Electrochemical Modification of Glassy Carbon

by Amethist S. Finch and James J. Sumner

ARL-TR-5697 September 2011

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ARL-TR-5697 September 2011 

Electrochemical Modification of Glassy Carbon 

Amethist S. Finch and James J. Sumner 

Sensors and Electron Devices Directorate, ARL 

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Electrochemical Modification of Glassy Carbon

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Amethist S. Finch and James J. Sumner

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14. ABSTRACT

With the sequencing of whole genomes now a reality, the push to synthesize genomes de novo is of great interest. Currently, 

state-of-the-art oligonucleotide synthetic methods allow for synthesis of up to 200 base pairs. In order to realize increased 

lengths of an order of magnitude or more, the development of new synthetic strategies and coupling mechanisms is necessary. 

This project aims to provide an alternative methodology for the synthesis of very long (>200 base pairs) deoxyribonucleic acid 

(DNA) oligonucleotides. This technique involves using a glass carbon rod as the support for the DNA synthesis and requires 

development of experimental techniques for irreversibly linking an organic molecule with an aniline-type moiety to the glassy 

carbon. By in situ conversion of the aniline functional group to its diazonium derivative, we demonstrate direct electrochemical 

modification of the glassy carbon rod. These preliminary results allowed for the transfer of these materials to collaborators at 

the Food and Drug Administration for use in their research on alternative methods for automated synthesis of oligonucleotides.

15. SUBJECT TERMS

Glassy carbon, electrochemistry, electrode passivation, oligonucleotide synthesis 

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Amethist S. Finch

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iii

Contents 

List of Figures iv

Acknowledgements v

1. Introduction 1

2. Materials and Methods 1

2.1 Alternating Current (AC) Voltammetry ..........................................................................2

2.2 Cyclic Voltammetry (CV) ...............................................................................................2

2.3 Electrode Testing .............................................................................................................3

3. Results and Discussion 3

3.1 Previous Results ..............................................................................................................3

3.2 Linker Moiety ..................................................................................................................4

3.3 Standard Glassy Carbon (GC) Electrode Experiments ...................................................5

3.3 Modified GC Rod Experiments .......................................................................................8

4. Conclusions 10

5. References 11

List of Symbols, Abbreviations and Acronyms 12

Distribution List 13
iv

List of Figures 

Figure 1. Diaminonaphthalene derivatives. ....................................................................................3

Figure 2. Representative composite AC voltammogram of DAN derivatives. All experiments 

were conducted at ambient temperature in a three-component electrode cell with a 

platinum working, a platinum wire counter, and a saturated calomel reference electrode. .......4

Figure 3. DLM provided by the FDA for coupling to GC electrodes via electrochemical 

methods. .....................................................................................................................................4

Figure 4. Schematic of standard GC electrode (BASi Inc.) (5). .....................................................5

Figure 5. Representative CV of DLM scanned one time with a standard GC electrode. All 

experiments were conducted at ambient temperature in a three-component electrode cell 

with a GC working, a platinum wire counter, and a saturated calomel reference electrode 

in 0.25 M KCl (pH 7.0) and 0.1% acetonitrile with an DLM concentration of 1 mM. .............6

Figure 6. Representative CV (scan 3) of DLM scanned with a standard GC electrode. All 

experiments were conducted at ambient temperature in a three-component electrode cell 

with a GC working, a platinum wire counter, and a saturated calomel reference electrode 

in 0.25 M KCl (pH 7.0) and 0.1% acetonitrile with an DLM concentration of 1 mM. .............7

Figure 7. Representative CV (scans 4 and 5) of DLM scanned with a standard GC electrode. 

All experiments were conducted at ambient temperature in a three-component electrode 

cell with a GC working, a platinum wire counter, and a saturated calomel reference 

electrode in 0.25 M KCl (pH 7.0) and 0.1% acetonitrile with an DLM concentration of 1 

mM. ............................................................................................................................................7

Figure 8. CV of DLM scanned five times with standard GC electrode 3. All experiments 

were conducted at ambient temperature in a three component electrode cell with a GC 

working, a platinum wire counter, and a saturated calomel reference electrode in 0.25 M 

KCl (pH 7.0) and 0.1% acetonitrile with an DLM concentration of 1 mM. ..............................8

Figure 9. Representative CV of DLM scanned five times with a GC rod 1. All experiments 

were conducted at ambient temperature in a three component electrode cell with a GC 

working, a platinum wire counter, and a saturated calomel reference electrode in 0.25 

KCl (pH 7.0) and 0.1% acetonitrile with an DLM concentration of 2 mM. ..............................9

Figure 10. Representative CV of DLM on scanned five times with a GC rod 2. All 

experiments were conducted at ambient temperature in a three component electrode cell 

with a GC working, a platinum wire counter, and a saturated calomel reference electrode 

in 0.25 M potassium chloride (pH 7.0) and 0.1% acetonitrile with an DLM concentration 

of 2 mM....................................................................................................................................10
v

Acknowledgements 

We acknowledge the support of the U.S. Army Research Laboratory (ARL), Sensors and 

Electron Devices Directorate (SEDD). We also acknowledge Dr. Serge Beaucage and Dr. 

