Development of Functional Materials from Rod - Like Viruses
Zhongwei Niu , Jianhua Rong , L. Andrew Lee , and Qian Wang
Cellular and Biomolecular Recognition: Synthetic and Non-Biological Molecules. Edited by Raz Jelinek
Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Developing functional materials at the nanometer (10 − 9 m) scale with well - defi ned
structures has a great impact on the fabrication of novel biomedical, optical, acous-
tic and electronic devices [1 – 6] . In particular, using biological building blocks as
templates in materials synthesis is an exciting and emerging area of research
[7 – 12] . Among all available scaffolds, viruses and virus - like particle s ( VLP s) have
attracted much attention due to their well - defi ned structural features, unique
shapes and sizes, genetic programmability, and simple and robust chemistries
[12 – 16] . The viruses provide a wide array of shapes such as rods and spheres, and
a variety of sizes spanning from tens to hundreds of nanometers. As naturally
available supramolecular systems, viruses are assembled by multiple noncovalent
interactions. These protein structures are evolutionary tested, multifaceted systems
with highly ordered spatial arrangement, and natural cell targeting and genetic
information storing capabilities. The years of dissecting the details of virus infec-
tion, replication and assembly pathways have imparted a wealth of information on
the stabilities and functionalities of these materials. The structural information
provided by X - ray crystallography, nuclear magnetic resonance studies and
previous mutagenesis studies lays the fi rm, primary foundation for viral vector
redesigns. Intricately fashioned, multifunctional viruses and VLPs for various
applications have spun off from viral vector - based gene therapy and vaccine devel-
opment founded on the polyvalent antigen display on virus coat proteins. Virus -
based assemblies and new materials development is a major hub of current
The aim of this chapter is to provide a brief overview of an important subset of
viruses, rod - like viruses, as building blocks for the development of novel nanoma-
terials through genetic and chemical modifi cations (covalent and noncovalent
chemistries), followed by the assembly of such particles into higher ordered struc-
tures (Scheme 1.1 ) . Rod - like tobacco mosaic virus ( TMV ) and M13 bacteriophage
are two leading examples as new bio - scaffolds owing to the combined chemical
2 1 Development of Functional Materials from Rod-Like Viruses
functionality of viral coat proteins, monodispersity, liquid crystalline - like organiza-
tion, and length scales that bridge the gap between top - down and bottom - up
strategies for materials development.
TMV, among other rod - like viruses (potato virus X and tomato mosaic virus),
shows an unheralded amount of research dating as far back as 1899 as an infec-
tious material  . The plant virus persists as a classic example of rod - like plant
viruses that has now been studied for over 100 years [18, 19] . Even so, the virus
as a supramolecular building block has only been recently envisioned. In this
section, we describe a simplifi ed overview of the virus pertinent to defi ning the
benefi ts of this virus as a supramolecular building block. For an in - depth review
of the virus, additional references are listed [20, 21] . The original, wild - type strain
(noted as the U1 strain) and many other variants have been extensively studied
Scheme 1.1 Schematic illustration of self - assembly and
preparation of functional materials using rod - like viruses.
1.2 Overview 3
for agricultural purposes, biopharmaceutical applications and recombinant protein
expression. The meta - stable structure, which unwinds when inside its host, exhib-
its some remarkable stability. TMV retains structural integrity even at pH from
3.5 to 9 and up to temperatures of 50 ° C. Its diameter measures around 18 nm
with a 4 - nm cylindrical cavity along the central core that runs through the entire
length of the virus (Figure 1.1 ). The length of native TMV (300 nm) is defi ned by
the encapsulated genomic RNA that stabilizes the 2130 coat proteins that assem-
ble helically around the single - stranded RNA. Interestingly, the coat protein of
TMV alone forms three different structural aggregates depending on solvent con-
ditions (i.e., helical, disk and A - protein). These structural variants and a four - layer
aggregate of TMV were crystallized and resolved at high resolution, yielding valu-
able information for understanding the assembly process of TMV  . Finally,
a great advantage has been that TMV can be economically and easily obtained in
large quantities (gram quantities) from infected tobacco plants with a simple
purifi cation procedure.
M 13 Bacteriophage
M13 is a fi lamentous bacteriophage composed of circular, single - stranded DNA,
which is 6407 nucleotides long encapsulated by approximately 2700 copies of the
major coat protein P8, and capped with fi ve copies of four different minor coat
proteins (P9, P7, P6 and P3) on the ends (Figure 1.2 ) [23, 24] . The minor coat
protein P3 attaches to the receptor at the tip of the F pilus of the host Escherichia
Figure 1.1 (a) Helical organization of TMV coat proteins and (b) cross - section of TMV.
4 1 Development of Functional Materials from Rod-Like Viruses
coli . The infection causes turbid plaques in E. coli . At other end of the fi lament are
fi ve copies of the surface exposed pIX (P9) and a more buried companion protein,
pVII (P7). These two proteins are very small, containing only 33 and 32 amino
acids, respectively, although some additional residues can be added to the N -
terminal portion of each which are then presented on the outside of the coat. The
major coat protein is primarily assembled from a 50 amino acid called pVIII (or
P8), which is encoded by gene VIII (or G8) in the phage genome. For a wild - type
M13 particle, it takes about approximately 2700 copies of P8 to make the coat
about 880 nm long. The diameter of M13 is around 6.6 nm. The coat ’ s dimensions
are fl exible and the number of P8 copies adjusts to accommodate the size of the
single - stranded genome it packages.
Programmable Protein Shells
Both viruses comprise of an outer protein shell, also known as the virus capsid,
which houses the genetic material (RNA in the case of TMV and DNA in M13).
These genetic materials possess all the essential information required for the virus
Figure 1.2 (a) TEM image of a M13 particle. (b) Schematic
illustration of the helical organization of M13 coat protein P8.
1.3 Programmable Protein Shells 5
to propagate within the host. Hence, by simply altering the genetic codes of the
viruses, in particular the gene encoding for the virus capsid, we can redesign the
outer shell of the virus with various functionalities. This trait provides an immense
advantage for biological systems over synthetic systems. By carefully manipulating
the template via genetic and chemical tools, M13 bacteriophage and TMV can be
molded with the precise control over the spatial layout of functional groups. Many
studies over the past few years highlight this ability of biological templates in
materials development. We begin with examples from chemical modifi cation of
TMV, followed by molecular cloning in combination with chemistries of both
viruses to yield highly uniform templates.
Chemical Modifi cations
Much of the initial virus chemistries resonate the conventional bioconjugation
strategies, targeting endogenous amino acids, such as lysines, glutamic or aspartic
acids and cysteines. Less commonly targeted functional groups, such as the phenol
ring of tyrosines, have also been incorporated into this chemistry strategy. The
systematic characterization on cowpea mosaic virus [25 – 29] , followed by studies
with cowpea chlorotic mottle virus, bacteriophage MS2, heat shock protein and
turnip yellow mosaic virus, has shed light on the unique chemical reactivities and
physical properties of these viruses. It has been reported that the lysines of some
fi lamentous bacteriophages could be addressed using similar bioconjugation strat-
egies [30, 31] . For TMV, only a selected tyrosine residue on the exterior of TMV
and glutamates 97 and 106 in the interior appear to be accessible based on the
crystal structure (Figure 1.3 a). Francis et al. showed that Glu97 and Glu106 can
be modifi ed by attaching amines through a carbodiimide coupling reaction  .
For the exterior surface modifi cation, Francis et al. have reported the tyrosine resi-
dues (Tyr139) of TMV as a viable site for chemical ligation using the electrophilic
substitution reaction at the ortho position of the phenol ring with diazonium salts
 . Although this reaction is very effi cient, it has two distinct disadvantages: the
synthesis of desired starting materials is diffi cult and the reaction is only suitable
for electron - defi cient anilines, which dramatically impedes its potential applica-
tions. Recently, Wang et al. have reported that an alkyne group can be quantita-
tively attached to tyrosine residues by diazonium coupling and a sequential
copper - catalyzed azide – alkyne cycloaddition reaction with azides can effi ciently
conjugate a wide range of compounds which include fl orescent dye molecules,
small peptides and polymers to the surface of TMV (Figure 1.3 )  .
Genetic Modifi cations
Many of the viruses in isolated forms are complex macromolecular assemblies of
metabolically inert molecules, which can be chemically modifi ed. Alternatively, the
viruses can be genetically reprogrammed in their hosts with foreign peptides to
express an antigen [34, 35] or to alter the affi nity of the recombinant viral particle for
6 1 Development of Functional Materials from Rod-Like Viruses
Figure 1.3 (a) Reactive sites for the covalent modifi cation of TMV, i.e., Tyr(Y)139, Glu(E)97
and Glu(E)106 are indicated in a single TMV capsid monomer. (b) Illustration of TMV
modifi cation by a two - step sequential reaction. (Part of this fi gure was adapted with
permission from  ).
different cell surface receptors [36, 37] . Furthermore, single amino acid substitu-
tion mutagenesis allows the site - specifi c incorporation of reactive amino acids,
such as lysines or cysteines, or non - natural amino acids  on the virus coat
protein for regioselective chemical modifi cations. Using such methods, Schultz
et al. have incorporated poly(ethylene glycol)  , alkyne modifi ed amino acids 
and photoisomerizable amino acids into the proteins  . In vivo and in vitro
protein expression systems derived from cell lysates have also been used to drive
viral protein synthesis with the non - natural amino acids [40, 42] . Many of the
viruses have their X - ray structures resolved at near - atomic resolution, facilitating
the generation of the recombinant nanoparticles. These alterations have ranged
from single amino acid substitutions to entire protein domain incorporations [43,
44] . To that end, the molecular cloning techniques are well integrated into the gen-
eration of hybrid viruses with novel biological, chemical and physical properties.
220.127.116.11 Genetic Modifi cation of TMV
TMV is highly immunogenic in mammalian hosts, which is ideal for adapting
TMV - based vectors for antigen display. An initial study by Haynes et al. demon-
strated the feasibility of incorporating immunogenic peptides as fusion proteins
on the plant virus capsids  . Short peptide fragments of up to 21 residues had
been repeatedly fused to the C - terminus of TMV using a leaky “ UAG ” stop codon
without losing viral replication or assembly [46, 47] . In other studies, a variety of
short inserts were made between Ser154 and Gly155 using polymerase chain
reaction - based site - directed mutagenesis [48, 49] . Longer peptide sequences of up
to 25 amino acids had also been fused to the C - terminus by deleting four to six
amino acids at the carboxyl end  . Culver et al. designed and functionalized the
cysteine - mutated TMV particles with fl uorescent dyes and the modifi ed TMV
particles were then partially disassembled to expose the single - stranded viral RNA.
The exposed single - stranded RNA strand was then utilized to hybridize to comple-
mentary DNA sequences patterned on surfaces [51, 52] . Francis et al. expressed
TMV coat protein in a bacterial system to generate cysteine - substituted TMV coat
proteins for the incorporation of light - harvesting motifs  .
18.104.22.168 M 13 Genetic Modifi cation
It is known that M13 phage is a high production rate virus, which has a single -
strand DNA, approximately 2700 copies of the P8 proteins, fi ve copies each of the
P3 and P6 proteins at one end, and fi ve copies each of the P7 and P9 proteins at
the other end. The functionalities of these protein groups localized at different
locations on a viral particle can be rationally altered independently via genetic
engineering  . One of the genetic engineering technologies, phage display, has
proven to be a powerful technology for selecting polypeptides with the desired
biological and physicochemical properties from large molecular libraries. The
phage display techniques have been reviewed extensively  . Basically, libraries
of random DNA sequences can be fused to the genes encoding coat proteins.
These are expressed and displayed as fusion peptides on the surface of the phage.
The phages are then passed over an immobilized target (such as a biological
1.3 Programmable Protein Shells 7
8 1 Development of Functional Materials from Rod-Like Viruses
receptor or inorganic substrate). Nonbinding phages are washed off, and binders
are eluted and amplifi ed in E. coli . After repeating this process several times, the
best binders are sequenced to deduce the amino acid sequences of the displayed
peptides. As an example, the type 3 library of M13 viruses is commercially avail-
able (New England BioLabs), in which the native M13 genome has been engi-
neered to express around 1 × 10 9 different random peptide sequences as N - terminal
fusions (three to fi ve copies) on the P3 viral protein coat.
In order to synthesize and assemble various inorganic nanowires, Belcher ’ s
group genetically modifi ed and expressed the P8 protein by using a phagemid
system, which resulted in the fusion of the substrate - specifi c peptides (e.g., A7,
Z8 and J140 peptides for ZnS and CdS, respectively) to the N - terminus of the P8
protein [12, 56] . A type 8 library was constructed by fusing eight random amino
acids into the N - terminus of all the P8 proteins with a random population of
10 7 – 10 8  . This library employs a modifi ed M13KE phage vector by generating
restriction sites, Pst I and Bam HI, in G8 through mutagenesis for the insertion of
random codons [G nm ( nnm ) 6 nn G], where n can be G, C, A or T and m can T or G.
Genome engineering phage employed in the type 8 library can produces 100%
expression and monodispersed viral particles  . In order to synthesize and
assemble various inorganic materials and structures, Belcher ’ s group used a
general biopanning technique to select some functional binding motifs on P8 by
exposing the type 8 phage library to certain substrate  . Weiss also reported
variants of the M13 bacteriophage that enable high - copy display of monometic and
oligomeric proteins, such as human growth hormone and streptavidin, on major
coat protein P8 of the surface of phage particles [59, 60] . Additionally, a type 8 - 3
phage could be produced with different binding motifs on both P3 and P8 proteins
by combining gene 3 (G3) and gene 8 (G8) insertions in a single viral genome
after specifi c binding motifs for targeted substrates were selected from separate
P3 and P8 libraries. Therefore, more complicated composite materials could be
produced  . In addition, P7 and P9 can also be amenable to modifi cation. Janda
et al. utilized P7 and P9 fusions to display antibody heavy and light chain variable
regions  . A hexahistidine peptide (AHHHHHH), which binds to Ni(II) - nitri-
lotriacetic ( Ni - NTA ) acid complex, was fused to the N - terminus of P9 reported by
Belcher ’ s group  .
Chemical Modifi cation in Combination with Genetic Mutation
For most of viral particles, there are no reactive cysteine residues exposed to exte-
rior surface – a reasonable assumption being that evolution had disfavored parti-
cles forming interparticle cross - links via disulfi de bonds. This presents the
unique opportunity to genetically insert the cysteine residue on strategic locations
of viruses and protein shells, after which the sulfhydryl group can be selectively
targeted with thiol - selective reagents. Culver et al. designed and functionalized
the cysteine - substituted TMV particles with fl uorescent dyes and the modifi ed
TMV particles were then partially disassembled to expose the single - stranded
1.4 Templated Syntheses of Composite Materials 9
viral RNA  . The exposed single - stranded RNA strand was then utilized to
hybridize to complementary DNA sequences patterned on surfaces [51, 52] .
Francis et al. expressed TMV coat protein in a bacterial system to generate
cysteine - substituted TMV coat proteins, which were modifi ed with fl uorescent
chromophores for the purpose of generating a light - harvesting system. By con-
trolling the pH and ionic strength, the proteins self - assembled into long fi brous
structures that were capable of positioning the chromophores for effi cient
energy transfer  . These studies highlight an important feature of viruses –
chemically reactive groups can be genetically engineered to selectively position
drug molecules, imaging agents and biologically relevant molecules on the
three - dimensional ( 3D ) template  .
Templated Syntheses of Composite Materials
Synthesis of Inorganic Materials Using TMV as the Template
The polar outer and inner surfaces of TMV have been widely exploited as templates
to grow metal or metal oxide nanoparticles such as CdS, PbS, gold, nickel, cobalt,
silver, copper, iron oxides, CoPt, FePt 3 and silica (Table 1.1 ) [13, 71 – 75] . From
electrophoretic measurements, the isoelectric point (p I ) of TMV is around 3.4. At
neutral pH, the TMV surface has net negative charge. In order to achieve success-
ful coating, the deposition conditions should be varied in order to match the
interaction between the viral surface and the deposition precursor. In the case of
silica coating, the reaction pH should be below 3  . As a result, the positively
charged TMV surface will have a strong interaction with anionic silicate sols
Figure 1.4 TEM images of (a) a single TMV containing a long
nickel wire inside the central channel and (b) nickel coated on
the outer surface of TMV. (Adapted with permission from  ).
