between enantioselectivities and DNA chiralities were proposed by using Cu(II) complex with 4,40 -dimethyl-2,20 -bipyridine and different DNA scaffolds, and the enantiomeric excess of product decreased in the following order: Bform duplex > Z-form duplex > G-quadruplex > singlestranded DNA [35]. Without organic ligands, Cu(II)bound G-quadruplexes also can accelerate D–A or F–C reactions. Interestingly, the absolute configuration and the enantioselectivity of the product were found to be greatly associated with the conformation of human telomeric G-quadruplex regulated by chemical environments [36]. Interestingly, one type of DNA-based electrochemical sensor was fabricated to distinguish chiral metallosupramolecular complexes, for example, the human telomeric antiparallel G-quadruplex can selectively interact with the P-Ni2L3 with an enantioselective recognition ratio higher than 5, whereas the DNA three-way junction preferentially binds to the M-Fe2L3 with the ratio of about 3.5 [37,38]. So far, a series of enantioselective DNA aptamers were selected against a target enantiomer using SELEX procedure [39]. These DNA aptamers exhibit high binding affinities and enantioselectivities, and have been successfully utilized as a new class of chiral stationary phases of high performance liquid chromatography. Inspired by special interactions of transition metal ions with DNA, recently we explored a DNA-based chiral separation method to ofloxacin racemates, for example, using Cu(II)-coordinated double helix as the chiral selector, both R- and S-ofloxacin can be directly enriched from the racemate, obtaining the enantiomeric excess of 59% (R) and 41% (S) respectively, through one adsorption– desorption separation [40].
Conclusions and perspectives Owing to the discoveries of structural polymorphism in the past decades, DNA molecules assembled via base pairings such as Watson–Crick, reverse Watson–Crick, Hoogsteen, and reverse Hoogsteen pairings, have attracted increasing interests in the fields of DNA nanotechnology. So far, DNA structures including the Gquadruplex, the i-motif, and the conventional Watson– Crick duplex, etc., have been extensively used as biotemplates to fabricate programmed DNA nanostructures as functional materials for sensing, computing, spatial positioning of proteins or nanoparticles, as well as artificial www.sciencedirect.com
Nanomaterials and nanoclusters based on DNA modulation Fu et al. 37
Figure 3
Acknowledgements Part of our polymorphic DNA research is supported by NSFC (21076141, 21176174, 21206107, 20836005).
Switchable nanomachines
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:
Stimuli-triggered interconversion
Su p
n io ion al at et in M rd o co
Nano/subnano clusters
ra ch mo ira le lit cu y la
r
of special interest of outstanding interest
Enantioselective platforms Current Opinion in Biotechnology
Intriguing features of polymorphic DNA structures provide novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/subnano clusters and enantioselective recognition platforms respectively.
building of smart nanomaterials. As illustrated in Figure 3, this review has attempted to highlight three key features of polymorphic DNA that provide the basis for its future implementations: The assembly–disassembly of Hoogsteen base pairings responses rapidly to various chemical stimuli, which can be used as ‘smart’ building blocks for nanofabrication. Thermodymamics and kinetics on the structural interconversions provide fundamental principles for the bottom-up construction of responsive DNA nanostructures, switchable nanomachines and stimuli-triggered nanomaterials. DNA scaffolds provide spatial constraints for controlled growth of metal nano/subnano clusters, whose physicochemical properties are modulated by sequence compositions and supramolecular structures, owing to the differences in the binding affinities of transition metal ions with polymorphic DNA. One major challenge in this area is to enable a bottom-up method to prepare nano/ subnano clusters with desirable distinct physicochemical properties using the programmable DNA scaffolds. Structural polymorphism leads to chiral diversity of DNA molecules, which can be served as stereoselective platforms for enantioseparation mainly through the specific interactions of ligand-/metal-nucleic acids. Recently, DNA-based construction of chiroptical plasmonic nanostructures and helical nanomaterials has emerged based on the mechanisms on chiral amplification, transfer and transcription, providing new application prospects of polymorphic DNA. www.sciencedirect.com
1. Choi J, Majima T: Conformational changes of non-B DNA. Chem Soc Rev 2011, 40:5893-5909. This review described the latest studies on the conformational changes of non-B DNAs, with a focus on the mechanism and dynamics of the structural changes involving G-quadruplex, i-motif, Z-DNA, A-motif, hairpin and triplex. 2.
Balasubramanian S, Hurley LH, Neidle S: Targeting Gquadruplexes in gene promoters: a novel anticancer strategy. Nat Rev Drug Discov 2011, 10:261-275.
3.
Liu W, Fu Y, Zheng B, Cheng S, Li W, Lau TC, Liang HJ: Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+. J Phys Chem B 2011, 115:13051-13056.
4.
Koirala D, Dhakal S, Ashbridge B, Sannohe Y, Rodriguez R, Sugiyama H, Balasubramanian S, Mao H: A single-molecule platform for investigation of interactions between Gquadruplexes and small-molecule ligands. Nat Chem 2011, 3:782-787. Here, using a laser tweezer method, the interactions between pyridostatin and telomeric G-quadruplex were investigated from the mechanical stability of ligand–DNA complex.
5.
Yu H, Gu X, Nakano S-I, Miyoshi D, Sugimoto N: Beads-on-astring structure of long telomeric DNAs under molecular crowding conditions. J Am Chem Soc 2012, 134:20060-20069.
6.
Zhang J, Fu Y, Zheng L, Li W, Li H, Sun Q, Xiao Y, Geng F: Natural isoflavones regulate the quadruplex–duplex competition in human telomeric DNA. Nucleic Acids Res 2009, 37:2471-2482.
7.
Zhang J, Zheng L, Wang X, Xiao Y, Lu Y, Li W: Branched silica nanostructures oriented by dynamic G-quadruplex transformation. Mater Res Bull 2010, 45:1954-1959.
8.
Xue Y, Liu J-Q, Zheng K-W, Kan Z-Y, Hao Y-H, Tan Z: Kinetic and thermodynamic control of G-quadruplex folding. Angew Chem Int Ed 2011, 50:8046-8050.
9.
Sobczak J-PJ, Martin TG, Gerling T, Dietz H: Rapid folding of DNA into nanoscale shapes at constant temperature. Science 2012, 338:1458-1461. Here hundreds of DNA strands can cooperatively fold a long template within minutes into origami objects, which enabled the rapid production of three-dimensional DNA objects with yields that approached 100%. 10. Fu Y, Wang X, Zhang J, Xiao Y, Li W, Wang J: Orderly microaggregates of G-/C-rich oligonucleotides associated with spermine. Biomacromolecules 2011, 12:747-756. 11. Zhou T, Chen P, Niu L, Jin J, Liang D, Li Z, Yang Z, Liu D: pH responsive size-tunable self-assembled DNA dendrimers. Angew Chem Int Ed 2012, 51:11271-11274. Here three-dimensional DNA dendrimers with size responsiveness were constructed through the assembly of Y-DNA, upon the folding/unfolding of i-motif in 1st generation.
12. Derr ND, Goodman BS, Jungmann R, Leschziner AE, Shih WM, Reck-Peterson SL: Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold. Science 2012, 338:662-665. Here a programmable synthetic cargo was built using 3D DNA origami with various binding sites for control of the type, number, spacing, and orientation of DNA-linked motors. Ensembles opposite-polarity motors engaged in a tug-of-war resolvable by disengaging one motor species. 13. Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Ho¨gele A, Simmel FC, Govorov AO, Liedl T: DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 2012, 483:311-314. Current Opinion in Biotechnology 2014, 28:33–38
38 Nanobiotechnology
Here rigid DNA origami enabled the high-yield production of tunable plasmonic structures comprised of metal nanoparticles arranged in nanometer scale helices.
In this review, the formation and stabilization of silver clusters using DNA templates were described, and the distinct spectroscopic and photophysical properties of the resulting hybrid fluorophores were highlighted.
14. Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, Simmel FC: Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 2012, 338:932-936. Here nanometer-scale transmembrane channels in lipid bilayers were created using self-assembled DNA-based nanostructures. The synthetic channels had similarities to natural ion channels, and can be used to discriminate single DNA molecules.
27. Kennedy TAC, MacLean JL, Liu J: Blue emitting gold nanoclusters templated by poly-cytosine DNA at low pH and poly-adenine DNA at neutral pH. Chem Commun 2012, 48:6845-6847.
15. Wang Z-G, Elbaz J, Willner I: DNA machines: bipedal walker and stepper. Nano Lett 2011, 11:304-309. Here a bipedal walker and a bipedal stepper were constructed based on the stimuli-responsive structural transition of i-motif and T-Hg2+-T, activated with H+/OH- and Hg2+/cysteine triggers. 16. Pei H, Liang L, Yao G, Li J, Huang Q, Fan C: Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. Angew Chem Int Ed 2012, 51:9020-9024. Here a series of reconfigurable DNA tetrahedra nanostructures were constructed containing dynamic sequences, and can be successfully used in intracellular detection.
28. Rotaru A, Dutta S, Jentzsch E, Gothelf K, Mokhir A: Selective dsDNA-templated formation of copper nanoparticles in solution. Angew Chem Int Ed 2010, 49:5665-5667. 29. Li T, Zhang L, Ai J, Dong S, Wang E: Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device. ACS Nano 2011, 5:6334-6338. 30. Fu Y, Zhang J, Chen X, Huang T, Duan X, Li W, Wang J: Silver nanomaterials regulated by structural competition of G-/C-rich oligonucleotides. J Phys Chem C 2011, 115:10370-10379. Here double-stranded DNA templates can generate distinct fluorescent Ag NCs modulated by the predominance among the structural competition of Watson-Crick duplex, G-quadruplex and i-motif.
17. Liu X, Niazov-Elkan A, Wang F, Willner I: Switching photonic and electrochemical functions of a DNAzyme by DNA machines. Nano Lett 2013, 13:219-225.
31. Li W, Liu L, Fu Y, Sun Y, Zhang J, Zhang R: Effects of polymorphic DNA on the fluorescent properties of silver nanoclusters. Photochem Photobiol Sci 2013, 12:1864-1872.
