A quartz crystal microbalance-based molecular ruler for biopolymersw

Hongwei Ma,*ab

Jian’an He,bZhiqiang Zhu,

cBei’er Lv,

aDi Li,

c

Chunhai Fancand Jing Fang

b

Received (in Cambridge, UK) 16th September 2009, Accepted 18th November 2009

First published as an Advance Article on the web 9th December 2009

DOI: 10.1039/b919179h

We developed a quartz crystal microbalance (QCM) based

molecular ruler that measures the length of surface immobilized,

hydrated biopolymers (DNA and proteins). These biopolymers

acted as stakes that solidified surrounding liquid at high

frequency vibration in QCM measurements, which led to a

simple linear frequency–thickness relation.

Many biopolymer interactions are accompanied with size

changes, such as antigen–antibody recognitions, RNA–protein

interactions and DNA hybridizations, etc. The ability to

accurately measure these changes greatly affects our under-

standing of the life process and our ability in designing

molecular machines. Sophisticated instrument and complex

techniques have been applied to measure the size change of

these activities, including neutron scattering,1 atomic force

microscopy,2,3 Forster resonance energy transfer and nano-

particle plasmonics.4,5 While proving efficient, these methods

are only affordable by a few laboratories and they do not

satisfy the routine need of many chemists and biologists.

Quartz crystal microbalance (QCM) is mainly used as a

mass sensor.6,7 It is also used as an online thickness-monitoring

device specifically in the vacuum deposition industry since the

Sauerbrey eqn (1) predicts a simple linear relationship between

the frequency change (Df) and area averaged mass change

(Dm = Tr), where T is the thickness increase and r is the

density of deposited metal:6

Dm = �CDfn/n (1)

where Dfn and fn are the frequency shift and the resonance

frequency at overtone number n, respectively; fn = nf0, n = 1,

3, 5, 7, 9, 11, 13. . .; constant C is 17.7 ng cm�2 Hz�1 for an

AT-cut, 5 MHz crystal. Recently, such simple linear frequency

and thickness change relation (f–T) was also found for

polymers in air.8–11 Furthermore, for QCM in liquid environ-

ment, such simple f–T relation was true but limited to a certain

working thickness range. For example, we found that a

number of polymers exhibited such simple f–T relation if the

dry film thickness was less than 40 nm (note that the wet

thickness would be much higher due to the swelling behavior

of polymer brushes).8–10 Those observations led us to explore

whether QCM operated in liquid environment could be used

as a molecular ruler. We will demonstrate below that QCM

could indeed measure the length of hydrated biopolymers.

A general physical image is shown in Scheme 1. For a QCM

chip immersed in liquid, biopolymers were covalently immobilized

on to the gold electrode surface of a QCM chip.

According to the continuous mechanical model,12 there are

two interfaces and two bodies. The first interface is between

the gold electrode and the first body (denoted as Box 1

thereafter) that contains biopolymers and surrounding liquid.

Box 1 is characterized by four parameters, namely elasticity

(m1), viscosity (Z1), density (r1) and thickness (T1), where the

subscript 1 indicates Box 1. The thickness of Box 1 is

determined by the length of hydrated biopolymers. The second

interface lies between Box 1 and the second body (Box 2),

which has a semi-infinite thickness compared with the

penetration depth of an acoustic wave.9,13 Note that Box 2

contains only liquid, characterized by two parameters, ZL and

rL, where the subscript L indicates liquid.9,14

We wish to propose a simple model that consists of two key

aspects: (i) the immobilized biopolymers acted as stakes that

solidified liquid under high frequency vibration, (ii) the

frequency change due to this solidified liquid (Box 1 in

Scheme 1) could be converted to mass change according to

eqn (2) and (3). Note that eqn (2) is similar to eqn (1):

Dm1 = r1T1 = ZqA/2f02 (2)

=�Dfn = A�n + B�n2 (3)

Scheme 1 Physical image of a continuum mechanical model is

presented with parameters that determine the frequency response of

quartz crystal microbalance. The stakes could be DNA and proteins.

See text for details.

a Suzhou Institute of Nano-Tech and Nano-Bionics,Chinese Academy of Sciences, Suzhou 215125, P.R. China.E-mail: hwma2008@sinano.ac.cn; Fax: 0086 512 62872562;Tel: 0086 512 62872539

b Biomed-X Research Center, Academy of Advanced InterdisciplinaryStudies, Peking University, Beijing 100871, P.R. China

c Shanghai Institute of Applied Physics Chinese Academy of Sciences,Shanghai 201800, P.R. Chinaw Electronic supplementary information (ESI) available: Materials,QCM monitoring of IgG and anti-IgG immobilization, stem-loopDNA immobilization and hybridization. See DOI: 10.1039/b919179h

This journal is �c The Royal Society of Chemistry 2010 Chem. Commun., 2010, 46, 949–951 | 949

COMMUNICATION www.rsc.org/chemcomm | ChemComm

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where r1 and T1 are the density and thickness of the solidified

liquid, respectively; Zq = 8.8 � 106 kg m�2 s�1 is the acoustic

impedance of the crystalline quartz.

