DNA-Guided Metallization of Nanomaterials and Their Biomedical Applications: Comparison
Please note this is a comparison between Version 1 by Zhenbao Liu and Version 2 by Peter Tang.

Precise control of the structure of metallic nanomaterials is critical for the advancement of nanobiotechnology. As DNA (deoxyribonucleic acid) can readily modify various moieties, such as sulfhydryl, carboxyl, and amino groups, using DNA as a directing ligand to modulate the morphology of nanomaterials is a promising strategy. 

  • DNA nanotechnology
  • nanomaterials
  • metallization
  • morphology
  • biomedical application

1. Introduction

The use of nanomaterials has brought significant advances in various fields, including biomedical applications. However, the synthesis of these materials often involves complex and expensive processes. Metallic nanomaterials are typically synthesized by wet chemistry or photolithography. However, metallic materials with complex shapes cannot be prepared by traditional wet chemical methods [1]. Although photolithography can control the structure of the material, it requires expensive production equipment and is limited by the optical diffraction limit [2][3][2,3]. DNA(deoxyribonucleic acid)-guided metallization of nanomaterials has emerged as a promising technique to overcome these challenges. DNA-guided metallization of nanomaterials refers to the process of using DNA molecules as templates to guide the synthesis and assembly of metallic nanoparticles [4][5][4,5]. This technique offers a simple, cost-effective, and efficient way to produce a wide range of nanomaterials with tailored shapes and sizes for various applications. The use of DNA as a template for metallization provides a high level of control over the properties of the resulting nanomaterials. Notably, DNA has been introduced during the growth phase of metal nanoparticles to control and regulate the morphology of the particles [6]. In this context, thwe researchers reeview the latest developments in DNA-guided metallization of nanomaterials and their biomedical applications, as well as outline future research directions to enhance the potential of this technology.
In 1998, Braun et al. [7] proposed the use of DNA as a template to guide the growth of metallic materials. However, in the early stages of development, metallization was usually uniformly deposited along the DNA scaffold, compromising its biorecognition and addressability. To address these issues, researchers have developed several new strategies. For instance, DNA can be specifically labeled with an aldehyde group (e.g., glutaraldehyde), which acts as a local reductant on DNA and can be programmed to direct the metallization process only on selected DNA strands [8][9][8,9]. Moreover, the difference in affinity between DNA bases and metals can be exploited to achieve sequence-selective metallization [10]. This is because various nucleic acid bases have different affinities for metallic materials. Generally, DNA-directed metal particle synthesis involves two steps: first, metal nanoseeds bind to DNA as nucleation sites for selective metal deposition, and then metal atoms will form a continuous metal structure along the shape of DNA [4]. For gold nanomaterials, the relative adsorption affinity of DNA bases is adenine (A) > cytosine (C) ≥ guanine (G) > thymine (T) [11]. In the case of silver nanomaterials, G and C bases exhibit higher affinities for silver ions, and guanine has the highest oxidation potential among the nucleic acid bases, which leads to the specific binding of metal ions to GC-rich DNA. Upon oxidation and binding to DNA, silver atoms can gain electrons from the reduced guanine base. A series of successive cycles of oxidation and the transfer of Ag atoms from nanoparticle to DNA results in the localization of atoms at specific sites along the DNA, or the formation of a small number of atomic silver clusters near the sites of particle binding on poly(dG)-poly(dC) molecules [10].
Continuous development has shown that DNA sequence combinations can control the different morphologies of nanoparticles during their growth, and that these effects can be synergistic or competitive. The DNA used to guide the growth of nanomaterials is stable and retains its biological recognition capabilities [12]. As a result, the synthesis of nanocrystals with controlled three-dimensional structures using DNA is both feasible and appealing. The approach using DNA enables the solution-based synthesis of nanocrystals with controlled three-dimensional structures in the desired orientation, and extends the current tools available for the design and synthesis of functionally rich nanomaterials for future translational biotechnology.
The unique properties of these DNA-guided metal nanomaterials have led to their exploration in a range of biomedical applications. Metal nanoparticles have unique optical, electronic and magnetic properties [13]. DNA-directed metallization of nanomaterials can combine the unique physicochemical properties of metal nanomaterials with the biological functions of DNA for biomedical applications, especially in biodetection, biosensing, therapy or medical imaging.

