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Studies of Surface Hybridization In a Model System

This research delves into surface hybridization regimes using innovative techniques and probe designs, demonstrating high reproducibility and preservation of probe activity. Various hybridization regimes such as noncompetitive, Langmuir, and electrostatically suppressed are explored, along with competitive hybridization scenarios. The study also highlights the discrimination capabilities of the system and the impact of temperature on signal detection.

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Studies of Surface Hybridization In a Model System

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  1. Studies of Surface Hybridization In a Model System Ping Gong, Damion Irving, DongbiaoGe, RastislavLevicky Polytechnic Institute of New York University This research was supported by the National Institutes of Health (HG003089 & HG004512) and by National Science Foundation (DMR 07-06170).

  2. Noncompetitive Hybridization Surface Hybridization Regimes • easy • highly reproducible • preserves probe activity HO-(CH2)3-SH DNA-SH a “DNA brush” Gold support thiol or disulfide * Herne T.M. & Tarlov M.J. JACS 1997 20mer Probe: 5’-TTTTAAATTCTGCAAGTGAT – (CH2)3-S-S-(CH2)3-OH -3’ 18mer Target: 3’-AATTTAAGACGTTCACTA-5’ 7 probe Coverages (S0) 5 ionic strengths (CB) CT = 100 nM

  3. Surface Hybridization Regimes L: Langmuir x = SD/S0 S0 (1012 cm-2) Gong, Levicky PNAS 2008 Irving, Gong, Levicky JPCB 2010 Gong, Wang, Liu, Shepard, Levicky JACS 2010

  4. Surface Hybridization Regimes PL: Pseudo-Langmuir x = SD/S0 S0 (1012 cm-2) surface DGSo = -44,000 kJ/mol vs -100,000 kJ/mol in solution (reference state 1 M Na+, 22 C) Gong, Levicky PNAS 2008 Irving, Gong, Levicky JPCB 2010 Gong, Wang, Liu, Shepard, Levicky JACS 2010

  5. Surface Hybridization Regimes SH-E:Electrostatically suppressed hybridization x = SD/S0 S0 (1012 cm-2) Gong, Levicky PNAS 2008 Irving, Gong, Levicky JPCB 2010 Gong, Wang, Liu, Shepard, Levicky JACS 2010

  6. Surface Hybridization Regimes SH-P: “Packing” suppressed hybridization x = SD/S0 S0 (1012 cm-2) CB = 0.63 mol L-1 Gong, Levicky PNAS 2008 Irving, Gong, Levicky JPCB 2010 Gong, Wang, Liu, Shepard, Levicky JACS 2010

  7. Competitive Hybridization 20mer Probe: 5' HS-(CH2)6-CAG GCA CAA ACA TGA ACC TC 3‘ 20mer Perfect Match (PM) Target: 5' GAG GTT CAT GTT TGT GCC TG-(CH2)3-NH2 3‘ 20mer Mismatch (MM) Target: 5' GAG GTT CGT GTT TGT GCC TG3' 0.2 M PB pH 7.0 10:1 MM:PM range of temperatures Thermally-stable Surface Immobilization DNA

  8. Solution Melt Transitions (o) Perfect match: DHPMo, DSPMo Mismatch: DHMMo, DSMMo Mismatch Penalty in Solution: DDHo = DHMMo - DHPMo DDSo = DSMMo - DSPMo PM Surface Melt Transition (*) Perfect match: DHPM*, DSPM* assume mismatch penalty same as in solution: DHMM*= DHPM* + DDHo DSMM*= DSPM* + DDSo

  9. 20mer Probe: 5' HS-(CH2)6-CAG GCA CAA ACA TGA ACC TC 3‘ 20mer Perfect Match (PM) Target: 5' GAG GTT CAT GTT TGT GCC TG-(CH2)3-NH2 3‘ 20mer Mismatch (MM) Target: 5' GAG GTT CGT GTT TGT GCC TG3' 0.2 M PB pH 7.0 10:1 MM:PM ● max discrimination ~ 20 C below solution TM for PM ● suppression of PM signal at lower temperatures ● enhancement of PM signal at higher temperatures

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