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. 1998 Feb 15;26(4):879–886. doi: 10.1093/nar/26.4.879

Combinatorial library diversity: probability assessment of library populations.

B Ward 1, T Juehne 1
PMCID: PMC147359  PMID: 9461443

Abstract

A method is described for measuring the diversity of combinatorial oligonucleotide libraries that entails extrapolating the base composition of a co-synthesized model library (dNC, N = A, C, G, T) to that of a multibase library template. The base composition of dNC was measured by HPLC. The ability of dNC to predict the base composition of a multibase library template was corroborated by measuring the composition of a 12 base combinatorial library. The base composition of the 12 base library was determined by several template dependent incorporation assays: measurement of restriction fragment specific activities from polymerase incorporation/restriction enzyme digests, template directed radionucleotide primer extension and quantitative dideoxynucleotide sequencing. Additionally, a convention for describing oligomeric combinatorial library (OCL) diversity is proposed. The convention uses a quantity termed the diversity quotient (Qd) to describe library breadth and the mole fraction of the least represented monomeric unit of the OCL to calculate minimum library quantity requirements. Similar methods/conventions could presumably be developed/adopted for non-nucleic acid libraries.

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Selected References

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  1. Abravaya K., Carrino J. J., Muldoon S., Lee H. H. Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res. 1995 Feb 25;23(4):675–682. doi: 10.1093/nar/23.4.675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barany F. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):189–193. doi: 10.1073/pnas.88.1.189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bartel D. P., Szostak J. W. Isolation of new ribozymes from a large pool of random sequences [see comment]. Science. 1993 Sep 10;261(5127):1411–1418. doi: 10.1126/science.7690155. [DOI] [PubMed] [Google Scholar]
  4. Brown M. A., Solomon E. Studies on inherited cancers: outcomes and challenges of 25 years. Trends Genet. 1997 May;13(5):202–206. doi: 10.1016/s0168-9525(97)01132-3. [DOI] [PubMed] [Google Scholar]
  5. Cavenee W. K., Dryja T. P., Phillips R. A., Benedict W. F., Godbout R., Gallie B. L., Murphree A. L., Strong L. C., White R. L. Expression of recessive alleles by chromosomal mechanisms in retinoblastoma. 1983 Oct 27-Nov 2Nature. 305(5937):779–784. doi: 10.1038/305779a0. [DOI] [PubMed] [Google Scholar]
  6. Chapman K. B., Szostak J. W. In vitro selection of catalytic RNAs. Curr Opin Struct Biol. 1994;4:618–622. doi: 10.1016/s0959-440x(94)90227-5. [DOI] [PubMed] [Google Scholar]
  7. Ciesiolka J., Illangasekare M., Majerfeld I., Nickles T., Welch M., Yarus M., Zinnen S. Affinity selection-amplification from randomized ribooligonucleotide pools. Methods Enzymol. 1996;267:315–335. doi: 10.1016/s0076-6879(96)67021-9. [DOI] [PubMed] [Google Scholar]
  8. Conrad R. C., Baskerville S., Ellington A. D. In vitro selection methodologies to probe RNA function and structure. Mol Divers. 1995 Sep;1(1):69–78. doi: 10.1007/BF01715810. [DOI] [PubMed] [Google Scholar]
  9. Conrad R. C., Giver L., Tian Y., Ellington A. D. In vitro selection of nucleic acid aptamers that bind proteins. Methods Enzymol. 1996;267:336–367. doi: 10.1016/s0076-6879(96)67022-0. [DOI] [PubMed] [Google Scholar]