In a recent report,10 we found that by fitting the data

according to eqn (3), the frequency changes contributed by

mass changes could be separated from that contributed by

viscoelasticity changes. The fitted value A contains only the

wet mass (i.e., biopolymers with solidified liquid), free of

viscoelastic contribution. Thus, one could calculate the

thickness of hydrated/swelled biopolymers if the density of

Box 1 was known. And we will prove below that the density of

Box 1 could be approximated as the density of liquid itself

(i.e., the density of PBS buffer). Two types of biopolymers,

namely DNA and protein IgG were tested to validate our

proposed model and their hydrated lengths were successfully

determined.

The first tested biopolymer was IgG immobilized to a

self-assembled monolayer of 11-mercaptoundecyl-tri(ethylene

glycol) (EG-SAM).15z This EG-SAM was further converted to

carboxyl acid terminated SAM so that IgG could be covalently

immobilized to the QCM surface. A high concentration of IgG

solution (50 mg mL�1) was used to ensure that a dense layer

of IgG was achieved. Anti-IgG at 50 mg mL�1 was then

followed that induced Df by specific interaction (Fig. 1). Both

immobilizations led to a thickness increase of Box 1. The

frequency changes were DfIgG = �122.1 Hz and Dfanti-IgG =

�160.4 Hz (overtone number n = 3), which were converted to

A values according to eqn (3): AIgG = 41.3 Hz and Aanti-IgG =

58.7 Hz. The negligible B values (BIgG = �0.04 Hz and

Banti-IgG = �0.45 Hz) indicated the viscoelasticity changes

were minimal. We noticed that according to our solidified

liquid model (i.e., taken the protein and PBS as Box 1 and

approximately the body density as of PBS at 1.100 g mL�1),

the thickness of Box 1 were 6.6 nm and 9.4 nm, very close to

the height of a densely packed layer of IgG and anti-IgG,

respectively.16 Furthermore, literature reports indicated the

density of this IgG layer was 1.47 ng mm�2,17 corresponding

to a dense packing of 1.27 � 1011 IgG molecules on the active

area of QCM electrode (a circle of diameter at 5 mm), which

would only cause 8.9 Hz change. This discrepancy (41.3 vs. 8.9 Hz)

was most commonly explained as 1 part protein had 4 parts of

entrapped liquid.18 Unfortunately, no attention was paid to

the coincidence of the thickness match between Box 1 and IgG

layer. Thus, one could immobilize any other proteins, measure

Dfprotein and calculate their hydrated lengths (note that it will

be an effective length or assuming all proteins shared the same

orientation).

Second, we applied DNA molecules with stem-loop struc-

ture to further validate our hypothesis. The DNA sequences

used here have been well studied. Therefore, their structural

changes upon hybridization of complementary strands were

quantitatively known.2,19,20 As illustrated in Fig. 2, the ssDNA

with preformed stem-loop structure was first co-immobilized

with 6-mercapto-1-hexanol (MCH), followed by the injection

of complementary strands. MCH was known to force ssDNA

extending from surface to solution, which would increase

the effectiveness of hybridization. Hybridization of the

complementary strand led to the formation of rigid dsDNA

that would again increase the effective thickness of Box 1.

Although mechanistically different, both the immobilization

of ssDNA and formation of dsDNA led to effective thickness

changes (DTeff) of Box 1.1,2 Two values were obtained: Dfim =

�95.5 Hz (i.e., S2 � S1) and Dfhy = �185.8 Hz (i.e., S3 � S1),

corresponding to 4.4 and 9.2 nm of the thickness increase of

the solidified layers S2 and S3 in Fig. 2, respectively. These two

thickness values agreed well with literature values determined

via neutron scattering method (4.7 and 9.4 nm).1 Furthermore,

the agreement between thickness change and frequency change

induced by hybridization also supports our hypothesis that

under specific conditions, QCM responds to layer’s thickness

change rather than mass change: the mass of DNA was

doubled if one assumed a 100% hybridization efficiency

but one could still use the density of PBS to get a correct

estimation of the length of hydrated dsDNA molecules.

In conclusion, we presented herein a QCM based molecular

ruler: surface tethered biopolymers could solidify liquid. QCM

sensed this Box 1 as a solid so that a simple f–T relation held

true. This simple f–T relation in turn enabled us to calculate

the length of hydrated biopolymers, which typically required

the use of sophisticated instrument and complex techniques.

