publication . Article . 2018

A calibrated diversity assay for nucleic acid libraries using DiStRO—a Diversity Standard of Random Oligonucleotides

Schütze, Tatjana; Arndt, Peter F.; Menger, Marcus; Wochner, Aniela; Vingron, Martin; Erdmann, Volker A.; Lehrach, Hans; Kaps, Christian; Glökler, Jörn;
Open Access
  • Published: 13 Nov 2018 Journal: Nucleic Acids Research, volume 38, pages e23-e23 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
We have determined diversities exceeding 10(12) different sequences in an annealing and melting assay using synthetic randomized oligonucleotides as a standard. For such high diversities, the annealing kinetics differ from those observed for low diversities, favouring the remelting curve after annealing as the best indicator of complexity. Direct comparisons of nucleic acid pools obtained from an aptamer selection demonstrate that even highly complex populations can be evaluated by using DiStRO, without the need of complicated calculations.
Subjects
Medical Subject Headings: human activitiesrespiratory system
free text keywords: Nucleic acid thermodynamics, SELEX Aptamer Technique, Molecular biology, Oligonucleotide, Genetics, Biology, Reference standards, Nucleic Acid Denaturation, Nucleic acid, Aptamer, Methods Online
16 references, page 1 of 2

Tuerk, C, Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990; 249: 505-510 [OpenAIRE] [PubMed]

Ellington, AD, Szostak, JW. In vitro selection of RNA molecules that bind specific ligands. Nature. 1990; 346: 818-822 [OpenAIRE] [PubMed]

Stoltenburg, R, Reinemann, C, Strehlitz, B. SELEX—a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng.. 2007; 24: 381-403 [OpenAIRE] [PubMed]

Mardis, ER. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet.. 2008; 9: 387-402 [OpenAIRE] [PubMed]

Britten, RJ, Kohne, DE. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science. 1968; 161: 529-540 [OpenAIRE] [PubMed]

Charlton, J, Smith, D. Estimation of SELEX pool size by measurement of DNA renaturation rates. RNA. 1999; 5: 1326-1332 [OpenAIRE] [PubMed]

Baum, PD, McCune, JM. Direct measurement of T-cell receptor repertoire diversity with AmpliCot. Nat. Methods. 2006; 3: 895-901 [OpenAIRE] [PubMed]

Ririe, KM, Rasmussen, RP, Wittwer, CT. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem.. 1997; 245: 154-160 [OpenAIRE] [PubMed]

Wochner, A, Cech, B, Menger, M, Erdmann, VA, Glökler, J. Semi-automated selection of DNA aptamers using magnetic particle handling. BioTechniques. 2007; 43: 344 [PubMed]

Wochner, A, Glökler, J. Nonradioactive fluorescence microtiter plate assay monitoring aptamer selections. BioTechniques. 2007; 42: 578 [PubMed]

Gupta, RD, Tawfik, DS. Directed enzyme evolution via small and effective neutral drift libraries. Nat. Methods. 2008; 5: 939-942 [OpenAIRE] [PubMed]

Lynch, SA, Gallivan, JP. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res.. 2009; 37: 184-192 [OpenAIRE] [PubMed]

Stein, V, Hollfelder, F. An efficient method to assemble linear DNA templates for in vitro screening and selection systems. Nucleic Acids Res.. 2009; 37: e122 [OpenAIRE] [PubMed]

Lister, R, Gregory, BD, Ecker, JR. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr. Opin. Plant Biol.. 2009; 12: 107-118 [OpenAIRE] [PubMed]

Shendure, J, Ji, H. Next-generation DNA sequencing. Nat. Biotechnol.. 2008; 26: 1135-1145 [OpenAIRE] [PubMed]

16 references, page 1 of 2
Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue