User:Jim892/sandbox2

:::::Group Page Talk link: {{Font color||yellow| Group_84D (talk)}}

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

• Inverted Repeats and DNA replication. 1996 review article. Might be good (or might be too old?) {{cite journal|title=Inverted repeats, stem-loops, and cruciforms: significance for initiation of DNA replication.|journal=Journal of Cellular Biochemistry|date=1996 Oct|volume=63|issue=1|pages=1–22|pmid=8891900|url=http://www.ncbi.nlm.nih.gov/pubmed/8891900|accessdate=19 October 2013 |last1=Pearson |first1=C. E. |last2=Zorbas |first2=H. |last3=Price |first3=G. B. |last4=Zannis-Hadjopoulos |first4=M. |doi=10.1002/(SICI)1097-4644(199610)63:1<1::AID-JCB1>3.0.CO;2-3 }}

• RNA related. Is CRISPR a potential category? CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats {{cite journal|last=Richter|first=C|coauthors=Chang, JT; Fineran, PC|title=Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems.|journal=Viruses|date=2012 Oct 19|volume=4|issue=10|pages=2291–311|doi=10.3390/v4102291|pmid=23202464|pmc=3497052|doi-access=free}}

• palindrome-mediated translocations are localized at the center of palindromic AT-rich repeats (PATRRs){{cite journal|title=Chromosomal translocations and palindromic AT-rich repeats.|journal=Current Opinion in Genetics & Development|date=2012 Jun|volume=22|issue=3|pages=221–8|pmid=22402448|last1=Kato|first1=T.|last2=Kurahashi|first2=H.|last3=Emanuel|first3=B. S.|doi=10.1016/j.gde.2012.02.004|pmc=3378763}}

• DNA inverted repeats in the genome. Might be a special category? {{cite journal|title=Palindromic gene amplification--an evolutionarily conserved role for DNA inverted repeats in the genome.|journal=Nature Reviews. Cancer|date=2009 Mar|volume=9|issue=3|pages=216–24|pmid=19212324|url=http://www.ncbi.nlm.nih.gov/pubmed/19212324|last1=Tanaka|first1=H.|last2=Yao|first2=M. C.|doi=10.1038/nrc2591}}

• Folded DNA - Hairpins {{cite journal|title=Folded DNA in action: hairpin formation and biological functions in prokaryotes.|journal=Microbiology and Molecular Biology Reviews : MMBR|date=2010 Dec|volume=74|issue=4|pages=570–88|pmid=21119018|last1=Bikard|first1=D.|last2=Loot|first2=C.|last3=Baharoglu|first3=Z.|last4=Mazel|first4=D.|doi=10.1128/MMBR.00026-10|pmc=3008174}}

• Inverted repeats in the male-specific region of the human chromosome Y(MSY) {{cite journal|title=Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions.|journal=PLOS Genetics|date=2013 Jul|volume=9|issue=7|pages=e1003666|pmid=23935520|last1=Hallast|first1=P.|last2=Balaresque|first2=P.|last3=Bowden|first3=G. R.|last4=Ballereau|first4=S.|last5=Jobling|first5=M. A.|doi=10.1371/journal.pgen.1003666|pmc=3723533}}

• Instability of palindromes by formation of a hairpin or cruciform structure and the resultant chromosomal deletion or translocation.{{cite journal|title=[The mechanisms of palindrome-stimulated mutation and related human diseases].|journal=Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji|date=2013 May|volume=35|issue=5|pages=571–7|pmid=23732662 |last1=Chen |first1=X. |last2=Xiao |first2=F. |last3=Guo |first3=J. |doi=10.3724/sp.j.1005.2013.00571 }}

• Holliday-junction resolution in homologous recombination and coding joint formation in rearrangement of antigen-receptor genes.{{cite journal|title=Two sequential cleavage reactions on cruciform DNA structures cause palindrome-mediated chromosomal translocations.|journal=Nature Communications|date=2013|volume=4|pages=1592|pmid=23481400|last1=Inagaki|first1=H.|last2=Ohye|first2=T.|last3=Kogo|first3=H.|last4=Tsutsumi|first4=M.|last5=Kato|first5=T.|last6=Tong|first6=M.|last7=Emanuel|first7=B. S.|last8=Kurahashi|first8=H.|doi=10.1038/ncomms2595}}

