Dizajn nukleinskih kiselina
![](http://upload.wikimedia.org/wikipedia/commons/thumb/c/c5/Mao-4armjunction-schematic.png/250px-Mao-4armjunction-schematic.png)
Dizajn nukleinskih kiselina je proces generisanja skupa nukleinskih kiselina koje formiraju željenu konformaciju. Dizajn nukleinskih kiselina je centralno polje DNK nanotehnologije i DNK računarstva.[2] Dizajn je neophodan jer postoji mnoštvo sekvenci nukleinskih kiselina koje će formirati datu sekundarnu strukturu, ali će većina njih imati dodatne neželjene interakcije koje se moraju izbeći. Pored toga postoji mnoštvo tercijarnih strukturnih razmatranja koja utiču na izbor sekundarne strukture datog dizajna.[3][4]
Dizajn nukleinskih kiselina ima slične ciljeve sa dizajnom proteina: u oba procesa, sekvenca monomera se racionalno dizajnira da bi se savila na željeni način i da bi se izbegle neželjene konformacije. Dizajn nukleinskih kiselina je znatno računski jednostavniji problem, usled jednostavnosti pravila uparivanja baza, te jednostavni heuristički metodi proizvode eksperimentalno robustne dizajne. Za rad većine računarskih modela za savijanje proteina je neophodan templet tercijarne strukture, dok se dizajn nukleinskih kiselina može izvoditi uglavnom na nivou sekundarne strukture. Strukture nukleinskih kiselina su znatno manje raznovrsne od proteina u pogledu njihove funkcionalnosti.[2][5]
Dizajn nukleinskih kiselina se može smatrati inverznim procesom od predviđanja strukture nukleinskih kiselina. U predviđanju strukture ona se određuje polazeći od poznate sekvence, dok se u dizajnu nukleinske kiseline, sekvenca generiše tako da formira željenu strukturu.[2]
Reference
- ↑ Mao, Chengde (December 2004). „The Emergence of Complexity: Lessons from DNA”. PLoS Biology 2 (12): 2036–2038. DOI:10.1371/journal.pbio.0020431. ISSN 1544-9173. PMC 535573. PMID 15597116.
- ↑ 2,0 2,1 2,2 Dirks, Robert M.; Lin, Milo; Winfree, Erik & Pierce, Niles A. (2004). „Paradigms for computational nucleic acid design”. Nucleic Acids Research 32 (4): 1392–1403. DOI:10.1093/nar/gkh291. PMC 390280. PMID 14990744.
- ↑ Seeman, N (1982). „Nucleic acid junctions and lattices”. Journal of Theoretical Biology 99 (2): 237–47. DOI:10.1016/0022-5193(82)90002-9. PMID 6188926.
- ↑ Sherman, W; Seeman, N (2006). „Design of Minimally Strained Nucleic Acid Nanotubes”. Biophysical Journal 90 (12): 4546–57. Bibcode 2006BpJ....90.4546S. DOI:10.1529/biophysj.105.080390. PMC 1471877. PMID 16581842.
- ↑ Brenneman, Arwen; Condon, Anne (2002). „Strand design for biomolecular computation”. Theoretical Computer Science 287: 39. DOI:10.1016/S0304-3975(02)00135-4.
Literatura
- Brenneman, Arwen; Condon, Anne (2002). „Strand design for biomolecular computation”. Theoretical Computer Science 287: 39. DOI:10.1016/S0304-3975(02)00135-4.
- Dirks, Robert M.; Lin, Milo; Winfree, Erik; Pierce, Niles A. (2004). „Paradigms for computational nucleic acid design”. Nucleic Acids Research 32 (4): 1392–1403. DOI:10.1093/nar/gkh291. PMC 390280. PMID 14990744.
- Seeman, N (1982). „Nucleic acid junctions and lattices”. Journal of Theoretical Biology 99 (2): 237–47. DOI:10.1016/0022-5193(82)90002-9. PMID 6188926.
- Andersen, Ebbe Sloth (2010). „Prediction and design of DNA and RNA structures”. New Biotechnology 27 (3): 184–193. DOI:10.1016/j.nbt.2010.02.012. PMID 20193785.
- Baker D and Sali A. Protein structure prediction and structural genomics. Science 2001; 294: 93-6.
- Chiu, D.K. and Kolodziejczak, T. (1991) Inferring consensus structure from nucleic acid sequences. Comput. Appl. Biosci, . 7, 347–352
- Do CB, Woods DA, Batzoglou S. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 22(14):e90-8.
- Gutell, R.R., et al. (1992) Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res, . 20, 5785–5795
- Leontis NB, Lescoute A, and Westhof E. The building blocks and motifs of RNA architecture. Curr Opin Struct Biol 2006; 16: 279-87.
- Lindgreen S, Gardner PP, Krogh A (2006). „Measuring covariation in RNA alignments: physical realism improves information measures”. Bioinformatics 22 (24): 2988–95. DOI:10.1093/bioinformatics/btl514. PMID 17038338.
- Macke T, Case D: Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. Edited by Leontes N, SantaLucia JJ. Washington, DC: American Chemical Society; 1998:379-393.
- Major F: Building three-dimensional ribonucleic acid structures. Comput Sci Eng 2003, 5:44-53.
- Massire C, Westhof E: MANIP: an interactive tool for modelling RNA. J Mol Graph Model 1998, 16:197-205, 255–257.
- Parisien M., Major F. (2008). „The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data”. Nature 452 (7183): 51–55. Bibcode 2008Natur.452...51P. DOI:10.1038/nature06684. PMID 18322526.
- Tuzet, H. & Perriquet, O., 2004. CARNAC: folding families of related RNAs. Nucleic Acids Research, 32(Web Server issue), W142-145.
- Touzet, H., 2007. Comparative analysis of RNA genes: the caRNAc software. Methods in Molecular Biology (Clifton, N.J.), 395, 465-474.
- Yingling YG, Shapiro BA (2006). „The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation”. J Mol Graph Model 25 (2): 261–274. DOI:10.1016/j.jmgm.2006.01.003. PMID 16481205.
- Zwieb C, Muller F (1997). „Three-dimensional comparative modeling of RNA”. Nucleic Acids Symp Ser 36 (36): 69–71. PMID 9478210.
- ModeRNA: A program for comparative RNA modeling
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