18. Zhou J, Amrane S, Korkut DN, Bourdoncle A, He H-Z, Ma D, Mergny J-L: Combination of i-motif and G-quadruplex structures within the same strand: formation and application. Angew Chem Int Ed 2013, 52:7742-7746.
32. Wu J, Fu Y, He Z, Han Y, Zheng L, Zhang J, Li W: Growth mechanisms of fluorescent silver clusters regulated by polymorphic DNA templates: a DFT study. J Phys Chem B 2012, 116:1655-1665.
19. He D, He X, Wang K, Cao J, Zhao Y: Photon-fueled gate-like delivery system using i-motif DNA functionalized mesoporous silica nanoparticles. Adv Funct Mater 2012, 22:4704-4710.
33. Zhang J, Wang X, Fu Y, Han Y, Cheng J, Zhang Y, Li W: Highly active subnano palladium clusters embeded in I-motif DNA. Langmuir 2013 http://dx.doi.org/10.1021/la402153b.
20. Li W, Wang J, Ren J, Qu X: Near-infrared- and pH-responsive system for reversible cell adhesion using graphene/gold nanorods functionalized with i-Motif DNA. Angew Chem Int Ed 2013, 52:6726-6730.
34. Rosati F, Roelfes G: Artificial metalloenzymes. ChemCatChem 2010, 2:916-927.
21. Berti L, Burley GA: Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles. Nat Nanotechnol 2008, 3:81-87. 22. Ma N, Tikhomirov G, Kelley SO: Nucleic acid-passivated semiconductor nanocrystals: biomolecular templating of form and function. Acc Chem Res 2010, 43:173-180. 23. Cha T-G, Baker BA, Salgado J, Bates CJ, Chen KH, Chang AC, Akatay MC, Han J-H, Strano MS, Choi JH: Understanding oligonucleotide-templated nanocrystals: growth mechanisms and surface properties. ACS Nano 2012, 6:8136-8143. 24. Wang Z, Zhang J, Ekman JM, Kenis PJA, Lu Y: DNA-mediated control of metal nanoparticle shape: one-pot synthesis and cellular uptake of highly stable and functional gold nanoflowers. Nano Lett 2010, 10:1886-1891. 25. Wang Z, Tang L, Tan LH, Li J, Lu Y: Discovery of the DNA genetic code for abiological gold nanoparticle morphologies. Angew Chem Int Ed 2012, 51:9078-9082. 26. Petty JT, Story SP, Hsiang J-C, Dickson RM: DNA-templated molecular silver fluorophores. J Phys Chem Lett 2013, 4:1148-1155.
Current Opinion in Biotechnology 2014, 28:33–38
35. Park S, Ikehata K, Watabe R, Hidaka Y, Rajendran A, Sugiyama H: Deciphering DNA-based asymmetric catalysis through intramolecular Friedel–Crafts alkylations. Chem Commun 2012, 48:10398-10400. 36. Wang C, Jia G, Zhou J, Li Y, Liu Y, Lu S, Li C: Enantioselective Diels–Alder reactions with G-quadruplex DNA based catalysts. Angew Chem Int Ed 2012, 51:9352-9355. 37. Feng L, Zhao C, Xiao Y, Wu L, Ren J, Qu X: Electrochemical DNA three-way junction based sensor for distinguishing chiral metallo-supramolecular complexes. Chem Commun 2012, 48:6900-6902. 38. Feng L, Xu B, Ren J, Zhao C, Qu X: A human telomeric DNA-based chiral biosensor. Chem Commun 2012, 48:9068-9070. 39. Peyrin E: Nucleic acid aptamer molecular recognition principles and application in liquid chromatography and capillary electrophoresis. J Sep Sci 2009, 32: 1531-1536. 40. Fu Y, Duan X, Chen X, Zhang J, Li W: Enantioselective separation of chiral ofloxacin using functional Cu(II)coordinated G-rich oligonucleotides. RSC Adv 2013 http:// dx.doi.org/10.1039/c3ra43251c.
www.sciencedirect.com
ScienceDirect Nanomaterials and nanoclusters based on DNA modulation Yan Fu, Xian Wang, Jinli Zhang and Wei Li Besides the inherent chirality, DNA is enriched by nitrogen and oxygen functional groups that are preferential to coordinate with transition metal ions, and its self-assembled structures, including the G-quadruplex, the i-motif, and the conventional Watson–Crick duplex, etc., can be adjusted via different base pairings. Recently biotemplating on the basis of DNA selfassembly has been considered as an attractive method to construct switchable nanomaterials, to direct crystal growth and to design enantioselective selectors/catalysts. This review briefly covers the recent progress relevant to DNA modulated nano/subnano materials. The long-term goal of this area of research is to explore novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/ subnano clusters and enantioselective recognition platforms respectively, through DNA-based modulation. Addresses Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People’s Republic of China Corresponding authors: Li, Wei ([email protected])
Current Opinion in Biotechnology 2014, 28:33–38 This review comes from a themed issue on Nanobiotechnology Edited by Jonathan S Dordick and Kelvin H Lee
0958-1669/$ – see front matter, # 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.copbio.2013.10.014
Introduction DNA can self-assemble into polymorphic supramolecular structures including the G-quadruplex, the i-motif, and the duplex and so on [1,2], via the conventional Watson– Crick base pairings but also reverse Watson–Crick, Hoogsteen, reverse Hoogsteen pairings in the presence of certain cations [3], or small-molecule ligands [4], or under cellular mimicking conditions (illustrated in Figure 1) [5]. On the basis of plenty of thermodynamic and kinetic studies on the structural transition [6–8,9], recently DNA self-assembly has been extensively explored as promising scaffolds, not only to design responsive nanostructures [10,11], but to direct controllable assembly of proteins, nanoparticles, or membrane channels [12,13,14]. This review will focus on the recent progress of nanomaterials and nanoclusters with distinct physicochemical properties modulated by structural interconversions of polymorphic DNA, in association with the metal-nucleic acid interactions, and inherent chirality of DNA. www.sciencedirect.com
Switchable nanomachines tuned via polymorphic DNA structures Polymorphic DNA structures such as i-motif and Gquadruplex, have been used to control functional nanomaterials that can respond to chemical stimulus on the time scales of minutes, based on the conformational switch. Numerous adaptive DNA-based nanomachines have been developed that can reversibly switch conformations, acting as walkers, steppers and intracellular detection systems [15,16]. Chemical stimulus involving protons, metal ions, etc., are inputted to activate DNA nanomachines based on the structural transition among polymorphic DNA. Meanwhile, signal such as color, fluorescence or chemiluminescence, can be generated from the complexation of G-quadruplex with catalytic hemin or luminescent dye, to output switching states (Figure 2a). Triggered by fuel/antifuel strands, DNA ‘walkers’ assembled on nucleic acid scaffolds were activated in solution or on surfaces including electrodes or CdSe/ZnS quantum dots (Figure 2b). The DNA machines led to the switchable formation or dissociation of the hemin/G-quadruplex on the scaffolds, which enabled fluorescence resonance energy transfer, electrochemical, chemiluminescence resonance energy transfer, and photoelectrochemical transduction of the switchable states [17]. Notably, the coexistence of a G-quadruplex and an i-motif in a single oligonucleotide was reported to be operated as a NOTIF logic gate stimulated by pH and cation, on the basis of fluorescent enhancement of crystal violet that selectively bound to the G-rich loop [18]. In addition polymorphic DNA can be utilized to modify surfaces/interfaces of inorganic materials, as well as to fabricate smart release systems and electrodes. A reversible photon-fueled controlled release vehicle was fabricated using photo-irradiated pH-jump system mediated by conformational switch of i-motif DNA, where malachite green carbinol base (MGCB) was immobilized on pore walls of mesoporous silica nanoparticles (MSN) as the reversible light-induced hydroxide ion emitter and imotif DNA was grafted on the surface of MSN as the cap material (Figure 2c). The release profile of Ru(bipy)32+ was strongly dependent on the unfolding of i-motif DNA due to the MGCB-mediated pH increase of solution in the presence of UV light, and the entrapped guest molecules could be delivered in small portions by turning the UV light on and off alternately [19]. A novel NIR and pH dual-responsive dynamic DNA system was constructed for controlled catch and release of cells, based on the NIR-induced dsDNA dissociation, and the pH-stimulated switching of i-motif [20]. Current Opinion in Biotechnology 2014, 28:33–38
34 Nanobiotechnology
Figure 1
(a)
(b)
N N H N H
H
N
H N
N
H N O H
H
N
N
N H
N
O
N H
O
+ N H
N
N H
O
N
N N
H N
N
H
H N
H
H
N O
M+
O
N
N
N
H
N
i-motif G-quadruplex (c)
to lf ta
H N
H
H
H
H
O
N
N
N
pl
O H
N
N O
N
Triplex
W at
so
N
H
du
N
ic k
O
N
ex
T×A·T
Cr
N
O
n-
N
N
N N
en
N
O
H
m
O
ro n
H
H
N
En vi
N+
N
ac
H
H N
rs
C+×G·C
Current Opinion in Biotechnology
Representative polymorphic DNA structures: (a) G-quadruplex (PDB id: 143D) and G-tetrad composed of four guanine bases through Hoogsteen base pairs; (b) i-motif (PDB id: 1EL2) and hemiprotonated C:C+ pairs; (c) parallel triplex (PDB id: 1BWG) and T AT and C+ GC pairs; Thermodynamic equilibrium between Watson-Crick duplex and these structures can be regulated by environmental factors such as cation, proton, small ligand, protein, hydration, etc.