Cristina Ausin of the Food and Drug Administration (FDA) for the collaboration opportunity as 

well as for providing the linker moiety, the electrode materials, and characterization of the 

modified glassy carbon rods. 
vi

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1

1. Introduction 

The field of biology has greatly pushed the envelope over the past decade with the ability 

sequence whole genomes in a matter of days (1). Many different competing technologies have 

been developed that allow for the sequencing of organism genomes and each of these 

technologies has its strengths (2). These sequencing technologies will allow for applications that 

go beyond de novo sequencing by tying genomics into lines of research on things such as 

chromatin structure, epigenomics, RNA transcription, immunology, and genomes of microbial 

communities. 

In contrast, the field of deoxyribonucleic acid (DNA) oligonucleotide synthesis has changed very 

little over the last decade. The same methodologies that were developed in the 1960s and 1970s 

are still in use for solid phase oligonucleotide synthesis today. While these methodologies are 

very well studied and each step proceeds with high yield when the steps are combined to make 

longer oligonucleotides, the intrinsic error is additive, prohibiting this technology from 

progressing towards longer sequences. Additionally, for DNA synthesis to reach the level of 

whole genome synthesis, great leaps in scientific understanding and alternative technologies are 

necessary. In order to move the field to the next level, there is a need to develop ultra high 

fidelity methodologies that will allow for the synthesis of ultra long oligonucleotides. 

This project aims to provide a scaffold that will allow for a revolution in DNA synthetic 

technology, ultimately allowing for the synthesis of very long (>200 base pairs) DNA 

oligonucleotides. This technique involves using a glassy carbon (GC) rod in a flow cell device 

as the support for the DNA synthesis and requires development of experimental techniques for 

irreversibly linking an organic molecule with an aniline-type moiety to the glassy carbon. By in 

situ conversion of the aniline functional group to its diazonium derivative, we demonstrate direct 

electrochemical modification of the GC rod. These preliminary results allowed for the transfer 

of these materials to collaborators at the Food and Drug Administration for use in their research 

on alternative methods for automated synthesis of oligonucleotides. 

2. Materials and Methods 

All chemicals were purchased from Thermo Fisher or Sigma-Aldrich and were of the highest 

grade available. Working, counter, and reference electrodes as well as a polishing kit were 

purchased from BASi (West Lafayette, IN). GC rods and diazonium linker moiety (DLM) were 

provided by Serge Beaucage and Cristina Ausin of the Food and Drug Administration (FDA). 

All electrochemical characterization measurements were carried out using a CH Instruments 
2

660A electrochemical workstation (Austin, TX) and data were processed using standard 

(OriginPro V. 8.5) graphing software. 

2.1 Alternating Current (AC) Voltammetry 

AC voltammetry experiments were run in a three-electrode cell with a GC working, a platinum 

wire counter, and a saturated calomel reference electrode. Phosphate buffered saline (PBS) pH 

7.4 (Sigma) was used as the electrolyte. One tablet of PBS was dissolved in 200 mL of doubledistilled water (ddH2O) to make a working solution of 10 mM potassium phosphate, 137 mM 

sodium chloride (NaCl), and 2.7 mM potassium chloride (KCl). Solutions of 

diaminonaphthalene (500 mM) were prepared in high performance liquid chromatography 

(HPLC)-grade acetonitrile. Diaminonaphthalene solutions (20 μL) were then mixed with 10 mL 

of PBS to final concentration of 1 mM in 0.2% acetonitrile. The following parameters were set 

for on the AC voltammetry workstation for all experiments: 