  10. Davies M. S., Wallis S. C., Driscoll D. M., Wynne J. K., Williams G. W., Powell L. M., Scott J. Sequence requirements for apolipoprotein B RNA editing in transfected rat hepatoma cells. J Biol Chem. 1989 Aug 15;264(23):13395–13398. [PubMed] [Google Scholar]
  11. Dille B. J., Butzen C. C., Birkenmeyer L. G. Amplification of Chlamydia trachomatis DNA by ligase chain reaction. J Clin Microbiol. 1993 Mar;31(3):729–731. doi: 10.1128/jcm.31.3.729-731.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ekland E. H., Szostak J. W., Bartel D. P. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science. 1995 Jul 21;269(5222):364–370. doi: 10.1126/science.7618102. [DOI] [PubMed] [Google Scholar]
  13. Fitzwater T., Polisky B. A SELEX primer. Methods Enzymol. 1996;267:275–301. doi: 10.1016/s0076-6879(96)67019-0. [DOI] [PubMed] [Google Scholar]
  14. Frenkel L. M., Wagner L. E., 2nd, Atwood S. M., Cummins T. J., Dewhurst S. Specific, sensitive, and rapid assay for human immunodeficiency virus type 1 pol mutations associated with resistance to zidovudine and didanosine. J Clin Microbiol. 1995 Feb;33(2):342–347. doi: 10.1128/jcm.33.2.342-347.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gold L., Polisky B., Uhlenbeck O., Yarus M. Diversity of oligonucleotide functions. Annu Rev Biochem. 1995;64:763–797. doi: 10.1146/annurev.bi.64.070195.003555. [DOI] [PubMed] [Google Scholar]
  16. Hardenbol P., Van Dyke M. W. Sequence specificity of triplex DNA formation: Analysis by a combinatorial approach, restriction endonuclease protection selection and amplification. Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2811–2816. doi: 10.1073/pnas.93.7.2811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Haris I. I., Green P. M., Bentley D. R., Giannelli F. Mutation detection by fluorescent chemical cleavage: application to hemophilia B. PCR Methods Appl. 1994 Apr;3(5):268–271. doi: 10.1101/gr.3.5.268. [DOI] [PubMed] [Google Scholar]
  18. Huizenga D. E., Szostak J. W. A DNA aptamer that binds adenosine and ATP. Biochemistry. 1995 Jan 17;34(2):656–665. doi: 10.1021/bi00002a033. [DOI] [PubMed] [Google Scholar]
  19. Ihalainen J., Siitari H., Laine S., Syvänen A. C., Palotie A. Towards automatic detection of point mutations: use of scintillating microplates in solid-phase minisequencing. Biotechniques. 1994 May;16(5):938–943. [PubMed] [Google Scholar]
  20. Kallansrud G., Ward B. A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients. Anal Biochem. 1996 Apr 5;236(1):134–138. doi: 10.1006/abio.1996.0141. [DOI] [PubMed] [Google Scholar]
  21. Kälin I., Shephard S., Candrian U. Evaluation of the ligase chain reaction (LCR) for the detection of point mutations. Mutat Res. 1992 Oct;283(2):119–123. doi: 10.1016/0165-7992(92)90143-6. [DOI] [PubMed] [Google Scholar]
  22. Laffler T. G., Carrino J. J., Marshall R. L. The ligase chain reaction in DNA-based diagnosis. Ann Biol Clin (Paris) 1993;51(9):821–826. [PubMed] [Google Scholar]
  23. Landegren U., Kaiser R., Sanders J., Hood L. A ligase-mediated gene detection technique. Science. 1988 Aug 26;241(4869):1077–1080. doi: 10.1126/science.3413476. [DOI] [PubMed] [Google Scholar]
  24. Minamitani S., Nishiguchi S., Kuroki T., Otani S., Monna T. Detection by ligase chain reaction of precore mutant of hepatitis B virus. Hepatology. 1997 Jan;25(1):216–222. doi: 10.1053/jhep.1997.v25.pm0008985293. [DOI] [PubMed] [Google Scholar]