2. Strategies of DNA Functionalized Nanoseeds

The formation of metal nucleation sites depends on the binding of metal ions or complexes to DNA and their subsequent reduction to form metal clusters, or on the binding of small metal particles to DNA. In the DNA-directed assembly of nanoparticles, chemical bonds are commonly used to connect DNA to nanoparticles, such as the Au-S bond commonly used in gold nanoparticles [14][15][16][14,15,16]. Silver nanoparticles are commonly modified with DNA using disulfide, lipoic acid, or cyclic disulfide bonds [17][18][19][17,18,19]. Compared to Au-S, Ag-S chemical bonding is less stable, and, hence, SH-DNA modification of silver nanoparticles is not commonly used. Chemically bonded covalent modifications possess better specificity, but they are cumbersome to pre-modify. However, when DNA is used to guide the growth of nanomaterials, it is more common to use electrostatic or ligand interactions to bind DNA to metallic nanomaterials [20][21][22][23][24][25][26][20,21,22,23,24,25,26]. This is because the process of metallization often occurs in a solution where DNA is added to a solution containing metal ions for co-incubation [27]. The positively charged ions are attracted to the negatively charged phosphate backbone in the DNA backbone, and the DNA catalyzes their reduction, leading to the formation of metal clusters along the DNA [9]. These small clusters tend to grow into nanoparticles, and DNA strands covered with negative charges on the surface prevent aggregation. Reduction methods include chemical reduction, photochemical reduction [28][29][28,29], and electrochemical deposition [30][31][30,31]. Additionally, polymorphic DNA chains, such as polyA chains, can be rapidly adsorbed on the surface of gold nanoparticles [32][33][32,33], while silver can be specifically ligated to C bases (Ag-C) [34]. In other words, DNA can be modified on the surface of silver nanoseeds by intrinsic Ag-C ligands. The strong Ag-C ligand not only makes Ag-DNA couples easy to form, but also shows good stability under high ionic strength and high-temperature conditions [35][36][35,36].

3. DNA as Director for Nanomaterials Metallization

In this section, thwe researchers mainly focus on the use of DNA to guide the metallization of metallic nanomaterials. So far, the main discussion has been on the functionalization of nanomaterials using DNA after their synthesis, where the morphology of the nanomaterials is already determined and DNA cannot influence it. The method of seed-mediated synthesis using DNA as a director can be used to prepare nanomaterials with controlled morphology [6]. The success of this approach is mainly based on the fact that different bases of DNA have different affinities for the surface of nanomaterials, resulting in different growth rates and morphologies. For instance, taking gold nanomaterials as an example, the adsorption affinities of different bases are as follows: A > C ≥ G > T [11]. Moreover, DNA can be easily modified with various groups such as thiol groups, carboxyl groups, and amino groups, which further extends the overgrowth method to regulate the morphology of nanoparticles using nanoparticles as seeds and DNA as a guiding agent. DNA metallization can be divided into two main steps: assembling the DNA template and organizing the nanoparticles [37][38][37,38]. The first step involves activation, in which the negatively charged DNA binds to cations or nanoparticles through coordination or electrostatic interactions. The next step is reduction, in which the reducing agent converts the metal cations into initial clusters. The commonly used reducing agents in this process include chemical reagents (e.g., NaBH4, ascorbic acid), UV light, and electricity [39][40][41][39,40,41]. Finally, in the growth step, unbound or newly introduced ions/nanoparticles are further reduced or deposited on the previous metal cluster sites [42]. The shape of the generated nanostructures is mainly influenced by two factors: the initial shape of the nano-seed and the sequence and secondary structure of the DNA. The size, orientation, and anisotropy of the crystals can be regulated by controlling nanoparticle concentration, solution ionic strength, and DNA grafting density on the particles and surface. In addition, metal nanocrystals with tunable surface plasmon resonance (SPR) can be obtained by using template molecules to guide the precise growth of metal atoms along a designed template [43][44][45][46][47][48][49][43,44,45,46,47,48,49]. Proper metallization of DNA can improve its electrical conductivity while maintaining the geometric features of DNA nanostructures. This imparts magnetic and optical properties to DNA and expands its potential applications. DNA-guided metal nanocrystals can be precisely controlled relative to the SPR peak position, and their optical properties can be further enhanced by controlling their morphology [50]. Currently, gold is one of the most widely investigated metal nanocrystals. Different DNA templates produce nanocrystals with various morphologies and specific SPRs by regulating the growth of gold along the DNA backbone. As the number of metal branches guided by the template DNA increases, the surface of the synthesized nanocrystals becomes rougher, enhancing the plasmon resonance between the nanoparticle core and the branches, and leading to the maximum absorption redshift peak. Moreover, different sizes of metal branches due to different DNA structures also cause the maximum absorption wavelength to change [49][51][52][49,51,52]. Potential DNA templates have different secondary structures, such as single-stranded (ss), double-stranded (ds), hairpin (hp), and triple-junction arms (ta). Researchers have successfully synthesized several shapes of DNA-directed nanostructures, including nanoflowers, nanopolygons, nanocaps with nanobridges, and sea cucumber-like structures [53]. Some examples related to these structures are listed in Table 1.
Table 1.
DNA as director for nanomaterials metallization.

