User:Jim892/sandbox2

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Unit 7 Assignment - (Outline, References, Images, Suggested Improvements)[edit]

Group Page Talk link: Group_84D (talk)

Outline for Article: Inverted Repeat --- (talk page for Inverted Repeat article)[edit]

  1. Lead paragraph (brief introduction)
  2. Definition & Examples
    1. cartoon to explain - Jim Perry has an idea for this - to be developed in future weeks
    2. Examples of Inverted Repeats
    3. Other types of repeats
      1. direct repeats vs. inverted repeats
      2. palindromes vs. inverted repeats
  3. Biological Features & Functionality
    1. Origin of Inverted Repeats - How they are introduced.
    2. Conditions that favor synthesis of Inverted Repeats.
    3. Most common biological functions using Inverted Repeats.
    4. Regions where presence is obligatory.
    5. Location of inverted repeats in the genome - how, why and where
    6. Inverted repeats common in different organisms
  4. Databases of Inverted Repeats (with External Links as appropriate)
  5. References

Information about the References[edit]

  • Inverted Repeats and DNA replication. 1996 review article. Might be good (or might be too old?) [1]
  • RNA related. Is CRISPR a potential category? CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats [2]
  • palindrome-mediated translocations are localized at the center of palindromic AT-rich repeats (PATRRs)[3]
  • DNA inverted repeats in the genome. Might be a special category? [4]
  • Folded DNA - Hairpins [5]
  • Inverted repeats in the male-specific region of the human chromosome Y(MSY) [6]
  • Instability of palindromes by formation of a hairpin or cruciform structure and the resultant chromosomal deletion or translocation.[7]
  • Holliday-junction resolution in homologous recombination and coding joint formation in rearrangement of antigen-receptor genes.[8]
  • Hypertensive crises caused by inverted left atrial appendage.[9]
  • Families of inverted repeat fold transporters.[10]
  • Size and distribution of inverted repeats in D. melanogaster DNA.[11]
  • Transient blindness and transurethral resection.[12]
  • Inverted sequences among families of repetition frequencies.[13]
  • Faulty application fork maintenance pathways at nonallelic repeats and cancer and genomic disorders and speciation.[14]
  • The properties of inverted repeat sequences in wheat nuclear DNA.[15]
  • Invereted repeats in spinach, corn and lettuce.[16]
  • Inverted repeats in MDg3 of Drosophila melanogaster.[17]

References:

  1. ^ Pearson, C. E.; Zorbas, H.; Price, G. B.; Zannis-Hadjopoulos, M. (1996 Oct). "Inverted repeats, stem-loops, and cruciforms: significance for initiation of DNA replication". Journal of Cellular Biochemistry. 63 (1): 1–22. doi:10.1002/(SICI)1097-4644(199610)63:1<1::AID-JCB1>3.0.CO;2-3. PMID 8891900. Retrieved 19 October 2013. {{cite journal}}: Check date values in: |date= (help)
  2. ^ Richter, C (2012 Oct 19). "Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems". Viruses. 4 (10): 2291–311. doi:10.3390/v4102291. PMC 3497052. PMID 23202464. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  3. ^ Kato, T.; Kurahashi, H.; Emanuel, B. S. (2012 Jun). "Chromosomal translocations and palindromic AT-rich repeats". Current Opinion in Genetics & Development. 22 (3): 221–8. doi:10.1016/j.gde.2012.02.004. PMC 3378763. PMID 22402448. {{cite journal}}: Check date values in: |date= (help)
  4. ^ Tanaka, H.; Yao, M. C. (2009 Mar). "Palindromic gene amplification--an evolutionarily conserved role for DNA inverted repeats in the genome". Nature Reviews. Cancer. 9 (3): 216–24. doi:10.1038/nrc2591. PMID 19212324. {{cite journal}}: Check date values in: |date= (help)
  5. ^ Bikard, D.; Loot, C.; Baharoglu, Z.; Mazel, D. (2010 Dec). "Folded DNA in action: hairpin formation and biological functions in prokaryotes". Microbiology and Molecular Biology Reviews : MMBR. 74 (4): 570–88. doi:10.1128/MMBR.00026-10. PMC 3008174. PMID 21119018. {{cite journal}}: Check date values in: |date= (help)
  6. ^ Hallast, P.; Balaresque, P.; Bowden, G. R.; Ballereau, S.; Jobling, M. A. (2013 Jul). "Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions". PLOS Genetics. 9 (7): e1003666. doi:10.1371/journal.pgen.1003666. PMC 3723533. PMID 23935520. {{cite journal}}: Check date values in: |date= (help)CS1 maint: unflagged free DOI (link)
  7. ^ Chen, X.; Xiao, F.; Guo, J. (2013 May). "[The mechanisms of palindrome-stimulated mutation and related human diseases]". Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. 35 (5): 571–7. doi:10.3724/sp.j.1005.2013.00571. PMID 23732662. {{cite journal}}: Check date values in: |date= (help)
  8. ^ Inagaki, H.; Ohye, T.; Kogo, H.; Tsutsumi, M.; Kato, T.; Tong, M.; Emanuel, B. S.; Kurahashi, H. (2013). "Two sequential cleavage reactions on cruciform DNA structures cause palindrome-mediated chromosomal translocations". Nature Communications. 4: 1592. doi:10.1038/ncomms2595. PMID 23481400.
  9. ^ Zhao, Q.; Hu, X. (2013 Sep). "Postoperative pulmonary hypertensive crisis caused by inverted left atrial appendage after cardiopulmonary bypass surgery for congenital heart disease in a neonate". Heart, Lung & Circulation. 22 (9): 781–3. doi:10.1016/j.hlc.2013.03.006. PMID 24054493. {{cite journal}}: Check date values in: |date= (help)
  10. ^ Saier Jr, M. H.; Saier, Milton H. (2013 Aug 28). "Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily". Proteins. 82 (2): 336–346. doi:10.1002/prot.24401. PMID 24038584. {{cite journal}}: Check date values in: |date= (help)
  11. ^ Biezunski, N (1981). "Structure and distribution of inverted repeats (Palindromes). I. Analysis of DNA of Drosophila melanogaster". Chromosoma. 84 (1): 87–109. doi:10.1007/BF00293365. PMID 6794998.
  12. ^ Appelt, GL (1979 Apr). "Transient blindness: unusual initial symptom of transurethral prostatic resection reaction". Urology. 13 (4): 402–4. doi:10.1016/0090-4295(79)90340-6. PMID 433047. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  13. ^ Dott, P. J.; Chuang, C. R.; Saunders, G. F. (1976 Sep 7). "Inverted repetitive sequences in the human genome". Biochemistry. 15 (18): 4120–5. doi:10.1021/bi00663a032. PMID 963027. {{cite journal}}: Check date values in: |date= (help)
  14. ^ Hu, L.; Kim, T. M.; Son, M. Y.; Kim, S. A.; Holland, C. L.; Tateishi, S.; Kim, D. H.; Yew, P. R.; Montagna, C.; Dumitrache, L. C.; Hasty, P. (2013 Sep 26). "Two replication fork maintenance pathways fuse inverted repeats to rearrange chromosomes". Nature. 501 (7468): 569–72. doi:10.1038/nature12500. PMC 3805358. PMID 24013173. {{cite journal}}: Check date values in: |date= (help)
  15. ^ Bazetoux, S.; Jouanin, L.; Huguet, T. (1978 Mar). "Characterization of inverted repeated sequences in wheat nuclear DNA". Nucleic Acids Research. 5 (3): 751–69. doi:10.1093/nar/5.3.751. PMC 342021. PMID 643618. {{cite journal}}: Check date values in: |date= (help)
  16. ^ Kolodner, R.; Tewari, K. K. (1979 Jan). "Inverted repeats in chloroplast DNA from higher plants". Proceedings of the National Academy of Sciences of the United States of America. 76 (1): 41–5. doi:10.1073/pnas.76.1.41. PMC 382872. PMID 16592612. {{cite journal}}: Check date values in: |date= (help)
  17. ^ Bayev Jr, A. A.; Krayev, A. S.; Lyubomirskaya, N. V.; Ilyin, Y. V.; Skryabin, K. G.; Georgiev, G. P. (1980 Aug 11). "The transposable element Mdg3 in Drosophila melanogaster is flanked with the perfect direct and mismatched inverted repeats". Nucleic Acids Research. 8 (15): 3263–73. doi:10.1093/nar/8.15.3263. PMC 324151. PMID 6255410. {{cite journal}}: Check date values in: |date= (help)

Possible Images[edit]

We will need to get permission before using these unless already under the proper license:

Hairpin Image: http://course1.winona.edu/sberg/ILLUST/hairpin.JPG

Open Access Article: http://www.biomedcentral.com/1471-2164/7/73/

See Figure 3 in this article for a good example of an inverted repeat
Here is the link to the photo: http://www.biomedcentral.com/1471-2164/7/73/figure/F3

Palidrome and mirror repeats: http://www.siumed.edu/~bbartholomew/images/Lehninger/img035.gif

Examples of inverted repeats: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/RecognitionHelix.gif

Suggested Improvements: These are listed on the talk page for the article[edit]

LINK: Article talk page (for the Inverted Repeat article)


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