我們觀察不同的聚合酵素連鎖反應(PCR) 的緩衝液, 如去離子水、TBE 緩衝液及膠體金溶液對於其反應之影響。並使用傳統熱循環式與自然對流式兩種不同的PCR 進行實驗。實驗得到的產物則應用電泳技術, 來觀察隨著反應循環數增加而產生的產量與特異性變化。結果發現TBE 緩衝液在超過標準的PCR 循環數(35個循環) 後, 仍可以保持PCR 中複製DNA 片段的特異性。接著並發現膠體金溶液及其中分離出來的金保存液, 兩者皆會對PCR 產生抑制力, 使得產量降低,但仍可以保持其特異性。而若是使用去離子水稀釋兩者, 再進行PCR 仍可以得到足夠的DNA 片段產量。我們使用粒子影像速度儀(Particle Image Velocimetry,PIV) 技術, 觀察自然對流式PCR 的流場結構, 了解以自然對流為主要機制的PCR, 是如何進行反應。並探討是什麼原因可以讓自然對流PCR 在較短的時間內, 達到與傳統PCR 同樣的複製DNA 效果。同時探討膠體金溶液對自然對流式PCR 流場結構的改變。

We investigate the effects of PCR (Polymerase Chain Reaction) buffer, such
as Deionized water (DI water), TBE buffer and nano gold colloid, on PCR. A conventional PCR and natural-convection PCR are considered to explore the effects.
Electrophoresis was conducted to analyze the PCR product. We found that the
amount of PCR product without any buffer and specificity were changed when the
number of cycle of PCR increased. In addition, we found that adding the TBE
buffer can keep the specificity even the number of PCR cycle exceeds 35 cycles. On the other hand, nano gold colloid and its buffer restrained PCR, but they still kept the specificity. It is, however, revealed that the enough PCR yield was obtained by diluted nano gold colloid. Subsequently, we utilized a PIV (Particle image velocimetry) technique to observe the flow structure of natural-convection PCR.
The mechanism why natural-convection PCR is more efficient than conventional
PCR was studied. The variation of flow structure of natural-convection PCR due
to nano gold colloids was found in PIV results.

[1] Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T.,
Mullis, K.B. and Erlich, H.A., 1988, Primer-directed enzymatic amplification
of DNA with a thermostable DNA polymerase. Science 239, 487-491.
[2] Wheeler, E.K., Benett, W., Stratton, P., Richards, J., Chen, A., Christian,
A., Ness, K.D., Ortega, J., Li, L.G., Weisgraber, T.H., Goodson, K. and
Milanovich, F., 2004, Convectively driven polymerase chain reaction thermal
cycler. Analytical Chemistry 76, 14, 4011-4016.
[3] Kubista, M., Andrade, J.M., Bengtsson, M., Forootan, A., Jon′ak, J., Lind,
K., Sindelka, R., Sj‥oback, R., Sj‥ogreen, B., Str‥ombon, L., St°ahlberg, A.,
Zoric, N., 2006, The real-time polymerase chain reaction. Molecular Aspects
of Medicine 27, 95-125.
[4] Pollack, M.G., Paik, P.Y., Shenderov, A.D., Pamula, V.K., Dietrich, F.S.
and Fair, R.B., 2003, Investigation of electrowetting-based microfluidics for
real-time PCR applications. Proceedings of the 7th International Conference
on Minialurized Chemical and Biochemical Analysis Systems, Squaw Valley,
California USA.
[5] M‥uller, G., Neumann, G. andWeber, W., 1984, Natural convection in vertical
Bridgman configurations. Journal of Crystal Growth 70, 78-93.
[6] Braun, D. and Libchaber, A., 2002, Trapping of DNA by thermophoretic
depletion and convection. Physical Review Letters 89, 188103.
[7] Krishnan, M., Ugaz, V.M. and Burns, M.A., 2002, PCR in a Rayleigh-B′enard
convection cell. Science 298, 793.
[8] Ugaz, V.M. and Krishnan, M., 2004, Novel convective flow based approaches
for high-throughput PCR thermocycling. Journal of the Association for Laboratory
Automation 9, 318-323.
· 77 ·
[9] Krishnan, M., Agrawal, N., Burns, M.A. and Ugaz, V.M., 2004, Reaction and
fluidics in miniaturized natural convection systems. Analytical Chemistry 76,
6254-6265.
[10] Braun, D., Goddard, N.L. and Libchaber, Albert., 2003, Exponential DNA
replication by laminar convection. Physical Review Letters 91, 158103.
[11] Braun, D., 2004, PCR by thermal convection. Modern Physics Letters B 18,
775-784.
[12] Chen, Z.Y., Qian, S.Z., Abrams, W.R., Malamud, D. and Bau, H.H. 2004,
Thermosiphon-based PCR reactor: experiment and modeling. Analytical
Chemistry 76, 3707-3715.