10 1 Development of Functional Materials from Rod-Like Viruses
Table 1.1 Summary of the inorganic nanowires synthesized with native TMV as template.
Composition a) Activation b) Reducing reagent pH c) Inner/outer d)
PbS none none 5 outer 
CdS none none 7 outer 
none none 9 outer 
Silica none none 2.5
CoPt none none NA inner 
FePt 3 none none NA inner 
Ni Pd(II) or Pt(II)
borane ( DMAB )
5 inner [67, 68]
inner [67, 68]
Co Pd(II) or Pt(II)
DMAB 5 inner 
inner and outer 
Ag none formaldehyde NA outer 
Au none ascorbic acid 6 inner and outer 
Ru none NaH 2 PO 2 or
NA inner and outer 
Cu Pd(II) DMAB 7.5 inner 
a) The fi nal composition of the surface coating on TMV.
b) The predeposition of reducing reagents; “ none ” = no a ctivation wa s neces sary.
c) NA = pH value not mentioned in the original literature.
d) Indicates the deposition was either inside the inner channel or at the outer surface of TMV.
formed by the hydrolysis of tetraethyl orthosilicate. In comparison, CdS, PbS and
iron oxide can be successfully coated on the outer surface at near - neutral pH by
specifi c metal - ion binding with the glutamate and aspartate residues  . As for
metal deposition, in some case, a suitable activation agent is needed in order to
realize successful coating  . Pd(II) and Pt(II) are two typical activation agents.
The metal deposition can happen either inside the inner channel or at the outer
surface of TMV (Figure 1.4 )  . Furthermore, genetically engineered TMV can
improve deposition of metal onto the surface [76, 77] . Basically, native TMV was
genetically altered to display multiple metal - binding sites through the insertion of
two cysteine residues within the N - terminus of the virus coat protein. In situ
chemical reductions can successfully deposit the silver, gold and palladium clus-
ters coating onto the genetically modifi ed TMV without any activation agent. In
comparison to native TMV, a much higher density of metal coating was observed
on the cysteine - inserted TMV.
Bacteriophage M 13 as the Template
The M13 viral system is an attractive template for the synthesis and assembly of
various materials and structures because of the programmable protein function-
alities by genetic engineering and chemical modifi cation, as mentioned previously.
In 1992, Stanley Brown pioneered the idea of using bacterial display for the screen-
ing and binding of inorganic materials  . Belcher et al. extended this phage
display technique to decorate M13 virus with different binding peptides with
specifi c recognition for inorganic materials, such as semiconductor materials (e.g.,
GaAs, InP, ZnS and CdS) and magnetic materials like FePt, CoPt, cobalt and metal
gold, or composites of them (Table 1.2 ) [14, 56, 76, 79, 82] . One of the advantages
of this idea is that exact genetic copies of the virus scaffold are easily reproduced
in the bacterial host because the protein sequences responsible for these attributes
are gene - linked and contained within the capsid of the virus. Another advantage
is that the exquisite structure of virus leads to a viable means of synthesizing and
1.4 Templated Syntheses of Composite Materials 11
Table 1.2 Summary of the inorganic nanowires synthesized with native M 13 as template.
Composition Location Binding
ZnS P3, P8 A7 CNNPMHQNC wurtzite [12, 14, 56, 79]
ZnS P3, P8 Z8 VISAHAGSSAAL zinc blend 
CdS P3, P8 J140 SLTPLTTSHLRS wurtzite 
Streptavidin P3 s1 SWDPYSHLLQHPQ [58, 80]
Ni P9 Ni -
CoPt P3, P8 CP7 CNAGDHANC 
FePt P3, P8 FP12 HNKHLPSTQPLA L10 [14, 81]
Au/CaSe P8/P3 P8#9/
Co 3 O 4 P8 E4 EEEE 
Au/Co 3 O 4 P8 AuE4 LKAHLPPSRLPS/
Single - letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp;
E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg;
S, Ser; T, Thr; V, Val; W, Trp; Y, Tyr.
12 1 Development of Functional Materials from Rod-Like Viruses
organizing materials on the nanometer scale. In contrast to traditional synthetic
methods, this approach allows for the precise control of the crystallinity of the
materials by directing nucleation of materials on the nanometer scale at low
temperature, which is an exciting new development.
The mineralization of the ZnS systems is a good example to show the merit of
M13 - based nanowire synthesis [14, 56] . In particular, one phage - bound peptide
sequence, named A7, was selected for ZnS, showing a nice control of the size and
shape of the fi nal ZnS particles at room temperature under aqueous conditions.
The synthesis process involved incubating the viral template with metal salt precur-
sors at low temperature and annealing the mineralized viruses at high temperature.
The results showed that the A7 peptide induced the nucleation and separated
wurtzite ZnS grown on the virus surface with preferential orientation before
annealing  . Upon annealing to remove the organic template and minimize of
the interfacial energy, the polycrystalline assembled to form single - crystal nanow-
ires still retaining the wurtzite phase and original orientation. The CdS nanowire
with the wurtzide phase and CoPt or FePt nanowires with the L1 0 phase prepared
from genetic modifi ed M13 virus were also prepared using similar method. Figure
1.5 and Table 1.2 show some representative results from Belcher ’ s group.