This molecular ruler is extremely sensitive in that only 0.16 nm

of length change is required to induce 1 Hz of frequency

change in PBS: the PBS/liquid acted as amplifier. This model is

proved to be true for cases where mass changes and

viscoelasticity changes were relative small or negligible and

Box 1 has a known density (i.e., that can be approximately

treated as the density of buffer used). This proposed approach

will meet the daily need of many chemists and biologists, who

study DNA and proteins. Although we obtained reasonably

well agreed thickness results by approximating the density

of Box 1 as of the surrounding liquid, we are aware of

the possibility that density could change significantly. In

addition to seeking help from impedance analysis or

Fig. 1 Protein IgG acted as stakes. (a) Schematic illustration of the

solidified liquid layer (Box 1) created upon the immobilization of IgG

to a EG-SAM and the extension of Box 1 due to the specific binding of

anti-IgG to IgG. Note that Box 2 has a semi-infinite thickness, which is

drawn to change so that the thickness change of Box 1 could be more

clearly visualized, (b) a representative QCM curve that recorded

the frequency changes induced by the IgG immobilization, Df =

�122.1 Hz (overtone number n = 3), (c) fitting of the frequency

changes at multiple overtones according eqn (3) gave A= 41.3 Hz and

B = �0.04 Hz.

950 | Chem. Commun., 2010, 46, 949–951 This journal is �c The Royal Society of Chemistry 2010

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dissipation monitoring, tuning of the density of immobilized

biopolymers may give some hints to this issue and we are

current working on this.

We thank the SINANO for the support of startup funds.

This project was also partially supported by 100 Talents

Programme of CAS (08BM031001), the NSFC grant

(20604002), NSFB grant (2072008) to H. M. and National

Basic Research Program of China (2009CB320305,

2007CB935602 and 2007CB936000), Ministry of Health

(2009ZX10004-301).

Notes and references

z Two models of QCM were used here, namely Q-Sense E4 (Q-Sense,Gothenburg, Sweden) and a home-built QCM with a control softwarepurchased from Resonant Probes GmbH (Goslar, Germany). Experi-ments were typically run at both machines and analysis indicatedno significant differences. All DNA solutions were diluted to theconcentration of 1 mM with PBS buffer before immobilization andhybridization. 6-Mercapo-1-hexanol (MCH) was diluted to 1 mMwith PBS before use. The 11-mercaptoundecyl-tri(ethylene glycol) self-assembled monolayer (EG-SAM) and poly(OEGMA) functionalizedchips (both SPR and QCM) were obtained from HRBio(Beijing, China).

IgG and anti-IgG. The functionalized QCM chip was placed in aQCM sensor chamber and the temperature was set to 25 1C. The QCMwas operated in a flow-through mode. A baseline was established bypassing PBS buffer (10 mM, pH= 7.4) at a speed of 40 mL min�1. Thecarboxyl groups were activated by a 5 min injection of an aqueousmixture of EDC (0.1 M) and NHSS (0.2 M). IgG was then pumped

through sensor chamber by a peristaltic pump. PBS buffer was finallypassed through to establish the second stable baseline. The remainingactive carboxyl groups were deactivated by ethanolamine (EtAmine at1 M, pH = 8.5). Anti-IgG was then introduced to the IgG surface.

DNA immobilization and hybridization. A QCM chip was firstloaded to a QCM sensor so that its absolute resonating frequencywas obtained. Then, PBS (pH 7.4) solution was pumped into the QCMchamber. After a stable baseline was established, a solution of 1 mMstem-loop DNA in PBS (0.1 M PB, 1 M NaCl, pH 7.4) was introducedand the immobilization of DNA on the chip was monitored online.Then, the DNA solution was replaced by PBS, and a solution of 1 mMMCH in PBS was pumped into the chamber and incubated for 20 min.The MCH solution was replaced by PBS to obtain a stable baseline,and the frequency shift induced by DNA immobilization was recordedas Dfim. After that, a solution of 1 mM complementary strands in PBSwas introduced and the DNA hybridization was also monitoredonline. Finally, PBS was introduced to obtain a baseline after20 min of hybridization, the corresponding frequency shift wasdenoted as Dfhy.

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Fig. 2 DNA acted as stakes. (a) the thickness changes of Box 1 were

realized through two ways: first was the immobilization of stem-loop

DNA (S2), second was the hybridization of complementary strand

(S3), (b) a representative QCM curve that recorded the frequency

changes induced by S2 and S3, Df = �95.5 and �185.8 Hz (overtone

number n = 3), equivalent to 4.4 and 9.2 nm.

This journal is �c The Royal Society of Chemistry 2010 Chem. Commun., 2010, 46, 949–951 | 951

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