• Hypertensive crises caused by inverted left atrial appendage.{{cite journal|title=Postoperative pulmonary hypertensive crisis caused by inverted left atrial appendage after cardiopulmonary bypass surgery for congenital heart disease in a neonate.|journal=Heart, Lung & Circulation|date=2013 Sep|volume=22|issue=9|pages=781–3|pmid=24054493|last1=Zhao|first1=Q.|last2=Hu|first2=X.|doi=10.1016/j.hlc.2013.03.006}}

• Families of inverted repeat fold transporters.{{cite journal|title=Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily.|journal=Proteins|date=2013 Aug 28|pmid=24038584|last1=Saier Jr|first1=M. H.|last2=Saier|first2=Milton H.|volume=82|issue=2|pages=336–346|doi=10.1002/prot.24401}}

• Size and distribution of inverted repeats in D. melanogaster DNA.{{cite journal|last=Biezunski|first=N|title=Structure and distribution of inverted repeats (Palindromes). I. Analysis of DNA of Drosophila melanogaster.|journal=Chromosoma|date=1981|volume=84|issue=1|pages=87–109|doi=10.1007/BF00293365|pmid=6794998}}

• Transient blindness and transurethral resection.{{cite journal|last=Appelt|first=GL|coauthors=Benson, GS; Corriere JN, Jr|title=Transient blindness: unusual initial symptom of transurethral prostatic resection reaction.|journal=Urology|date=1979 Apr|volume=13|issue=4|pages=402–4|doi=10.1016/0090-4295(79)90340-6 |pmid=433047}}

• Inverted sequences among families of repetition frequencies.{{cite journal|title=Inverted repetitive sequences in the human genome.|journal=Biochemistry|date=1976 Sep 7|volume=15|issue=18|pages=4120–5|pmid=963027 |last1=Dott |first1=P. J. |last2=Chuang |first2=C. R. |last3=Saunders |first3=G. F. |doi=10.1021/bi00663a032 }}

• Faulty application fork maintenance pathways at nonallelic repeats and cancer and genomic disorders and speciation.{{cite journal|title=Two replication fork maintenance pathways fuse inverted repeats to rearrange chromosomes.|journal=Nature|date=2013 Sep 26|volume=501|issue=7468|pages=569–72|pmid=24013173|last1=Hu|first1=L.|last2=Kim|first2=T. M.|last3=Son|first3=M. Y.|last4=Kim|first4=S. A.|last5=Holland|first5=C. L.|last6=Tateishi|first6=S.|last7=Kim|first7=D. H.|last8=Yew|first8=P. R.|last9=Montagna|first9=C.|last10=Dumitrache|first10=L. C.|last11=Hasty|first11=P.|doi=10.1038/nature12500|pmc=3805358}}

• The properties of inverted repeat sequences in wheat nuclear DNA.{{cite journal|title=Characterization of inverted repeated sequences in wheat nuclear DNA.|journal=Nucleic Acids Research|date=1978 Mar|volume=5|issue=3|pages=751–69|pmid=643618|last1=Bazetoux|first1=S.|last2=Jouanin|first2=L.|last3=Huguet|first3=T.|doi=10.1093/nar/5.3.751|pmc=342021}}

• Invereted repeats in spinach, corn and lettuce.{{cite journal|title=Inverted repeats in chloroplast DNA from higher plants.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=1979 Jan|volume=76|issue=1|pages=41–5|pmid=16592612|last1=Kolodner|first1=R.|last2=Tewari|first2=K. K.|doi=10.1073/pnas.76.1.41|pmc=382872|doi-access=free}}

• Inverted repeats in MDg3 of Drosophila melanogaster.{{cite journal|title=The transposable element Mdg3 in Drosophila melanogaster is flanked with the perfect direct and mismatched inverted repeats.|journal=Nucleic Acids Research|date=1980 Aug 11|volume=8|issue=15|pages=3263–73|pmid=6255410 |last1=Bayev Jr |first1=A. A. |last2=Krayev |first2=A. S. |last3=Lyubomirskaya |first3=N. V. |last4=Ilyin |first4=Y. V. |last5=Skryabin |first5=K. G. |last6=Georgiev |first6=G. P. |doi=10.1093/nar/8.15.3263 |pmc=324151 }}

References:

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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 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

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