Module 2: Analyzing Cloned NBS Sequences

References

1. Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975;98(3):503–17. doi:10.1016/s0022-2836(75)80083-0

2. Struhl K. Subcloning of DNA fragments. Curr Protoc Mol Biol. 2001;3(1):3.161-3.16.2. doi:10.1002/0471142727.mb0316s13

3. Novelli VM, Cristofani-Yaly M, Bastianel M, Palmieri DA, Machado MA. Screening of genomic libraries. Microsatellites. Methods Mol Biol. 2013;1006:17–24. doi:10.1007/978-1-62703-389-3_2

4. Shimizu N, Maekawa M, Asai S, Shimizu Y. Multicolor FISHs for simultaneous detection of genes and DNA segments on human chromosomes. Chromosome Res. 2015;23:649–62. doi:10.1007/s10577-015-9473-9

5. Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol. 2017;43(3):263–93. doi:10.3109/1040841X.2016.1169990

6. Gebbie L. Genomic Southern blot analysis. In: Henry, R., Furtado, A. (eds) Cereal Genomics. Methods Mol Biol v. 1099. Totowa, NJ: Humana Press; 2014. p.159–77. doi:10.1007/978-1-62703-715-0_14

7. Chang MM. Plasmid‐to‐plasmid Southern blot analysis validates the presence of nucleotide binding site (nbs) sequences in cloned plasmids. Biochem Mol Biol Educ. 2022;50(4):373–80. doi:10.1002/bmb.21642

8. Chang MM, DiGennaro P, Macula A. PCR cloning of partial nbs sequences from grape (Vitis aestivalis Michx). Biochem Mol Biol Educ. 2009;37(6):355–60. doi:10.1002/bmb.20320

9. Protocol – Plasmid Isolation by Boiling Method (Miniprep) [Internet]. Laboratory Notes; 2021 [accessed 2023 Feb 9]. Available from: https://www.laboratorynotes.com/protocol-plasmid-isolation-by-boiling-method-miniprep/

10. Ehrt S, Schnappinger D. Isolation of plasmids from E. coli by alkaline lysis. In: Casali, N., Preston, A. (eds) E. coli Plasmid Vectors. Methods Mol Biol v. 235. Totowa, NJ: Humana Press; 2003. p. 75–8. doi:10.1385/1-59259-409-3:75

11. Wang B, Merva M, Williams WV, Weiner DB. Large-scale preparation of plasmid DNA by microwave lysis. Biotechniques. 1995;18:554–5.

12. Ford T. Plasmids 101: Restriction Cloning [Internet]. Cambridge (MA): Addgene Blog; 2016 Feb 16 [accessed 2023 Mar 20]. Available from: https://blog.addgene.org/plasmids-101-restriction-cloning

13. Yu J, Zhang Z, Cao K, Huang X. Visualization of alkali-denatured supercoiled plasmid DNA by atomic force microscopy. Biochem Biophys Res Commun. 2008;374(3):415–8.

14. Southern blot. In: Wikipedia [Internet]. 2023 Jun 14 [accessed 2023 Feb 10]. Available from: https://en.wikipedia.org/wiki/Southern_blot

15. Transfer of DNA to a solid support [Internet]. ALPF Medical; 2014 [accessed 2023 Feb 10]. Available from: https://web.archive.org/web/20160510180823/https://www.alpfmedical.info/microsatellite-instability/transfer-of-dna-to-a-solid-support.html

16. GeneJET Gel Extraction Kit [Internet]. Waltham (MA): Thermo Fisher Scientific [accessed 2023 Feb 10]. Available from: https://www.thermofisher.com/order/catalog/product/K0691

17. Harwood AJ. End-labeling of DNA fragments. In: Harwood, AJ (ed) Basic DNA and RNA Protocols. Methods Mol Biol v.58. Totowa, NJ: Humana Press; 1996. p.105–10. doi:10.1385/0-89603-402-X:105

18. Rapley R, Theophilus BD. Internal labeling of DNA probes. In: Theophilus, BDM, Rapley, R (eds) PCR Mutation Detection Protocols. Methods Mol Biol v.187. Totowa, NJ: Humana press; 2002. p.13–5. doi:10.1385/1-59259-273-2:013

19. T4 Polynucleotide Kinase [Internet]. Waltham (MA): Thermo Fisher Scientific [accessed 2023 Apr 10]. Available from: https://www.thermofisher.com/order/catalog/product/EK0031

20. Green MR, Sambrook J. Labeling the 3′ Termini of Oligonucleotides Using Terminal Deoxynucleotidyl Transferase. Cold Spring Harb Protoc. 2021 Aug 2;2021(8). doi: 10.1101/pdb.prot100685. PMID: 34341178

21. Rigby PW, Dieckmann M, Rhodes C, Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977;113(1):237–51. doi:10.1016/0022-2836(77)90052-3

22. Smith DR. Random primed labeling of DNA. In: Murphy D, Carter DA (eds) Transgenesis Techniques. Methods Mol Biol v.18. Totowa, NJ: Humana Press; 1993. p.445–7. doi:10.1385/0-89603-245-0:445

23. Lion T, Haas OA. Nonradioactive labeling of the probe with digoxigenin by polymerase chain reaction. Anal Biochem. 1990;188(2):335–7. doi:10.1016/0003-2697(90)90616-h.

24. Technical guide for nonradioactive nucleic acid labeling and detection [Internet]. Milford (MA): SeraCare [accessed 2023 Feb 10]. Available from: https://www.seracare.com/globalassets/seracare-resources/tg-non-radioactive-nucleic-acid-labeling-and-detection.pdf

25. DIG application manual for filter hybridization [Internet]. Darmstadt (Germany): Sigma-Aldrich; [accessed 2023 Feb 11]. Available from: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/marketing/global/documents/199/985/dig-application-manual-for-filter-hybridisation-iris.pdf

26. Image of colorimetric substrates for alkaline phosphatase [Internet]. Darmstadt (Germany): Sigma-Aldrich; [accessed 2023 Feb 11]. Available from: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/marketing/global/images/technical-documents/articles/protein-biology/immunohistochemistry/figure-1-v3a4.gif

27. Translate tool – ExPASy [Internet]. Geneva (Switzerland): Swiss Institute of Bioinformatics; [accessed 2023 Feb 11]. Available from: https://web.expasy.org/translate/

28. Analyze Sequence – Addgene [Internet]. Cambridge (MA): Addgene [accessed 2023 Feb 11]. Available from: https://www.addgene.org/analyze-sequence/

29. BLAST: Basic Local Alignment Search Tool [Internet]. Bethesda (MD): National Center for Biotechnology Information [accessed 2023 Feb 11]. Available from: https://blast.ncbi.nlm.nih.gov/

30. Clustal Omega < Multiple Sequence Alignment < EMBL-EBI [Internet]. Hinxton (UK): European Bioinformatics Institute [accessed 2023 Feb 11]. Available from: https://www.ebi.ac.uk/Tools/msa/clustalo/

31. EMBOSS Needle < Pairwise Sequence Alignment < EMBL-EBI [Internet]. Hinxton (UK): European Bioinformatics Institute [accessed 2023 Feb 11]. Available from: https://www.ebi.ac.uk/jdispatcher/psa

32. StrataClone PCR Cloning Kit. [accessed 2023 February 8]. https://www.agilent.com/cs/library/usermanuals/public/240205.pdf

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