Nanomaterials/clusters stabilized via the coordination of nucleotides Polymorphic DNAs are distinguished from other capping agents in the synthesis of metallic nanomaterials because they not only present nitrogen and oxygen functional groups that coordinate with metal, but also assemble to supramolecular structures via unique base pairings to provide spatial constraints. In the field of bioinorganic chemistry, according to different binding models of metal–nucleic acids, three kinds of metal ions can be classified as the phosphate binding group (Na+, K+, Mg2+, etc.), the nucleobase and phosphate binding group (Ni2+, Zn2+, Cu2+, etc.), and the exclusive nucleobase binding group (Ag+, Pt2+, Hg2+, etc.). At neutral pH, it is suggested that the binding stability for nucleobase complexes with transition metals decreases in the order: N7/O6(G) > N3(C) > N7(A) > N1(A) > N3(A,G) [21]. Therefore, DNA and their components have been widely used as biotemplates to control the crystal growth of Current Opinion in Biotechnology 2014, 28:33–38
semiconductor nanomaterials [22]. Functional groups such as carbonyl and amine/nitrogen moieties on the nucleobases primarily coordinate cations on the nanocrystal for surface passivation, and the overhanging phosphate backbones prevent irreversible aggregation of nanoparticles. Physicochemical properties including fluorescence emission as well as particle size, were dependent upon the surface reactivities of DNA templates with growing nanocrystals, for example, PbS capped by poly A without carbonyl groups, exhibited very dim emission properties compared to those formed with other sequences including poly GT, poly T, and poly C. Moreover, the backbone twist or the secondary structure formation was also detected for the capping DNA, for example, TBA and AS1411 strands can fold into G-quadruplex on the PbS surface [23]. The interactions between DNA sequences and surfaces of metal nanocrystals were shown to be highly www.sciencedirect.com
Nanomaterials and nanoclusters based on DNA modulation Fu et al. 35
Figure 2
(a)
3′
(II)
(I)
3′
3′
H2O2
Substrate
+
Chemiluminescence
5′
G-quadruplex Random coil
Mn+
Hemin
3′ 5′ 3′
5′
5′
Mn+
H2O
+
H+ 5′
i-motif
G-quadruplex
+ Duplex H
(III)
hν
3′
Oxidized Substrate
hν ’
3′
5′ 3′
Output
+
Input
Dye
Random coil
i-motif 5′
(b) (I)
Color Fluorescence
5′
(c) (II)
hν
T
E FR
Hemin
Acceptor Electrode
Donor
hν ’ Electrode
e-
e-
Luminol Hemin
QD
UV light
H2O Current
Fluorescence (III)
Release
H2O2
H2O2
CR
ET
hν
Dark H2O MGCB
Ru(bipy)32+
Photocurrent (d)
G-quadruplex
Outside-growth
i-motif
duplex
Inside-growth Current Opinion in Biotechnology
Principles on the construction of DNA-based nanomachines or nanomaterials. (a) (I) Stimuli-triggered interconversions among duplex, G-quadruplex, i-motif, etc.; (II) G-quadruplex combines with the catalytic cofactor hemin and exhibits peroxidase activity in the presence of different substrates, resulting in a change in color, fluorescence or chemiluminescence; (III) G-quadruplex also can selectively bind to different luminescent dyes, resulting in an enhanced fluorescence. (b) Different approaches on generating readout signals for a ‘DNA walker’, of which the core is the G-quadruplex formation/dissociation, (I) FRET between a pair of donor and acceptor, (II) hemin/G-quadruplex-generated current, (III) hemin/G-quadruplex-generated chemiluminescence, and subsequent CRET-generated photocurrent. (c) Photon-fueled release of guest molecules from the pores of mesoporous silica nanoparticles capped with i-motif. (d) Illustration of Ag clusters encapsulated in polymorphic DNA. www.sciencedirect.com
Current Opinion in Biotechnology 2014, 28:33–38
36 Nanobiotechnology
sequence-dependent, for example, the purines adsorbed on the gold surface more strongly than the pyrimidines, in the order of G > A > C > T. Therefore, oligonucleotides have been successfully used to control the morphologies of metal nanomaterials during seedmediated growth [24]. A new DNA-encoding scheme for controlling the synthesis of gold nanomaterials was discovered through governing the morphological controls by different DNA molecules as well as their combinations. A variety of novel shapes involving flat nanohexagons, round rough plates, round flat plates and six-pointed nanostars, can be obtained through the controllable growth on the surface of gold nanoprisms by poly G, poly A, poly C and poly T, respectively [25]. Metal clusters consisting of a few to several hundred metal atoms, have received increasing interests due to their unique physical, electrical, and optical properties, promising for use in catalysis, imaging, and sensing. In recent years, DNA oligonucleotides have been recognized as efficient templates to embed Ag [26], Au [27], Cu [28] clusters, of which fluorescent properties have been proven to be modulated by the sequence composition as well as the DNA conformation [29]. It is illustrated that fluorescent stabilities of Ag clusters, with the cluster size of Ag3–Ag6, were associated with the binding affinities between DNA templates and Ag+ [30,31]. On the basis of DFT calculations, it is indicated that Ag atoms tend to aggregate inside the encapsulated spaces of i-motif or duplex, and the formed Ag clusters were positively charged with high fluorescent spectral features; whereas Ag atoms were preferential to aggregate outside of the G-tetrad, resulting in the formation of Ag nanoparticles without fluorescence (Figure 2d) [32]. In addition, polymorphic DNA has also been used as a unique spatial constraint to stabilize highly active nano/ subnano catalysts. Since the interval between two neighboring CH+C pairings of i-motif was very close to the Pd– Pd bond distance (2.8 A˚) in bulk metal, i-motif-encapsuled Pd8–Pd9 clusters were designed consisting of metallic atoms as well as positively charged Pd ligated by N3 of cytosines. This subnano catalyst facilitated the activation of nitryl group of 4-nitrophenol with a relative rate constant of 2034 min1 (mM Pd)1, higher than other Pd nanocatalysts synthesized with other templates of peptides, proteins, polymers or dendrimers with the relative rate constant ranged from 5 to 1221 min1 mM1 in literatures [33].
