跳到主要內容

臺灣博碩士論文加值系統

(44.211.117.197) 您好!臺灣時間:2024/05/21 03:31
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

我願授權國圖
: 
twitterline
研究生:陳淑姿
研究生(外文):Chen Shu Tzu
論文名稱(外文):The Analysis of SELEX by statistical models: Aptamers are selected at pre-equilibrium state
指導教授:林良盈林良盈引用關係陳齊康陳齊康引用關係
學位類別:碩士
校院名稱:國立中興大學
系所名稱:應用數學系
學門:數學及統計學門
學類:數學學類
論文種類:學術論文
論文出版年:2005
畢業學年度:93
語文別:英文
外文關鍵詞:SELEXaptamerligandaffinitybinding ratedissociation rate.
相關次數:
  • 被引用被引用:0
  • 點閱點閱:165
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
We develop a new mathematical model and computer simulations for SELEX (Systematical Evolution of Ligands by EXponential enrichment) experiments. By considering binding and dissociation rates of ligands and targets, we investigate quantitatively the effect of incubation time of binding reactions on the enrichment of high affinity ligands. We incorporate partition efficiency, background contamination and initial winner frequency in our simulations. In most cases, we find that with insufficient incubation times SELEX can still generate aptamers for targets, yet the full enrichment of the ligand library is at the expense of selection cycles.
Contents
 Introduction .........................................1
Preliminary and background .......3
Model ……………………………………………………………………….5
a. Binding and dissociation rate profiles ..5
b. Modeling the selection and amplification of ligands..6
Simulation ......................................8
Result ……………………………………………………………11
Discussion ………………………………………………………15
Figure ……………………………………………………………17
Reference …………………………………………………………30
Appendix …………………………………………………………………..32



Table of figures
Figure 1. An illustration of the scheme of SELEX experiment………17
Figure 2. The pooling of nucleic acid ligands………………………….18
Figure 3. The evolution of frequency of the nucleic acids subpools..20
Figure 4: The evolution of frequency of affinity subpools…………...22
Figure 5: The evolution of frequencies of affinity subpools
with specific incubation time (90 minutes)………………..23
Figure 6: The evolution of frequencies of affinity subpools
with specific incubation time (180 minutes)………………..24
Figure 7: The evolution of frequencies of affinity subpools
with specific incubation time (270 minutes)………………..25
Figure 8. The effect of incubation time on the enrichment
of aptamers……………………………………………………….26
Figure 9. The evolution of frequencies of affinity subpools
with instant incubation (1 minutes)…………………………27
Figure 10. The evolution of frequencies of affinity subpools
with instant incubation (3 minutes)…………………………28
Figure 11. The evolution of frequencies of affinity subpools
with instant incubation (10 minutes)……………………….29
1.Bartel, D. P. and J. W. Szostak (1993). Isolation of new ribozymes from a large pool of random sequences. Science, 261, 1411-1418.
2.Beaudry, A. A. and G. F. Joyce (1992). Directed evolution of an RNA enzyme. Science, 257 (5070), 635-641.
3.Blackwell, T. K. and H. Weintraub (1990). Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science, 250(4984), 1104-1110.
4.Breaker, R. R. and G. F. Joyce (1994). Emergence of a replicating species from an in vitro RNA evolution reaction. Proc. Natl Acad. Sci. U S A, 91(13), 6093-6097.
5.Cuenoud, B. and J. W. Szostak (1995). A DNA metalloenzyme with DNA ligase activity. Nature, 375(6532), 611-614.
6.Irvine, D., C. Tuerk, and L. Gold, SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J Mol Biol, 1991. 222(3), p. 739-61.
7.Joyce, G. F. (1989a). Amplification, mutation and selection of catalytic RNA. Gene, 82(1), 83-87.
8.Joyce, G. F. (1989). RNA evolution and the origins of life. Nature, 338(6212), 217-224.
9.Kinzler, K. W. and Vogelstein B. (1989). Whole genome PCR: application to the identification of sequences bound by gene regulatory proteins. Nucleic Acids Res. 17(10), 3645-3653.
10.Kinzler, K. W. and Vogelstein B. (1990). The GLI gene encodes a nuclear protein which binds specific sequences in the human genome. Mol. Cell. Biol. 10(2), 634-642.
11.Lehman, N. and G. F. Joyce (1993). Evolution in vitro of an RNA enzyme with altered metal dependence. Nature, 361(6408), 182-185.
12.Lin, C. W., M. Hanna, et al. (1994). Evidence that the guanosine substrate of the Tetrahymena ribozyme is bound in the anti conformation and that N7 contributes to binding. Biochemistry, 33(9), 2703-2707.
13.Lorsch, J. R. and J. W. Szostak (1994). In vitro selection of RNA aptamers specific for cyanocobalamin. Biochemistry, 33(4), 973-982.
14.Murtin, M., Galas, D, J., Arnheim, N. & Prentki, P. (1989). In vitro selection of protein binding sites: IHF-DNA interaction. UCLA workshop: the Polymerase Chain Reaction, April 1989, Keystone, Colorado.
15.Peterson, R. D., D. P. Bartel, et al. (1994). 1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding element. Biochemistry, 33(18), 5357-5366.
16.Pollock, R. and R. Treisman (1990). A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res. 18(21), 6197-6204.
17.Prudent, J. R., T. Uno, et al. (1994). Expanding the scope of RNA catalysis. Science, 264(5167), 1924-1927.
18.Rebar, E. J. and C. O. Pabo (1994). Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science, 263(5147), 671-673.
19.Rosenwald, S., R. Kafri, et al. (2002). Test of a statistical model for molecular recognition in biological repertoires. J. Theor. Biol, 216(3), 327-36.[1]
20.Sun, F., D. Galas, et al. (1996). A mathematical analysis of in vitro molecular selection-amplification. J. Mol. Biol. 258(4), 650-660.
21.Thiesen, H. J. and C. Bach (1990). Target Detection Assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein. Nucleic Acids Res. 18(11), 3203-3209.
22.Tuerk, C. & Gold L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249(4968), 505-510.
23.Vant-Hull, B., A. Payano-Baez, et al. (1998). The mathematics of SELEX against complex targets. J. Mol. Biol. 278(3), 579-597.
24.Wilson, C. and J. W. Szostak (1995). In vitro evolution of a self-alkylating ribozyme. Nature, 374(6525), 777-782.
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top