  25. Nakabayashi Y., Nishigaki K. Single-strand conformation polymorphism (SSCP) can be explained by semistable conformation dynamics of single-stranded DNA. J Biochem. 1996 Aug;120(2):320–325. doi: 10.1093/oxfordjournals.jbchem.a021416. [DOI] [PubMed] [Google Scholar]
  26. Osborne Scott E., Ellington Andrew D. Nucleic Acid Selection and the Challenge of Combinatorial Chemistry. Chem Rev. 1997 Apr 1;97(2):349–370. doi: 10.1021/cr960009c. [DOI] [PubMed] [Google Scholar]
  27. Powell S. M., Petersen G. M., Krush A. J., Booker S., Jen J., Giardiello F. M., Hamilton S. R., Vogelstein B., Kinzler K. W. Molecular diagnosis of familial adenomatous polyposis. N Engl J Med. 1993 Dec 30;329(27):1982–1987. doi: 10.1056/NEJM199312303292702. [DOI] [PubMed] [Google Scholar]
  28. Redston M. S., Papadopoulos N., Caldas C., Kinzler K. W., Kern S. E. Common occurrence of APC and K-ras gene mutations in the spectrum of colitis-associated neoplasias. Gastroenterology. 1995 Feb;108(2):383–392. doi: 10.1016/0016-5085(95)90064-0. [DOI] [PubMed] [Google Scholar]
  29. Samiotaki M., Kwiatkowski M., Parik J., Landegren U. Dual-color detection of DNA sequence variants by ligase-mediated analysis. Genomics. 1994 Mar 15;20(2):238–242. doi: 10.1006/geno.1994.1159. [DOI] [PubMed] [Google Scholar]
  30. Sharma P. M., Bowman M., Madden S. L., Rauscher F. J., 3rd, Sukumar S. RNA editing in the Wilms' tumor susceptibility gene, WT1. Genes Dev. 1994 Mar 15;8(6):720–731. doi: 10.1101/gad.8.6.720. [DOI] [PubMed] [Google Scholar]
  31. Syvänen A. C. Detection of point mutations in human genes by the solid-phase minisequencing method. Clin Chim Acta. 1994 May;226(2):225–236. doi: 10.1016/0009-8981(94)90217-8. [DOI] [PubMed] [Google Scholar]
  32. Syvänen A. C., Sajantila A., Lukka M. Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am J Hum Genet. 1993 Jan;52(1):46–59. [PMC free article] [PubMed] [Google Scholar]
  33. Tabler M., Benos P., Dörr M. Representation of unique sequences in libraries of randomized nucleic acids. Nucleic Acids Res. 1996 Sep 1;24(17):3437–3438. doi: 10.1093/nar/24.17.3437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Tanno Y., Yoneda M., Tanaka K., Tanaka H., Yamazaki M., Nishizawa M., Wakabayashi K., Ohama E., Tsuji S. Quantitation of heteroplasmy of mitochondrial tRNA(Leu(UUR)) gene using PCR-SSCP. Muscle Nerve. 1995 Dec;18(12):1390–1397. doi: 10.1002/mus.880181208. [DOI] [PubMed] [Google Scholar]
  35. Trotta P. P., Beutel B. A., Sherman M. I. Oligonucleotide diversity and drug discovery. Med Res Rev. 1995 Jul;15(4):277–298. doi: 10.1002/med.2610150403. [DOI] [PubMed] [Google Scholar]
  36. Ward B. Type IIS restriction enzyme footprinting I. Measurement of a triple helix dissociation constant with Eco57I at 25 degrees C. Nucleic Acids Res. 1996 Jun 15;24(12):2435–2440. doi: 10.1093/nar/24.12.2435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Wiedmann M., Barany F., Batt C. A. Detection of Listeria monocytogenes with a nonisotopic polymerase chain reaction-coupled ligase chain reaction assay. Appl Environ Microbiol. 1993 Aug;59(8):2743–2745. doi: 10.1128/aem.59.8.2743-2745.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wu D. Y., Wallace R. B. Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene. 1989;76(2):245–254. doi: 10.1016/0378-1119(89)90165-0. [DOI] [PubMed] [Google Scholar]
  39. Wu D. Y., Wallace R. B. The ligation amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics. 1989 May;4(4):560–569. doi: 10.1016/0888-7543(89)90280-2. [DOI] [PubMed] [Google Scholar]

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