• Init E (V) = 0 

• Final E (V) = 0.7 

• Incr E (V) = 0.004 

• Amplitude (V) = 0.025 

• Frequency (Hz) = 10 

• Sample Period (s) = 1 

• Quiet Time (s) = 2 

• Sensitivity (A/V) = 1e-5 

2.2 Cyclic Voltammetry (CV) 

Experiments were carried out in a three-electrode cell with a GC working, a platinum wire 

counter, and a saturated calomel reference electrode. A 1 M stock solution of the DLM was 

prepared by dissolving 0.6 mg in 1 mL of HPLC-grade acetonitrile. This stock solution was used 

to make the working solutions of 1 and 2 mM in 0.25 M KCl in 0.1% acetonitrile. The following 

parameters were set for CV on the workstation for all experiments: 

• Init E (V) = –0.4 to 0 

• High E (V) = 0.7 

• Low E (V) = –0.3 

• Init P/N = P 

• Scan Rate (V/s) = 0.05 
3

• Segment = 2 

• Sample Interval (V) = 0.001 

• Quiet Time (s) = 2 

• Sensitivity (A/V) = 1e-5 to 1e-7

2.3 Electrode Testing 

Coverage DLM on standard electrodes and GC rods was determined via fluorescence 

experiments conducted at the FDA. 

3. Results and Discussion 

3.1 Previous Results 

Figure 1 illustrates the compounds used in initial CV experiments for determining Eox of 

diaminonaphthalene (DAN) and DAN derivatives (figure 1) using CV. This proved to be 

problematic due to polymer film formation of DAN upon the surface of the GC and platinum 

electrode (3). This polymer was not conductive under aqueous conditions; therefore, the reverse 

scan and subsequent scans showed diminishing current. In order to determine that 

instrumentation was not the cause of the erratic scans and polymer formation, Eox determinations 

were repeated under the CV conditions outline in reference 3 (3a). The data were successfully 

reproduced using AC voltammetry coupled with an exhaustive process of cleaning and polishing 

the electrode surface after each scan (figure 2) (4). 

Figure 1. Diaminonaphthalene derivatives.
4

Figure 2. Representative composite AC voltammogram of DAN derivatives. All experiments 

were conducted at ambient temperature in a three-component electrode cell with a 

platinum working, a platinum wire counter, and a saturated calomel reference 

electrode.

This polymer film formation was a hindrance in Eox determinations; however, for the purposes of 

linking the DLM to the GC electrode surface, this film formation was seen as an advantageous 

occurrence. The methodologies used for these experiments were translated to the 

electrochemistry on the DLM compound with GC electrodes.

3.2 Linker Moiety

The DLM compound (figure 3) was synthesized and provided in its diazonium form by the FDA. 

The DLM was dissolved directly into acetonitrile and used in all subsequent electrochemistry 

experiments.

Figure 3. DLM provided by the FDA for coupling to GC electrodes via 

electrochemical methods.
5

3.3 Standard Glassy Carbon (GC) Electrode Experiments 

Initial experiments were conducted on standard GC electrodes as supplied by the manufacturer. 

These electrodes (figure 4) are manufactured in a solvent-resistant chlorotrifluoroethylene 

(CTFE) plastic body (7.5 cm length x 6 mm outer diameter [OD]), which is embedded with 

highly polished 3.0-mm GC disks. 

Figure 4. Schematic of standard GC 

electrode (BASi Inc.) (5). 

Three standard electrodes were scanned under varying conditions in order to determine the 

optimal scanning parameters. Electrode 1 was scanned a single time while electrodes 2 and 3 

were each scanned five times. The plot of the single scan on electrode 1 is illustrated in figure 5. 

Note the redox activity around 0.8 V riding the background with a dramatically increasing slope. 
6

0.0 0.2 0.4 0.6 0.8 1.0

-6.0x10-6

-5.0x10-6

-4.0x10-6

-3.0x10-6

-2.0x10-6

-1.0x10-6

0.0

1.0x10-6 Current (A)

Potential vs SCE (V)

 Scan 1

Glassy Carbon Electrode 1

Figure 5. Representative CV of DLM scanned one time with a standard GC electrode. All experiments 

were conducted at ambient temperature in a three-component electrode cell with a GC working, a 

platinum wire counter, and a saturated calomel reference electrode in 0.25 M KCl (pH 7.0) and 

0.1% acetonitrile with an DLM concentration of 1 mM.

Electrode 2 was scanned a total of five times. The scan range was optimized from electrode 1. 