Furthermore, more complicated nanostructures can be produced by incorporat-
ing two or more fusion proteins. The engineering of specifi c receptors at the ends
of the phage enables networks and other assemblies with predictable structures,
specifi c characteristics and defi ned properties to be created. For example, Belcher
et al. have used mutated M13 phages with both P8 and P3 engineered as templates
to assemble gold and CdSe nanocrystal/hetero - nanocrystal arrays and gold nanow-
ires [58, 83] . In another example, two kinds of materials - specifi c peptide motifs
(AuE4) were engineered together into the major coat P8 protein, which resulted
in a hybrid Au − Co 3 O 4 nanowire  . Those works demonstrate that various
substrate - specifi c motifs can be independently selected from type 8 or type 3 librar-
ies and then genetically incorporated into M13 structures to produce versatile
hybrid materials with heterofunctionality.
Self - Assembly of Rod - Like Viruses
Compared to synthetic particles, viruses are truly monodisperse at the nanometer
scale, and are thus ideal for the self - assembly study and construction of uniform
nanostructured materials. TMV and M13 bacteriophage are widely used as build-
ing blocks to construct unique one - dimensional ( 1D ) fi bers, two - dimensional ( 2D )
thin fi lms and 3D liquid crystal - like structures.
Figure 1.5 (a) I llustration d epicting A 7 pept ide
expression on the P8 upon phage amplifi cation
and assembly, and then the subsequent
nucleation of ZnS nanocrystals. Call - outs
depict insertion of the A7 nucleotide
sequences, resulting in A7 fusion protein
shown as green - shaded areas. Additionally,
the call - out of the engineered virus shows
detail of the wild - type P8 and the A7 -
engineered P8 composing the viral coat.
(b) Higher magnifi cation scanning TEM
( STEM ) im ages o f A 7 – P8 - engineered v iruses
directing ZnS nanocrystal synthesis at 0 ° C,
showing an individual viral ZnS – virus
nanowire. (c) High - angle annular dark fi eld
( HAADF ) STEM image of a straight region of a
viral nanowire at higher magnifi cation showing
the close - packed ZnS nanocrystal morphology.
(Inset) Electron diffraction pattern, taken from
the area shown in (c), shows the hexagonal
wurtzite ZnS structure. (d) Images and
characterization of ZnS – CdS hybrid nanowires
prepared from viruses expressing a stochastic
mixture of both the A7 – P8 and J140 – VIII
fusion proteins by using CdS/ZnS nanocrystal
synthesis at 25 ° C. HAADF STEM image of a
viral CdS and ZnS hybrid layered structure.
Inset: Electron diffraction pattern of the
layered structure showing the coexistence of
wurtzite CdS and ZnS phases. (e) HAADF
STEM image of the layered structure at higher
magnifi cation. Inset: Cartoon illustrating the
layered structure composed of viruses and
nanocrystals. (Adapted with permission from
1.5 Self-Assembly of Rod-Like Viruses 13
14 1 Development of Functional Materials from Rod-Like Viruses
Controlled 1 D Assembly
Developing 1D functional structures on nanometer scales defi nes a new paradigm
in the fabrication of novel biomedical, optical, acoustic, electronic and magnetic
materials and devices. Numerous methods have been developed for the synthesis
of 1D nanostructures, with advances often being sought in terms of structural
control and ease of processing. Using biological building blocks as templates in
1D materials synthesis is an exciting and emerging area of research. In addition
to using native viral particles as templates to construct inorganic nanowires, a
number of efforts have been reported to control the 1D assembly of TMV and M13
22.214.171.124 TMV Head - to - Tail Assembly
A head - to - tail ordered assembly of wild - type TMV has often been observed as very
likely a product of complementary hydrophobic interactions between the dipolar
ends of the helical structure [64, 84 – 87] . In particular, the 1D assembly is dramati-
cally favored in an acidic environment due to the minimization of the repulsion
between the carboxylic residues at the assembly interface  . The exterior surface
of TMV is highly charged and hydrophilic. The particles carry negative charges at
neutral pH since the p I of TMV is around 3.4  . Therefore, a monomeric mol-
ecule with an amino group (or other positive charged groups), such as aniline, can
accumulate on the surface of TMV due to the electrostatic attraction or hydrogen
bonding to the negatively charged surface residues of TMV. An in situ polymeriza-
tion should be able to produce a homogenous layer of polymers on the surface of
TMV and fi x the head - to - tail assembled tube - like structure.
For example, TMV/ polyaniline ( PANI ) composite fi bers were produced by the
attraction of aniline (and also PANI) to the surface of TMV at neutral pH and a
sequential in situ polymerization. As shown by transmission electron microscopy
( TEM ) and atomic force microscopy ( AFM ), the length of such fi bers can reach
several micrometers (Figure 1.6 ). The diameter of fi bers increased to 20 nm in
comparison to 18 nm of the original TMV measured with TEM (Figure 1.6 b). The
inner channel could not be detected even after negative staining and no visible
gap could be detected from a long composite fi ber (Figure 1.6 d). This indicates
that the head - to - tail protein – protein interaction leads to the formation of fi ber - like
structures. Such interaction, in principle, is identical to the subunit interactions
at any cross - section of the native TMV [85, 90] . In addition, there was no solution
PANI formed in the reaction. It is possible that the local concentration of aniline
on the TMV surface was much higher than in solution; therefore, in situ polym-
erization was able to produce a thin layer of polymers exclusively on the surface
of TMV and fi x the head - to - tail assembled tube - like structure. The intrinsic aniso-
tropic morphology of PANI at dilute polymerization conditions further assisted
the 1D nanofi ber formation.