DNA-based enantioselective recognition and its applications Supramolecular chirality is intrinsic to natural DNA, therefore, DNA exhibit stereoselective response for chiral molecules. Owing to the intriguing feature of structural polymorphism, DNA molecules are promising for Current Opinion in Biotechnology 2014, 28:33–38
exploration of new methodologies on enantiomeric resolution. DNA-based chiral catalysts, which are selfassembled from DNA and a metal complex with a specific ligand through covalent anchoring strategies, exhibit high stereoselectivity and rate enhancement in asymmetric carbon–carbon or carbon–heteroatom bond-forming reactions, such as Diels–Alder (D–A), Friedel–Craft (F–C) alkylations, and Michael addition [34]. In asymmetric intramolecular F–C reactions, the relationships between enantioselectivities and DNA chiralities were proposed by using Cu(II) complex with 4,40 -dimethyl-2,20 -bipyridine and different DNA scaffolds, and the enantiomeric excess of product decreased in the following order: Bform duplex > Z-form duplex > G-quadruplex > singlestranded DNA [35]. Without organic ligands, Cu(II)bound G-quadruplexes also can accelerate D–A or F–C reactions. Interestingly, the absolute configuration and the enantioselectivity of the product were found to be greatly associated with the conformation of human telomeric G-quadruplex regulated by chemical environments [36]. Interestingly, one type of DNA-based electrochemical sensor was fabricated to distinguish chiral metallosupramolecular complexes, for example, the human telomeric antiparallel G-quadruplex can selectively interact with the P-Ni2L3 with an enantioselective recognition ratio higher than 5, whereas the DNA three-way junction preferentially binds to the M-Fe2L3 with the ratio of about 3.5 [37,38]. So far, a series of enantioselective DNA aptamers were selected against a target enantiomer using SELEX procedure [39]. These DNA aptamers exhibit high binding affinities and enantioselectivities, and have been successfully utilized as a new class of chiral stationary phases of high performance liquid chromatography. Inspired by special interactions of transition metal ions with DNA, recently we explored a DNA-based chiral separation method to ofloxacin racemates, for example, using Cu(II)-coordinated double helix as the chiral selector, both R- and S-ofloxacin can be directly enriched from the racemate, obtaining the enantiomeric excess of 59% (R) and 41% (S) respectively, through one adsorption– desorption separation [40].
Conclusions and perspectives Owing to the discoveries of structural polymorphism in the past decades, DNA molecules assembled via base pairings such as Watson–Crick, reverse Watson–Crick, Hoogsteen, and reverse Hoogsteen pairings, have attracted increasing interests in the fields of DNA nanotechnology. So far, DNA structures including the Gquadruplex, the i-motif, and the conventional Watson– Crick duplex, etc., have been extensively used as biotemplates to fabricate programmed DNA nanostructures as functional materials for sensing, computing, spatial positioning of proteins or nanoparticles, as well as artificial www.sciencedirect.com
Nanomaterials and nanoclusters based on DNA modulation Fu et al. 37
Figure 3
Acknowledgements Part of our polymorphic DNA research is supported by NSFC (21076141, 21176174, 21206107, 20836005).
Switchable nanomachines
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:
Stimuli-triggered interconversion
Su p
n io ion al at et in M rd o co
Nano/subnano clusters
ra ch mo ira le lit cu y la
r
of special interest of outstanding interest
Enantioselective platforms Current Opinion in Biotechnology
Intriguing features of polymorphic DNA structures provide novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/subnano clusters and enantioselective recognition platforms respectively.
building of smart nanomaterials. As illustrated in Figure 3, this review has attempted to highlight three key features of polymorphic DNA that provide the basis for its future implementations: The assembly–disassembly of Hoogsteen base pairings responses rapidly to various chemical stimuli, which can be used as ‘smart’ building blocks for nanofabrication. Thermodymamics and kinetics on the structural interconversions provide fundamental principles for the bottom-up construction of responsive DNA nanostructures, switchable nanomachines and stimuli-triggered nanomaterials. DNA scaffolds provide spatial constraints for controlled growth of metal nano/subnano clusters, whose physicochemical properties are modulated by sequence compositions and supramolecular structures, owing to the differences in the binding affinities of transition metal ions with polymorphic DNA. One major challenge in this area is to enable a bottom-up method to prepare nano/ subnano clusters with desirable distinct physicochemical properties using the programmable DNA scaffolds. Structural polymorphism leads to chiral diversity of DNA molecules, which can be served as stereoselective platforms for enantioseparation mainly through the specific interactions of ligand-/metal-nucleic acids. Recently, DNA-based construction of chiroptical plasmonic nanostructures and helical nanomaterials has emerged based on the mechanisms on chiral amplification, transfer and transcription, providing new application prospects of polymorphic DNA. www.sciencedirect.com
1. Choi J, Majima T: Conformational changes of non-B DNA. Chem Soc Rev 2011, 40:5893-5909. This review described the latest studies on the conformational changes of non-B DNAs, with a focus on the mechanism and dynamics of the structural changes involving G-quadruplex, i-motif, Z-DNA, A-motif, hairpin and triplex. 2.