Seeds

Type of DNA Templates

Shape of Nanomaterials

References

AuNPs/AuNRs functionalized with thiol-DNA

Ribbon-like DNA origami nanostructures

1D AuNPs/AuNRs lines or

2D AuNPs lattices

[54]

30 nm AuNPs

Rectangular DNA origami

AuNP chains

[47]

Graphdiyne and HAuCl4

ssDNAs (A20)

Decahedrons, icosahedrons, or flower-like Au nanoparticles

[55]

Gold nanorods

ssDNA, dsDNA, hpDNA, and taDNA

Trepang-like AuNCs

[41]

AuNPs and Cu

Bar-shaped DNA origami

Cu-Au metal junction

[56]

Ag Nanocube

10-mer oligo-A, -T, -C

Edge-truncated octahedral, and truncated tetrahedral AgNPs

[57]

AgNO3

G-/C-Rich oligonucleotides

Silver clusters

[39]

AgNO3

Triangular DNA origami template

Ag nanoclusters

[58]

AgNO3

target DNA, its complementary sequence parts, and probe DNA G4)

Colloidal silver solution

[59]

AgNO3

Telomerase primer oligonucleotides

Silver NPs

[40]

4. Biomedical Applications

The biomedical applications of DNA-guided metallized nanomaterials are diverse and promising, with potential applications in biosensing, bioimaging, and therapy [60][61][70,71].