The initial and third scans were conducted under the same parameters as electrode 1 and there 

was little or no change between these plots from that of electrode 1. Scan 3 (figure 6) was 

conducted in an increased potential window from –0.4 to 1 V and scans 4 and 5 were conducted 

in a reduced potential window from 0 to 0.6 V. A representative CV of scans 4 and 5 are 

illustrated in figure 7. Figure 6 shows a scan in which the potential window is too large. There 

is hysteresis near –0.3 V and the rapidly changing slopes at both extremes indicate solvent or 

electrode breakdown. These scans suggest that the most optimal window for scanning may be 

between 0 to 0.7 V. 
7

-0.6 -0.4 -0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2

-8.0x10-6

-6.0x10-6

-4.0x10-6

-2.0x10-6

0.0

2.0x10-6

4.0x10-6

6.0x10-6

8.0x10-6

1.0x10-5

1.2x10-5

1.4x10-5 Glassy Carbon Electrode 2 Current (A)

Potential vs SCE (V)

 Scan 2

Figure 6. Representative CV (scan 3) of DLM scanned with a standard GC electrode. 

All experiments were conducted at ambient temperature in a threecomponent electrode cell with a GC working, a platinum wire counter, and a 

saturated calomel reference electrode in 0.25 M KCl (pH 7.0) and 0.1% 

acetonitrile with an DLM concentration of 1 mM.

0.0 0.1 0.2 0.3 0.4 0.5 0.6

-1.50E-007

-1.00E-007

-5.00E-008

0.00E+000

5.00E-008

1.00E-007

 scan 4 Current (A) Current (A)

Potential vs SCE (V)

Glassy Carbon Electrode 2

 scan 5

Figure 7. Representative CV (scans 4 and 5) of DLM scanned with a standard GC 

electrode. All experiments were conducted at ambient temperature in a threecomponent electrode cell with a GC working, a platinum wire counter, and a

saturated calomel reference electrode in 0.25 M KCl (pH 7.0) and 0.1% 

acetonitrile with an DLM concentration of 1 mM.
8

Electrode 3 was scanned five times all under the same parameters from 0 V to 0.7 V. Figure 8 

shows the results of the 5 scans. These scans clearly show redox activity at 0.45 V and each 

subsequent scan illustrates that there is less chemistry occurring on the surface of the GC 

electrode. This was due to the polymerization on the electrode surface. 

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7

-4.0x10-7

-3.0x10-7

-2.0x10-7

-1.0x10-7

0.0

1.0x10-7

 Scan 1

 Scan 2 Current (A)

 Potential vs SCE(V)

 Scan 3

Combined Electrode 3 Scans

 Scan 4

 Scan 5

Figure 8. CV of DLM scanned five times with standard GC electrode 3. All experiments 

were conducted at ambient temperature in a three component electrode cell with 

a GC working, a platinum wire counter, and a saturated calomel reference 

electrode in 0.25 M KCl (pH 7.0) and 0.1% acetonitrile with an DLM 

concentration of 1 mM.

All three DLM passivated standard GC electrodes were provided to our collaborators at the 

FDA, where they conducted standard fluorescence measurements to determine extent of 

coverage on the GC surface. Initial results indicate that that all electrodes were covered,

although second and third electrodes provided the most uniformity by fluorescence experiments. 

These preliminary results allowed for us to move the technical methods determined from these 

control experiments to the full GC rods.

3.3 Modified GC Rod Experiments

Prior to testing the electrochemical coupling strategy on the GC rods, a methodology for 

protecting the ends rods needed to be developed. This methodology was necessary because the 

design of the flow cell required the GC rods to be fully functionalized except on the ends of the 

rods. This was to prohibit chemistry on the ends of the rods, which was hypothesized to be 

lower yielding due to steric constraints. Additionally, because of the cost of the ultra high purity 

and polished GC rods, the initial studies were conducted on less expensive graphite rods. The 
9

graphite rods were first wrapped with conductive wire (platinum) in order to create an electrical 

connection, wrapped with parafilm, and capped with shrink wrap tubing. This entire assembly 

was immersed in a 0.25-M KCl solution for testing of the passivation technique. The graphite 

rods were tested for their conductivity to determine the ability of the rods to act as electrodes 

after capping and checked to ensure the rod remained dry underneath the cap. Upon successful 

testing of the capping methodologies on the graphite rods, the subsequent experiments were 

conducted on GC rods. 

GC rod 1 was capped by the method described above and the sample was scanned five times 

from 0 to 0.7 V. Figure 9 illustrates these scans. After the first scan, there does not appear to be 

much change in CV, indicating that there is little or no change in the surface chemistry of the GC 

rod. The capping was removed and the GC rod 1 was then stored in a microfuge tube filled with 

fresh 0.25 M KCl.