By combining electron microscopy and AFM, the length and surface morphol-
ogy of TMV and composite fi bers can be readily investigated. However, samples
1.5 Self-Assembly of Rod-Like Viruses 15
prepared on substrates for electron microscopy and AFM characterization upon
drying can potentially alter both their diameter and surface morphology due to the
interaction between the surface proteins and substrate  . To complement the
TEM data, small angle X - ray scattering ( SAXS ) and in situ time - resolved SAXS
( TRSAXS ) on solution samples were performed to understand the kinetics of
PANI/TMV composite nanofi ber formation  . The difference in cross - sectional
structure between wild - type TMV and PANI/TMV was revealed by fi tting of the
SAXS data using GNOM software [92, 93] . The largest dimension along the cross -
section ( D ) obtained for TMV was around 18 nm, which was consistent with the
TMV crystal structure. For the PANI/TMV, the maximum cross - sectional dimen-
sion was 30 nm and this increase in length scale could be attributed to the PANI
coating of TMV.
Therefore, there are two crucial factors that facilitate the formation of long 1D
TMV - composite fi bers: (i) accumulation and polymerization of monomers on the
surface of TMV, and (ii) prolongation and stabilization of TMV helices. The inter-
action between monomers and TMV is essential for the long fi ber formation. For
example, when thiophene was employed as the monomer under a similar polym-
erization condition, there was no formation of any fi ber - like structures, likely due
to the much weaker interaction between thiophene and the surface of TMV. To
Figure 1.6 TEM images (a and b) and AFM images (c and d) of PANI/TMV nanofi bers.
16 1 Development of Functional Materials from Rod-Like Viruses
further confi rm this, an amino - functionalized thiophene salt was used as the
charged monomer, and 1D long fi bers were readily observed when a mixture
of TMV and amino - functionalized thiophene salt was treated with oxidative
regents  .
126.96.36.199 Conductive 1 D TMV Composite Fibers
It is known that the pH of the polymerization reaction has a great infl uence on
the structure and conductivity of PANI. At near - neutral reaction pH, long 1D
PANI - coated TMV single nanofi bers formed upon treating TMV with a dilute
solution of aniline and ammonium persulfate. However, such nanofi bers
exhibited a homogeneous diameter and high aspect ratio, but no conductivity,
likely due to the branched structures of PANI. In order to form conductive
PANIs, polymerization reactions were performed under acidic conditions.
However, at low reaction pH, only bundle - like structures consisting of parallel
arrays of nanofi bers were formed. A standard four - probe method was employed
to measure the conductivity of PANI/TMV composite nanofi bers. At room
temperature, the bulk DC conductivities measured were in the range of 0.01 –
0.1 S cm − 1 for composite nanofi bers synthesized at low reaction pH (2.5 and 4.0).
This is comparable to the PANI nanofi bers synthesized by other methods  .
No conductivity was observed for the composite nanofi bers formed at a higher
To generate well - dispersed conductive fi bers, highly negative charged poly -
(sulfonated styrene) ( PSS ) was used both as the dopant acid to enhance the con-
ductivity of PANI and to improve the stability of composite fi bers in aqueous
solution. The resulted PSS/PANI/TMV composite was formed as predominantly
isolated fi ber, which could be well - dispersed in a dilute water solution (Figure 1.7 ).
Electronic properties measured using scanning spreading resistance microscopy
indicated a conductivity of around 1 × 10 − 5 Ω − 1 cm − 1  .
188.8.131.52 Weaving M 13 Bacteriophage into Robust Fibers
Silk spiders and silk worms can spin highly engineered continuous fi bers by
passing aqueous liquid crystalline protein solution through their spinneret. By
mimicking this process, Belcher et al. used the electrospinning method or wet -
spinning process to spin native M13, genetically engineered M13 and quantum
dot s ( QD s) conjugated M13 into robust 1D long fi bers with the diameters from
tens of nanometers to micrometers [96, 97] . In order to obtain continuous fi ber,
the virus solution was mixed with polyvinylpyrolidone ( PVP ) to improve process-
ing ability  . The resulting virus - blended PVP fi bers were transformed into
nonwoven fabrics that retained their ability to infect bacterial hosts. By chemically
conjugated amine - terminated cadmium selenide QDs to M13 templates via the
carboxylic acid side groups displayed on the P8 proteins, a continuous fi ber
of micrometer - scale diameter (microfi ber) was created through a wet - spinning
process while a concentrated QD - conjugated virus solution was spun vertically into
glutaraldehyde solution (Figure 1.8 )  . The M13 fi bers containing QDs emitted
red light under exposure to ultraviolet ( UV ) light. These composite fi bers have
potential applications in optical devices and advanced sensors.
184.108.40.206 Nanoring Structure
As described earlier, both P3 and P9 proteins that reside at the end of the M13
virus can be used to display peptide, which enable the creation of some other
interesting structures, such as rings, squares and other arrays. For example, the
bifunctional viruses displayed an anti - streptavidin peptide (binding streptavidin)
and hexahistidine peptide (binding to Ni - NTA) at opposite ends of the virus as P3
and P9 fusions, respectively. Stoichiometric addition of the streptavidin – Ni - NTA
linker molecule led to the reversible formation of nanorings with circumferences
corresponding to the lengths of the DNAs  .