4.1. Biosensing

DNA-guided metallized nanomaterials can also be used for biosensing applications, such as detecting biomolecules or pathogens in biological samples. By attaching DNA or antibodies to the surface of metal nanoparticles, specific interactions with target molecules can be detected using techniques such as surface plasmon resonance or electrochemistry. Chen et al. [59] utilized Exonuclease III (Exo III) biocatalysts and silver metallization of DNA to scale up biomercaptans at picomolar concentrations. The scale-up process relies primarily on the recovery of biomercaptans, the recovery of target DNA from silver deposits, and specific interactions between the quadchain and its binding ligands. DNA-silver nanohybrids are synthesized via NaBH4 reduction of AgNO3. Building upon this research, Wu et al. [40] developed a DNA metallization-based telomerase activity assay. The method utilizes a highly characteristic solid-state electrochemical process that utilizes DNA template deposition of silver nanoparticles as an electroactive label with enzyme-assisted suppression of background signals. The ion exchange process is highly selective and limited to the DNA template, significantly improving sensing performance and reducing non-specific adsorption. Furthermore, this test does not require PCR amplification, thus avoiding related errors and contamination, and enabling a more reliable evaluation of telomerase activity in circulating tumor cells (CTCs).
DNA has a high affinity for silver ions, and these local cations can be reduced to form silver nanostructures that follow the profile of the DNA template. Thus, the formation of silver nanoparticles in the DNA scaffold would block the binding of ligands embedded in DNA and may also act as a fluorescent bursting agent when some ligands are embedded in the silver-adsorbed DNA. Lin et al. [62][72] first described the use of DNA-mediated silver nanostructures as a platform for simple, reliable, highly sensitive, and selective fluorescence-on detection of dopamine (DA). The method relies on large fluorescence enhancement through specific binding of the small molecule genefinder (GF) to dsDNA, which is released from the silver nanoparticles by DA. Hao et al. [63][73] introduced multiple electroactive probes for the rapid detection of Cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA by surface-initiated reversible addition fragmentation chain transfer (SI-RAFT) polymerization and in situ DNA metallization as a signal amplification strategy, using C3H4O as a monomer. In the case of C3H4O as a monomer, SI-RAFT polymerization can bring a large number of aldehyde sites to the subsequent silver mirror reaction. The acrolein polymer acts as a reducing agent to reduce Ag+ to AgO, and then silver particles are deposited on the polymer backbone, which significantly amplifies the electrochemical signal. Gong et al. [64][74] used the DNA-guided growth of silver nanoclusters as a template to label catalytic and molecular beacons as an amplified biosensing platform for the detection of DNAzyme cofactors such as Pb2+ and L-histidine. The introduction of target cofactors triggers enhanced the fluorescence of AgNCs, thus providing an “on” fluorescence response to the target biomolecule. The proposed sensing system shows a highly sensitive response to the target cofactor by cyclic amplification using multiple enzymatic conversions of the DNAzyme. Chen et al. [65][75] presented the first method to implement a simple and label-free bio-thiol detection platform based on silver metallization of G-quadruplex DNA to control conformational switching. A simple, label-free, highly sensitive, and selective sensor was demonstrated for the detection of biothiols based on G-quadruplex conformational transitions designed by silver metallization. The method relies on a significant fluorescence enhancement resulting from a specific interaction between the NMM and the G-quadruplex, whose conformation is recovered after the release of the biothiols from the silver deposition.
After using dsDNA to guide copper ions for metallization, they can also be used as detection probes [66][63]. Chen et al. [67][64] designed a new and simple strategy for highly sensitive and selective detection of Pb2+ using dsDNA-CuNPs as fluorescent probes. dsDNA can be used as an effective template to reduce Cu2+ by ascorbic acid to form CuNPs, and the formed dsDNA-CuNPs have superior fluorescence. Interestingly, it was found that Pb2+ could quench the fluorescence of dsDNA-CuNPs. Based on this phenomenon found in this work, a very simple and rapid method for Pb2+ monitoring was established.

4.2. Bioimaging

Similarly, DNA-guided metallized nanomaterials can also be used as contrast agents in biomedical imaging techniques such as magnetic resonance imaging (MRI) and computed tomography (CT). By attaching metal nanoparticles to DNA templates, contrast agents with high specificity and sensitivity can be designed for use in diagnostic imaging. Zhang et al. [41] produced sea cucumber-like gold nanocrystals (AuNC) with tunable plasmonic properties using DNA as a template. These sea cucumber-like AuNCs exhibit a broad absorption band in the near-infrared range (700–1100 nm) and possess good thermal stability, high photothermal conversion efficiency, and biocompatibility. They were utilized for in vitro CT imaging, dark field imaging, and photothermal therapy.
Silver nanoclusters (AgNCs) prepared using DNA as a template have become an important tool for the development of biomarkers and molecular sensors because of their good fluorescence properties, excellent photostability, sub-nanometer size, and low cytotoxicity [68][69][76,77]. The fluorescent nature of silver nanoclusters is highly dependent on the DNA sequence and sensitive to the oligonucleotide environment, which gives them potential for genetic diagnostics. It was shown that strong base-Ag+ binding and the formation of stable supramolecular structures such as i-motifs and G-quadruplexes are two important prerequisites for the formation of bright photoluminescent AgNC [70][78]. Based on this principle, combining functional motifs of DNA (e.g., aptamers) with DNA templates for fluorescent DNA/AgNCs has been used for cell type-specific imaging. Han et al. [71][79] reported the first synthesis of aptamer-AgNCs using L-DNA as a template. Compared with natural D-DNA-templated AgNCs, L-DNA-templated aptamer-AgNCs have higher nuclease resistance. This advantage makes the aptamer-AgNCs obtained by L-DNA templating more suitable for achieving cell type-specific imaging. Ran et al. [72][80] used multicolor C-rich DNA template AgNCs for the first time to simultaneously image the exogenous components of the latent fingerprint (LFP) and the LFP itself. Visualization and detection of potential fingerprints are achieved by combining DNA-regulated AgNCs with molecular conjugates.
The versatility of DNA can also be exploited to combine different functional DNAs in a single structure for bioimaging. Li et al. [73][81] designed a multifunctional DNA scaffold to synthesize AgNCs for intracellular imaging of tumor-associated mRNAs. The DNA scaffold contains three functional parts: SGC8c aptamer as a specific internalization part, fluorescent AgNCS nucleating sequences, and complementary sequences (CDNAs) that can hybridize with target DNA or RNA to alter the fluorescent properties of AgNCS. In addition, DNA-AgNCs combined with other nanomaterials can be combined to design FRET-based fluorescent probes for the fluorescent labeling of folate receptors on cancer cells [68][76].