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7

-5.0x10-6

-4.0x10-6

-3.0x10-6

-2.0x10-6

-1.0x10-6

0.0

1.0x10-6 Current (A)

Potential vs SCE (V)

 Scan 1

 Scan 2

Combined GC Rod 1

 Scan 3

 Scan 4

 Scan 5

Figure 9. Representative CV of DLM scanned five times with a GC rod 1. All experiments 

were conducted at ambient temperature in a three component electrode cell with a GC 

working, a platinum wire counter, and a saturated calomel reference electrode in 0.25 

KCl (pH 7.0) and 0.1% acetonitrile with an DLM concentration of 2 mM.

GC rod 2 was also capped by the method described previously and this sample was scanned five 

times with an increased potential scan window. The initial scan was conducted with a range of 

–0.4 to 0.7 V and subsequent scans (2–5) were conducted from –0.3 to 0.7 V. Figure 10 

illustrates the results of these sets of scans. As before, there appears to be little or no change in

the CV after the initial scan. The end capping was removed and GC rod 2 was stored in a 

microcentrifuge tube filled with fresh 0.25 M KCl.
10

-0.4 -0.2 0.0 0.2 0.4 0.6

-2.0x10-5

-1.5x10-5

-1.0x10-5

-5.0x10-6

0.0

5.0x10-6

1.0x10-5

Potential vs SCE (V)

 Scan 1 Current (A)

 Scan 2

 Scan 3

 Scan 4

 Scan 5

Combined GC Rod 2

Figure 10. Representative CV of DLM on scanned five times with a GC rod 2. All experiments 

were conducted at ambient temperature in a three component electrode cell with a 

GC working, a platinum wire counter, and a saturated calomel reference electrode in 

0.25 M potassium chloride (pH 7.0) and 0.1% acetonitrile with an DLM 

concentration of 2 mM.

Both GC 1 and 2 rods were then provided to the FDA for further characterization via 

fluorescence measurements. The rods were tested by the FDA and both were adequately coated 

with the DLM. Our FDA collaborators were then able to attach a nucleoside (~1 nmol based on 

fluorescence measurements) to each rod and manually synthesize a dinucleotide. They also 

checked the recyclability of one of the rods, by cleaving the dinucleotide from the rod and 

successfully reattaching a new nucleoside afterwards with consistent yields. Currently, we are in 

the process of optimizing the design of the synthesis cell and will soon proceed with the 

automated synthesis of oligonucleotides.

4. Conclusions

In conclusion, we were able to quickly determine an electrochemical coupling strategy that can 

be translated to a variety of linker arms similar to DLM for passivation of GC surfaces. We 

transitioned GC rod passivated with DLM samples to the FDA for further testing and all the 

experiments were successful. The ease and versatility of this methodology provides a strong 

framework for future work.
11

5. References 

1. Shendure, J.; Ji, H. Next-generation DNA sequencing. Nature Biotechnology 2008, 26 (10), 

1135–1145.

2. Mukhopadhyay, R. DNA sequencers: the next generation. Analytical Chemistry 2009, 81, 

1736–1740.

3. (a) Abdel-Azzem, M., Electrooxidative oligomerization of 1,5-diaminonapthalene in 

acetonitrile medium. J. Electroanal. Chem. 1996, 417, 163–173; (b) Abdel-Azzem, M.; 

Yousef, U. S.; Pierre, G., A cyclic voltammetric and coulometric study of a modified 

electrode prepared by electrooxidative polymerization of 1,5-diaminonapthalene in aqueous 

acidic medium. Eur. Polym. J. 1998, 34, 819–826; (c) Yousef, U. S.; Abdel-Azzem, M., A 

cyclic voltammetric and coulometric study of a modified electrode prepared by 

electrooxidative polymerization of nickel complex of 1,5-diaminonapthalene inacetonitrile. 

Pol. J. Chem. 1998, 72, 2583–2596.

4. Campbell, N. P.; Finch, A. S.; Rokita, S. E. Modulating the ground- and excited-state 

oxidation potentials of diaminonaphthalene by sequential N-methylation. Chemphyschem

2010, 11 (8), 1738–1773. 

5. BASi Stationary Voltammetry Electrodes. http://www.basinc.com/products/ec/sve.php

(August 2011). 
12

List of Symbols, Abbreviations and Acronyms 

AC alternating current 

CTFE chlorotrifluoroethylene 

CV cyclic voltammetry 

DAN diaminonaphthalene 

ddH2O double-distilled water 

DLM diazonium linker moiety 

DNA deoxyribonucleic acid 

FDA Food and Drug Administration 

GC glassy carbon 

HPLC high performance liquid chromatography 

KCl potassium chloride 

NaCl sodium chloride 

OD outer diameter 

PBS phosphate buffered saline 
13

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