Fabrication of Thin Films by 2 D Self - Assembly
Mirkin ’ s research group reported a direct - write lithographic method that can
directly write TMV onto a nanopatterned surface  . This method was the so - called
dip - pen nanolithography ( DPN ). TMV nanoarrays were fabricated by initially gen-
erating chemical templates of 16 - thiohexadecanoic acid ( MHA ) on a gold thin fi lm
by using DPN. By immersing the substrate in an alkanethiol solution, the regions
surrounding these features were passivated with a monolayer of 11 - thioundecyl -
penta (ethylene glycol). The passivation layer can avoid nonspecifi c binding between
TMV and the unpatterned areas. The carboxylic acid groups of MHA were coordi-
nated to Zn 2+ ions. The metallated substrate was then exposed to TMV solution.
Individual TMV particles can be selectively attached to the substrate (Figure 1.9 ).
Using this method, it was possible to isolate and control the orientation of TMV
Figure 1.7 (a) Schematic illustration of 1D conductive
polymer/TMV composite fi ber. (b) TEM image of PSS/PANI/
TMV composite long fi ber. (c) TEM image of PSS/polypyrrole/
TMV composite long fi ber.
1.5 Self-Assembly of Rod-Like Viruses 17
18 1 Development of Functional Materials from Rod-Like Viruses
Figure 1.8 Images and schematic design of
chemically and engineered functional fi bers.
(a) Fluorescence microscopy image of a
genetically engineered M13 virus fi ber
conjugated with QDs excited by using UV
light. (b) Under exposure to UV light, virus
fi bers conjugated with QDs emit red light and
nonconjugated virus fi bers emit blue light.
(c) The mutated M13 shows a relatively
higher intensity of light emission than the
wild - type M13KE virus after QD conjugation.
(d) Schematic illustration of electric spinning
and genetic modifi cation of M13. LC = liquid
crystalline. (Adapted with permission from
particles in a well - defi ned manner. Culver ’ s research group reported another
method to align genetically modifi ed TMV on the substrate  . Briefl y, genetically
modifi ed TMV nanotemplates were fi rst labeled with fl uorescent markers and
partially disassembled by alkaline treatment. Results demonstrated that high
spatial and sequence specifi city are obtained during nanotemplate hybridization,
including density control through the modulation of capture DNA concentration.
Recently, Velev et al. reported a single - step technique for depositing hierarchi-
cally ordered and aligned arrays of TMV particles over macroscopic length scales
using convective alignment  . Shear - induced alignment is responsible for the
long - range organization during the coating process with viscous TMV suspen-
sions. The overall assembled fi lm structure was controlled by the operational
parameters, including withdrawal speed and substrate wettability. Gold nanopar-
ticles could be selectively attached onto the fi ber surface. This allowed the forma-
tion of large uniform coatings with anisotropic conductivity. Using a similar
methodology, well - ordered monolayer fi lms were generated using the TMV as a
model anisotropic colloid. This convective assembly process rapidly generated
fi lms several centimeters in length with all the rods aligned parallel to the direction
of assembly  .
The self - assembly of nanoparticles at fl uid interfaces, driven by the reduction in
interfacial energy, has been well established. The energetic penalty associated with
the formation of an interface is given by the product of the total area of the inter-
face and the interfacial energy [101, 102] . Particles dispersed in one of the phases
will segregate to an interface so as to mediate interactions between the fl uids.
Consequently, the segregation of particles to the interface acts to stabilize the
interface. Rod - like TMV can self - assemble at the interface of water and hexane to
give a long - range parallel structure.
Controlling the 3 D Assembly of TMV and M 13
TMV can be arranged in 3D structures [103 – 105] . Nematic liquid crystals of TMV
were used to prepare silica mesostructures and nanoparticles with parallel or radial
arrays of linear channels, respectively  . The mesostructures were produced as
micrometer - size inverse replicas of the nematic phase and had a periodicity of
Figure 1.9 Schematic illustration of selective immobilization
of a single virus on DPN - generated MHA nanotemplates
treated with Zn(NO 3 ) 2 · 6H 2 O. PEG - SH = poly(ethylene
glycol) - thiol. (Adapted with permission from  ).
1.5 Self-Assembly of Rod-Like Viruses 19
20 1 Development of Functional Materials from Rod-Like Viruses
approximately 20 nm. The general stability of TMV liquid crystals suggests that
this approach may also be used to prepare a wide range of inorganic oxides,
semiconductors and metal - based mesoporous materials.
Just like any rod - like viruses, fd and M13 phages can also form liquid crystals
[79, 107, 108] . Belcher ’ s group reported the evidence of chiral smectic C structures
of M13 virus - based fi lms – a conformation arising from the helical structure of
M13 [79, 109] . The most interesting work was that they had used the viral –
inorganic hybrid materials prepared from genetically modifi ed viruses as the basic
building block for materials design, which will show great potential for tunable
devices. For example, high concentrations of genetically engineered viruses were
suspended in ZnS precursor solutions to form viral – ZnS nanocrystal liquid crys-
talline suspensions with smectic to cholesteric phases at different concentrations
of virus. The ZnS nanocrystals and M13 viral systems could form a self - supporting
hybrid fi lm material retaining the smectic - like lamellar morphologies when dried
in high concentration. Optical characterization revealed that the fi lms were com-
posed of around 72 - µ m periodic dark and bright band patterns that corresponded
to the chiral smectic C structure (Figure 1.10 ). A periodic length of 895 nm was
observed, corresponding to the combination of virus length (860 – 880 nm) and
nanocrystal aggregates (around 20 nm) by scanning electron microscopy. The
surface morphology of the viral fi lm exhibited zig - zag chiral smectic O patterns
due to the long rod shape of the viruses conjugated to an inorganic head group
composed of ZnS nanocrystals. The viral fi lm cast on different substrates could
form different liquid crystal phases.