[13] Li, H.K. Huang, J.H., Lv, J.H., An, H.J., Zhang, X.D. Zhang, Z.Z., Fan, C.H.
and Hu, J., 2005, Nanoparticle PCR: nanogold-assisted PCR with echanced
specificity. Angewandte Chemie International Edition 44, 5100-5103.
[14] Li, M., Lin, Y.C. Wu, C.C., and Liu, H.S., 2005, Enhancing the efficiency of
a PCR using gold nanoparticles. Nucleic Acids Research 33, 21.
[15] Vu, B.V., Litvinov, D. and Willson, R.C., 2008, Gold Nanoparticle Effects
in Polymerase Chain Reaction: Favoring of Smaller Products by Polymerase
Adsorption. Analitical chemistry 80, 5462-5467.
[16] Patel, H.E., Das, S.K., and Sundararajan, T., Nair, A.S., George, B. and
Pradeep, T., 2008, Thermal conductivities of naked and monolayer protected
metal nanoparticle based nanofluids: Manifestation of anomalous enhancement
and chemical effects. Applied physics letters 83, 2931-2933.
[17] Hu, M. and Hartland, G.V. 2002, Heat Dissipation for Au Particles in Aqueous
Solution: Relaxation Time versus Size. The journal of physical chemistry B
106, 7029-7033.
[18] Keblinski, P., Phillpot, S.R., Choi, S.U.S., Eastman, J.A., 2002, Mechanisms
of heat flow in suspensions of nano-sized particles (nanofluids). Journal of
heat and mass transfer 45, 855-863.
[19] Watson, J.D. and Crick, F.H., 1953, Molecular structure of nucleic acids.
Nature 171, 737-738.
[20] Janes, H. W., Chen, B. Y., PCR Cloning protocols.
· 78 ·
[21] Nikoobakht, B. and El-Sayed, M.A., 2003, Preparation and growth mechanism
of gold nanorods (NRs) using seed-mediated growth method. Chemistry
of Materials 15, 1957-1962.
[22] Reynolds, R.A. III, Mirkin, C.A., and Letsinger, R.L., 2000, Homogeneous,
nanoparticle-based quantitative colorimetric detection of oligonucleotides.
Journal of the American Chemical Society 122, 3795-3796.
[23] Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger, R.L. and Mirkin,
C.A., 2000, Selective colorimetric detection of polynucleotides based on the
distance-dependent optical properties of gold nanoparticles. Science 277,
1078-1081.
[24] Li, H.X. and Rothberg, L., 2004, Colorimetric detection of DNA sequences
based on electrostatic interactions with unmodified gold nanoparticles. Science
101, 14036-14039.
[25] Zhu, H.P., Mi, L.J., Chen, S.M., Wang, W.F., Yao, S.D., 2007, Study on the
Interaction of Colloidal Gold with Taq DNA Polymerase. Chinese Journal of
Chemistry 25, 1233-1237.
[26] Sun, C. and Xia, K.Q., 2005, Three-dimensional flow structures and dynamics
of turbulent thermal convection in a chlindrical cell. Physical Review E 72,
026302.
[27] Adrian, R.J., 1991, Particle-imaging techniques for experimental fluid mechanics.
Annual Reviews of Fluid Mechanics 23, 261-304.
[28] Jana, N.R., Gearheart, L. and Murphy, C.J. 2001, Seed-Mediated Growth
Approach for Shape-Controlled Synthesis of Spheroidal and Rod-like Gold
Nanoparticles Using a surfactant Template. Advanced Materials 13, 1390-
1393.
[29] He, Y.Q., Liu, S.P., Kong, L., Liu, Z.F., 2005, A study on the sizes and concentrations
of gold nanoparticles by spectra of absorption, resonance Rayleigh
scattering and resonance non-linear scattering. Spectrochimica Acta Part A
61, 2861-2866.
[30] Haiss, W., Thanh, N.T.K., Aveyard, J. and Fernig, D.G., 2007, Determination
of Size and Concentration of Gold Nanoparticles from UV-Vis Spectra.
Analytical Chemistry 79, 4215-4221.
· 79 ·
[31] Maaloum, M., Pernodet, N., Tinland, B., 1998, Agarose gel structure using
atomic force microscopy: gel concentration and ionic strength effects. Electrophoresis
19, 1606-1610.
[32] Pernodet, N., Maaloum, M., Tinland, B., 1996, Pore size of agarose gels by
atomic force microscopy. Electrophoresis 18, 55-58.
[33] Http://users.ugent.be/ avierstr/index.html
[34] Chen, B.Y. and Janes, H.W., PCR Cloning Protocols Second Edition., 192
[35] Http://en.wikipedia.org/wiki/PID controller
[36] Http://en.wikipedia.org/wiki/Electromagnetic spectrum
[37] Http://en.wikipedia.org/wiki/DNA