Balasubramanian S, Hurley LH, Neidle S: Targeting Gquadruplexes in gene promoters: a novel anticancer strategy. Nat Rev Drug Discov 2011, 10:261-275.
3.
Liu W, Fu Y, Zheng B, Cheng S, Li W, Lau TC, Liang HJ: Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+. J Phys Chem B 2011, 115:13051-13056.
4.
Koirala D, Dhakal S, Ashbridge B, Sannohe Y, Rodriguez R, Sugiyama H, Balasubramanian S, Mao H: A single-molecule platform for investigation of interactions between Gquadruplexes and small-molecule ligands. Nat Chem 2011, 3:782-787. Here, using a laser tweezer method, the interactions between pyridostatin and telomeric G-quadruplex were investigated from the mechanical stability of ligand–DNA complex.
5.
Yu H, Gu X, Nakano S-I, Miyoshi D, Sugimoto N: Beads-on-astring structure of long telomeric DNAs under molecular crowding conditions. J Am Chem Soc 2012, 134:20060-20069.
6.
Zhang J, Fu Y, Zheng L, Li W, Li H, Sun Q, Xiao Y, Geng F: Natural isoflavones regulate the quadruplex–duplex competition in human telomeric DNA. Nucleic Acids Res 2009, 37:2471-2482.
7.
Zhang J, Zheng L, Wang X, Xiao Y, Lu Y, Li W: Branched silica nanostructures oriented by dynamic G-quadruplex transformation. Mater Res Bull 2010, 45:1954-1959.
8.
Xue Y, Liu J-Q, Zheng K-W, Kan Z-Y, Hao Y-H, Tan Z: Kinetic and thermodynamic control of G-quadruplex folding. Angew Chem Int Ed 2011, 50:8046-8050.
9.
Sobczak J-PJ, Martin TG, Gerling T, Dietz H: Rapid folding of DNA into nanoscale shapes at constant temperature. Science 2012, 338:1458-1461. Here hundreds of DNA strands can cooperatively fold a long template within minutes into origami objects, which enabled the rapid production of three-dimensional DNA objects with yields that approached 100%. 10. Fu Y, Wang X, Zhang J, Xiao Y, Li W, Wang J: Orderly microaggregates of G-/C-rich oligonucleotides associated with spermine. Biomacromolecules 2011, 12:747-756. 11. Zhou T, Chen P, Niu L, Jin J, Liang D, Li Z, Yang Z, Liu D: pH responsive size-tunable self-assembled DNA dendrimers. Angew Chem Int Ed 2012, 51:11271-11274. Here three-dimensional DNA dendrimers with size responsiveness were constructed through the assembly of Y-DNA, upon the folding/unfolding of i-motif in 1st generation.
12. Derr ND, Goodman BS, Jungmann R, Leschziner AE, Shih WM, Reck-Peterson SL: Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold. Science 2012, 338:662-665. Here a programmable synthetic cargo was built using 3D DNA origami with various binding sites for control of the type, number, spacing, and orientation of DNA-linked motors. Ensembles opposite-polarity motors engaged in a tug-of-war resolvable by disengaging one motor species. 13. Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Ho¨gele A, Simmel FC, Govorov AO, Liedl T: DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 2012, 483:311-314. Current Opinion in Biotechnology 2014, 28:33–38
38 Nanobiotechnology
Here rigid DNA origami enabled the high-yield production of tunable plasmonic structures comprised of metal nanoparticles arranged in nanometer scale helices.
In this review, the formation and stabilization of silver clusters using DNA templates were described, and the distinct spectroscopic and photophysical properties of the resulting hybrid fluorophores were highlighted.
14. Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, Simmel FC: Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 2012, 338:932-936. Here nanometer-scale transmembrane channels in lipid bilayers were created using self-assembled DNA-based nanostructures. The synthetic channels had similarities to natural ion channels, and can be used to discriminate single DNA molecules.
27. Kennedy TAC, MacLean JL, Liu J: Blue emitting gold nanoclusters templated by poly-cytosine DNA at low pH and poly-adenine DNA at neutral pH. Chem Commun 2012, 48:6845-6847.
15. Wang Z-G, Elbaz J, Willner I: DNA machines: bipedal walker and stepper. Nano Lett 2011, 11:304-309. Here a bipedal walker and a bipedal stepper were constructed based on the stimuli-responsive structural transition of i-motif and T-Hg2+-T, activated with H+/OH- and Hg2+/cysteine triggers. 16. Pei H, Liang L, Yao G, Li J, Huang Q, Fan C: Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. Angew Chem Int Ed 2012, 51:9020-9024. Here a series of reconfigurable DNA tetrahedra nanostructures were constructed containing dynamic sequences, and can be successfully used in intracellular detection.
28. Rotaru A, Dutta S, Jentzsch E, Gothelf K, Mokhir A: Selective dsDNA-templated formation of copper nanoparticles in solution. Angew Chem Int Ed 2010, 49:5665-5667. 29. Li T, Zhang L, Ai J, Dong S, Wang E: Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device. ACS Nano 2011, 5:6334-6338. 30. Fu Y, Zhang J, Chen X, Huang T, Duan X, Li W, Wang J: Silver nanomaterials regulated by structural competition of G-/C-rich oligonucleotides. J Phys Chem C 2011, 115:10370-10379. Here double-stranded DNA templates can generate distinct fluorescent Ag NCs modulated by the predominance among the structural competition of Watson-Crick duplex, G-quadruplex and i-motif.
17. Liu X, Niazov-Elkan A, Wang F, Willner I: Switching photonic and electrochemical functions of a DNAzyme by DNA machines. Nano Lett 2013, 13:219-225.
31. Li W, Liu L, Fu Y, Sun Y, Zhang J, Zhang R: Effects of polymorphic DNA on the fluorescent properties of silver nanoclusters. Photochem Photobiol Sci 2013, 12:1864-1872.
18. Zhou J, Amrane S, Korkut DN, Bourdoncle A, He H-Z, Ma D, Mergny J-L: Combination of i-motif and G-quadruplex structures within the same strand: formation and application. Angew Chem Int Ed 2013, 52:7742-7746.
32. Wu J, Fu Y, He Z, Han Y, Zheng L, Zhang J, Li W: Growth mechanisms of fluorescent silver clusters regulated by polymorphic DNA templates: a DFT study. J Phys Chem B 2012, 116:1655-1665.
19. He D, He X, Wang K, Cao J, Zhao Y: Photon-fueled gate-like delivery system using i-motif DNA functionalized mesoporous silica nanoparticles. Adv Funct Mater 2012, 22:4704-4710.
33. Zhang J, Wang X, Fu Y, Han Y, Cheng J, Zhang Y, Li W: Highly active subnano palladium clusters embeded in I-motif DNA. Langmuir 2013 http://dx.doi.org/10.1021/la402153b.
20. Li W, Wang J, Ren J, Qu X: Near-infrared- and pH-responsive system for reversible cell adhesion using graphene/gold nanorods functionalized with i-Motif DNA. Angew Chem Int Ed 2013, 52:6726-6730.
34. Rosati F, Roelfes G: Artificial metalloenzymes. ChemCatChem 2010, 2:916-927.
21. Berti L, Burley GA: Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles. Nat Nanotechnol 2008, 3:81-87. 22. Ma N, Tikhomirov G, Kelley SO: Nucleic acid-passivated semiconductor nanocrystals: biomolecular templating of form and function. Acc Chem Res 2010, 43:173-180. 23. Cha T-G, Baker BA, Salgado J, Bates CJ, Chen KH, Chang AC, Akatay MC, Han J-H, Strano MS, Choi JH: Understanding oligonucleotide-templated nanocrystals: growth mechanisms and surface properties. ACS Nano 2012, 6:8136-8143. 24. Wang Z, Zhang J, Ekman JM, Kenis PJA, Lu Y: DNA-mediated control of metal nanoparticle shape: one-pot synthesis and cellular uptake of highly stable and functional gold nanoflowers. Nano Lett 2010, 10:1886-1891. 25. Wang Z, Tang L, Tan LH, Li J, Lu Y: Discovery of the DNA genetic code for abiological gold nanoparticle morphologies. Angew Chem Int Ed 2012, 51:9078-9082. 26. Petty JT, Story SP, Hsiang J-C, Dickson RM: DNA-templated molecular silver fluorophores. J Phys Chem Lett 2013, 4:1148-1155.
Current Opinion in Biotechnology 2014, 28:33–38
35. Park S, Ikehata K, Watabe R, Hidaka Y, Rajendran A, Sugiyama H: Deciphering DNA-based asymmetric catalysis through intramolecular Friedel–Crafts alkylations. Chem Commun 2012, 48:10398-10400. 36. Wang C, Jia G, Zhou J, Li Y, Liu Y, Lu S, Li C: Enantioselective Diels–Alder reactions with G-quadruplex DNA based catalysts. Angew Chem Int Ed 2012, 51:9352-9355. 37. Feng L, Zhao C, Xiao Y, Wu L, Ren J, Qu X: Electrochemical DNA three-way junction based sensor for distinguishing chiral metallo-supramolecular complexes. Chem Commun 2012, 48:6900-6902. 38. Feng L, Xu B, Ren J, Zhao C, Qu X: A human telomeric DNA-based chiral biosensor. Chem Commun 2012, 48:9068-9070. 39. Peyrin E: Nucleic acid aptamer molecular recognition principles and application in liquid chromatography and capillary electrophoresis. J Sep Sci 2009, 32: 1531-1536. 40. Fu Y, Duan X, Chen X, Zhang J, Li W: Enantioselective separation of chiral ofloxacin using functional Cu(II)coordinated G-rich oligonucleotides. RSC Adv 2013 http:// dx.doi.org/10.1039/c3ra43251c.
www.sciencedirect.com
