Photolithographic synthesis of high-density DNA probe arrays: Challenges and opportunities

Pawloski, Adam R.; McGall, Glenn H.; Kuimelis, Robert G.; Barone, Dale; Cuppoletti, Andrea; Ciccolella, Paul; Spence, E.; Afroz, Farhana; Bury, Paul A.; Chen, Christy; Chen, Chuan; Pao, Dexter; Le, Michael; McGee, Becky; Harkins, Elizabeth; Savage, Michael P.; Narasimhan, Sim; Goldberg, Martin W.; Rava, Richard P.; Fodor, Stephen P. A.

doi:10.1116/1.2794325

Cited by 12 publications

(16 citation statements)

References 16 publications

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“…Although this strategy did not improve the activity of cluster II or cluster III RIPtides, a significant increase in potency was observed for clusters IV and V RIPtides. Interestingly, we found that several sequenceextended versions of cluster IV RIPtides showed nanomolar IC 50 values in TRAP assays (supplemental Table 1, entries [35][36][37][38][39][40]. These observations are consistent with previous observations that longer DNA oligonucleotides targeting an overlapping region in hTR exhibit inhibitory activity against telomerase in vitro (45).…”

Section: -Ome Riptide Microarrays and Telomerase Inhibitionsupporting

confidence: 81%

“…Microarray Manufacture-For the fabrication of 2Ј-OMe oligonucleotide-based high density microarrays, a photoresist technique based in I-line (365 nm) projection lithography was utilized (35). This method (supplemental Fig.…”

Section: Methodsmentioning

confidence: 99%

“…To avoid this laborious operation, we used a recently developed microarray fabrication technology that employs photochemical generation of an acid to deprotect DMT groups (35). This method (supplemental Fig.…”

Section: Journal Of Biological Chemistry 18845mentioning

confidence: 99%

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Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2′-OMe RNA-interacting Polynucleotide (RIPtide) Microarrays

Gude

Berkovitch

Santos

et al. 2012

Journal of Biological Chemistry

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Background: Identification of targetable regions in folded RNAs remains a challenge. Results: A novel RIPtide microarray comprising all 2Ј-O-methylated RNAs 4 -8 nucleotides in length has been used to discover biologically active antagonists of human telomerase. Conclusion: RIPtide microarrays can identify nucleic acid-based ligands that bind folded RNA structures. Significance: RIPtide technology provides the first completely sequence-unbiased screen for targetable sites on folded RNA targets.

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Section: -Ome Riptide Microarrays and Telomerase Inhibitionsupporting

confidence: 81%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2′-OMe RNA-interacting Polynucleotide (RIPtide) Microarrays

Gude

Berkovitch

Santos

et al. 2012

Journal of Biological Chemistry

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“…Whether their function is to diagnose disease, detect specific DNA sequences, screen for bioterrorism agents, or identify specific cancer variants, biochips of all types are ushering in a new era of medical and biological research. Several different biochip variations are now commercially available [2][3][4][5] and have been used in clinical and research settings. These biochips exploit a complimentary relationship between a probe and labeled target to produce a sensing response upon interaction of the probe/target pair.…”

Section: Introductionmentioning

confidence: 99%

Pattern recognition of shape-encoded hydrogel biosensor arrays

et al. 2009

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A pattern-recognition and encoding system has been developed for a biochip platform using shaped hydrogel sensors batch produced via photolithography. Each sensor shape is fashioned with a unique pattern of dots that makes it identifiable to a pattern recognition system. By linking the sensor's function to its shape, "random" arrays can be created ͑i.e., arrays that do not require sensors to be located at specific positions͒. Random arraying can be quickly and cost-effectively achieved via self-assembly methods. Pattern-recognition software was written to perform automated recognition of micrographs exhibiting fluorescing sensors. As a test of the recognition process, an array of shapeencoded DNA sensors was fabricated using lithography. Fluorescent micrographs were taken of a DNA-sensing experiment, and then processed with the pattern-recognition software. The results show that this process is quite viable with 98% recognition accuracy of the nondefective sensors in both images.

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“…Today, stepper-based lithography in combination with solid-phase photoacid generating polymer films has demonstrated submicron DNA patterns. 19 Other examples of increasing the resolution of photolithographic DNA chips have been accomplished by including reduction optics in maskless projection lithography systems. However, these results are limited to CDs greater than 2 m. 20,21 For the in situ synthesis of nanoscale DNA patterns, photomask engineering or developing higher magnification projection optics would be impractical.…”

Section: Introductionmentioning

confidence: 99%

In situ synthesis and direct immobilization of ssDNA on electron beam patterned hydrogen silsesquioxane

Negrete

Önses

Nealey

et al. 2009

Journal of Vacuum Science &Amp; Technology B: Microelectronics and Nanometer Structures Processing, Measurement, and Phenomena

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In addition to being a high-resolution negative-tone electron beam resist, hydrogen silsesquioxane (HSQ) has chemical properties similar to glass, making it useful for integration with biodevice fabrication. The authors demonstrate the use of electron beam patterned HSQ as a solid support for light-directed in situ ssDNA synthesis and ssDNA immobilization, creating submicron HSQ structures (ranging from 1μmto40nm) that are functionalized with ssDNA. After ssDNA synthesis, the hybridization of Cy-3 labeled complementary strands reveals that the synthesis is indeed localized to the HSQ. They observed relatively low background fluorescence from the supporting silicon substrate or from HSQ where no DNA synthesis was performed. In the course of the experiment they surveyed several materials as support for the HSQ patterning. In addition, the support substrate must be resistant to DNA synthesis. They found that piranha cleaned silicon, glassy carbon, hydrogen plasma treated glassy carbon, and hexamethyldisilazane primed silicon allow little or no synthesis when examined by hybridization with fluorescent labeled complement DNA. This work is relevant to the fabrication of devices that may require submicron patterns of structures functionalized with ssDNA for hybridization assays or DNA self-assembly applications and demonstrates a novel use of a commonly used negative-tone resist.

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Photolithographic synthesis of high-density DNA probe arrays: Challenges and opportunities

Cited by 12 publications

References 16 publications

Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2′-OMe RNA-interacting Polynucleotide (RIPtide) Microarrays

Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2′-OMe RNA-interacting Polynucleotide (RIPtide) Microarrays

Pattern recognition of shape-encoded hydrogel biosensor arrays

In situ synthesis and direct immobilization of ssDNA on electron beam patterned hydrogen silsesquioxane

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