In situ oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication

In this paper, we demonstrate in situ synthesis of oligonucleotide probes on poly(dimethylsiloxane) (PDMS) microchannels through use of conventional phosphoramidite chemistry. PDMS polymer was moulded into a series of microchannels using standard soft lithography (micro-moulding), with dimensions <100 μm. The surface of the PDMS was derivatized by exposure to ultraviolet/ozone followed by vapour phase deposition of glycidoxypropyltrimethoxysilane and reaction with poly(ethylene glycol) spacer, resulting in a reactive surface for oligonucleotide coupling. High, reproducible yields were achieved for both 6mer and 21mer probes as assessed by hybridization to fluorescent oligonucleotides. Oligonucleotide surface density was comparable with that obtained on glass substrates. These results suggest PDMS as a stable and flexible alternative to glass as a suitable substrate in the fabrication and synthesis of DNA microarrays

Confocal image following hybridization indicating non-uniform synthesis of 6mer oligonucleotides (5′-CTACGC) on HBAPTES deposited via solution-phase silanization

<p><b>Copyright information:</b></p><p>Taken from " oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication"</p><p>Nucleic Acids Research 2005;33(8):e75-e75.</p><p>Published online 3 May 2005</p><p>PMCID:PMC1088307.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Confocal images showing the effect of () GPTMS only and () GPTMS with surface spacer, PEG, on the synthesis of 6mer oligonucleotides (5′-CTACGC) followed by hybridization

<p><b>Copyright information:</b></p><p>Taken from " oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication"</p><p>Nucleic Acids Research 2005;33(8):e75-e75.</p><p>Published online 3 May 2005</p><p>PMCID:PMC1088307.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> In (a), the epoxide groups on GPTMS were opened by washing with aqueous HCl before synthesis ()

Influence of ‘hydrophobic recovery’ of derivatized-PDMS (PEG/GPTMS on UVO-treated PDMS) towards oligonucleotide synthesis of 6mer probes (5′-CTACGC) following () 7 days, () 14 days and () 60 days storage in a desiccator

<p><b>Copyright information:</b></p><p>Taken from " oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication"</p><p>Nucleic Acids Research 2005;33(8):e75-e75.</p><p>Published online 3 May 2005</p><p>PMCID:PMC1088307.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Demonstration of target/probe fidelity and lack of non-specific binding through synthesis of an oligo-A (5′-AAAAAA) on PEG/GPTMS/PDMS followed by attempted hybridization to 5′-CTACGC target

<p><b>Copyright information:</b></p><p>Taken from " oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication"</p><p>Nucleic Acids Research 2005;33(8):e75-e75.</p><p>Published online 3 May 2005</p><p>PMCID:PMC1088307.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> Lack of differentiation between blocked and unblocked channels indicates non-hybridization

Qualitative comparison of confocal images of () glass versus () PDMS (both PEG/GPTMS) as a substrate for oligonucleotide synthesis of 5′-CTACGC following hybridization with complement target

<p><b>Copyright information:</b></p><p>Taken from " oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication"</p><p>Nucleic Acids Research 2005;33(8):e75-e75.</p><p>Published online 3 May 2005</p><p>PMCID:PMC1088307.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> The rippled effect in Figure 3.3.1 (a) is attributed to slight loss of sealing between the PDMS microchannels and glass microscope slides during synthesis

Confocal images with corresponding intensity plots showing synthesis/hybridization of 6mer oligonucleotides (5′-CTACGC) on PEG/GPTMS/PDMS microchannels using () 3% TCA/DCM and () 10% TFA/HO deblocking reagents

<p><b>Copyright information:</b></p><p>Taken from " oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication"</p><p>Nucleic Acids Research 2005;33(8):e75-e75.</p><p>Published online 3 May 2005</p><p>PMCID:PMC1088307.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> The blocked channels provide a control surface for the background fluorescence signal. The resulting stripes in (a) are thinner due to channel swelling occurring during synthesis