4.3. Therapy

The use of DNA-guided metallized nanomaterials in therapy has the potential to improve efficacy and specificity. By attaching drugs to the surface of metal nanoparticles guided by DNA templates, targeted drug delivery to specific tissues or cells can be achieved [74][82]. Additionally, DNA-guided metallized nanomaterials can be designed to respond to specific environmental stimuli, such as changes in pH or temperature, leading to controlled drug release. In addition, the photothermal properties of metallic materials make them well-suited for photothermal therapy. Silver nanoparticles grown with DNA as a template are excellent platforms for gene delivery; DNA has a high affinity for silver ions and these local cations can be reduced to form silver nanostructures that follow the contours of the DNA template; the formation of silver nanoparticles (AgNP) in the DNA scaffold can spontaneously induce DNA bending and cohesion as well as negative charge shielding, which facilitates cellular internalization. Based on this, Tao et al. [75][83] reported a simple one-pot synthesis of plasmid DNA template silver nanoparticles (pDNA-AgNPs), which can be used as a platform for efficient gene delivery. The intracellular repair of plasmid DNA (pDNA) can be achieved through a glutathione (GSH)-mediated ligand exchange process, which can facilitate efficient gene delivery. The ease of synthesis and low cytotoxicity of metallized pDNA structures compared to conventional gene carriers make them suitable biocompatible nanomaterials for biomedical applications.
The nanoparticles obtained by the metallization of DNA can be used in combination with other materials for photothermal therapy. Wang et al. [76][84] combined DNA-functionalized SWCNT with DNA-guided synthesis of noble metal (Ag or Au) nanoparticles to form nanocomposites by an in situ liquid-phase synthesis method. The nanocomposites also exhibited significantly enhanced photothermal cancer cell killing due to the strong surface plasmon resonance absorption generated by the gold shells grown on the nanotube surface.
DNA-templated metallized materials can be used to act as gatekeepers for drug delivery systems. Mesoporous silica is often used to deliver drugs; however, its porous structure is prone to drug leakage. Liu et al. [77][85] proposed a method to construct silver nanoparticles (AgNP) on mesoporous silica nanospheres (MSN) through a DNA templating process. The DNA strands bound to the MSN surface can form AgNP to close the pores and reduce drug leakage. Drug release is determined by specific Ag-S interactions. Subject to varying degrees of glutathione within the tumor environment, site-specific drug release can be achieved using a controlled exchange process mediated by GSH through ligand breakdown of AgNP. This interaction does not result in the formation of toxic -SH components, making it more biocompatible. Decorating MSNs with AgNPs via a DNA templating process provides a more labor-intensive yet cost-effective and robust method of nanocarrier construction, unlike traditional covalent or non-covalent strategies. This approach can also be extended to other DNA metallization nanomaterials.
Overall, these recent examples demonstrate the potential of DNA-guided metallized nanomaterials in various biomedical applications and provide a foundation for further research and development in this field.
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