Using the streptavidin - binding M13 mutants, Belcher et al. showed a universal
approach with which any materials, such as inorganic gold nanoparticles, organic
fl uorescent dyes (fl uorescein) and biological molecules ( R - phycoerythrin), were
able to be aligned in a similar fashion as the ZnS was in viral fi lms  . Moreover,
because of the ease of genetic engineering of M13, it is possible to assemble a
diversity of M13 - based composites with more complex structural features and
specifi c functions [16, 97] .
Virus - Based Device and Applications
The practical use of rod - like viruses is to render them with new functionalities, to
assemble them into different hierarchical structures and to incorporate them into
devices. Balandin et al. reported that hybrid virus – inorganic nanostructures, which
consist of silica or silicon nanotubes deposited on TMV, had potential application
in nanostructure - based nanocircuits  . The confi ned acoustic phonons were
found to be redistributed between the nanotube shell and the acoustically soft virus
enclosure. As a result, the low - temperature electron mobility in the hybrid virus –
silicon nanotube increased by a factor of 4 compared to that of an empty silicon
nanotube. Recently, Francis et al. reported that TMV could be used for the con-
struction of light - harvesting systems through self - assembly  . The building
1.6 Virus-Based Device and Applications 21
Figure 1.10 Characterization of mutant
M13 – ZnS fi lm. (a) Photograph of A7 – ZnS
viral fi lm. (b) POM (203) birefringent dark
and bright band patterns (periodic length
72.8 mm) were observed. These band patterns
are optically active, and their patterns reverse
depending on the angles between polarizer
and analyzer. (c) Schematic structural
diagram of the A7 – ZnS composite fi lm.
(d) AFM image of the free surface. The M13
phage forms parallel aligned herringbone
patterns that have almost right angles
between the adjacent director (arrows).
(Adapted with permission from  ,
Copyright by AAAS).
blocks were prepared by attaching fl uorescent chromophores to cysteine residues
introduced on TMV coat proteins. When placed under the appropriate buffers,
these conjugates could be re - assembled into stacks of disks or into rod - like par-
ticles that reached hundreds of nanometers in length. By controlling the assembly
state, the effi ciency of energy transfer could be controlled.
Yang et al. recently reported that TMV, decorated with platinum nanoparticles,
could be embedded in a nonconductive polymer to form a sandwich - like structures
between two metallic electrodes  . It was a prototype of memory device based
on conductance switching, which leads to the occurrence of bistable states with
an on/off ratio larger than three orders of magnitude. The mechanism of this
process was attributed to charge trapping in the nanoparticles for data storage and
a tunneling process in the high conductance state. Although many questions
22 1 Development of Functional Materials from Rod-Like Viruses
concerning the switching mechanism were not answered, this research directed
the use of biological objects as basic building blocks in electronic memory devices.
As described above, Co 3 O 4 and hybrid Au − Co 3 O 4 - based composite nanowires
can be fabricated using genetically engineered M13 virus as template  . These
wires had very good specifi c capacity, and the Au − Co 3 O 4 hybrid composite gener-
ated higher initial and reversible lithium storage capacity than the pure Co 3 O 4
nanowires when tested at the same current rate. Combining the self - assembly of
M13 phages on polyelectrolyte multilayers  and the nanowire synthesis, 2D
ordered monolayers of Co 3 O 4 or Au – Co 3 O 4 nanowires were produced, which were
utilized as electrodes for lithium - ion batteries  . The capacity test showed that
the assembled monolayer of Co 3 O 4 nanowires/Li cells could sustain and deliver
94% of its theoretical capacity at a rate of 1.12 C and 65% at a rate of 5.19 C, dem-
onstrating the capability for a high cycling rate. These results show that basic
biological principles can be applied to the rational design and assembly of nanoscale
battery components, leading to improved performance in properties such as spe-
cifi c capacity and rate capability. Additionally, the ease of genetic modifi cation of
the M13 virus allows for the preparation and assembly of many functional nano-
materials for applications such as light emitting displays, optical detectors, photo-
voltaic devices, magnetic storage, high - surface - area catalysts, medical diagnostics
Nanotechnology revolves around the controlled design, synthesis, and application
of particles at the atomic and molecular scales. Viruses decorated with various
small molecules to target cells have already demonstrated specifi c cell - targeting
ability. Furthermore, the nanosized probes can be modifi ed with bioimaging
agents such as near - infrared fl uorescent dyes and magnetic contrast imaging
agents at high local concentrations to increase detection sensitivity [113 – 115] .
In particular, rod - like viruses, including TMV and M13, which are extremely dif-
fi cult to synthesize in the laboratory, are attractive for use as scaffolds for the
development of novel functional materials at the nanometer level due to their
anisotropic structural features. They have four unique advantages compared to
most synthetic particles:
(1) The 3D structures can be characterized at the atomic or near - atomic level.
(2) Potential of controlled self - assembly in a broad length scale.
(3) Genetic control over the composition and surface properties.
(4) Monodispersed particles and economic large - scale production in gram and
Therefore, by embracing surface modifi cation to further enhance their physical
properties and retaining the biological origins for genetic alterations, rod -
like viruses will have great potential in the development of new materials for
biomedical and electronic applications.
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