multi stranded dna
TRANSCRIPT
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Multistranded DNA
for 10th Craiova International
Medical Students Conference
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There are 28 possible base pairs thatinvolve at least two hydrogen bonds.
Base pairs
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Watson-Crick,Reverse Watson-Crick,Hoogsteen,Reverse Hoogsteen,Wobble,Reverse Wobble
10 possible purine-pyrimidinebase pairs
Image: http://www.imb-jena.de/
Base pairs
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Homo purines
7 possible homo purine-purinebase pairs
Base pairs
Image: http://www.imb-jena.de/
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Homo- and heteropyrimidines
7 possible pyrimidine-pyrimidinebase pairs
Base pairs
Image: http://www.imb-jena.de/
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4 possible hetero purine-purinebase pairs
Base pairs
Hetero purines
Image: http://www.imb-jena.de/
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The structure ofoligonucleotide
Source: Saenger,W., Principles of Nucleic Acid Structure, Springer Verlag New York
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The structure ofsugar
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anti and syn conformational ranges for
glycosydic bonds in pyrimidine (left) andpurine (right) nucleosides
Chi angle
Source: Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University
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moving in concert moving in opposition steps between two base-pairs translocational movement of base-pairs relative to
the helix axis
movemen obases
Tip Inclination Opening
Propeller Buckle Twist
Roll Tilt Slide
Rise Shift -
movements of bases in sequence-dependent structures :
http://www.imb-jena.de/ImgLibDoc/nana/IMAGE_NASP.html
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Co-ordinate
frame
Tip Inclination
movemen obases
Rotationmotions are co-
coordinated
Image: http://www.imb-jena.de/
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Co-ordinate
frame
Opening
movemen obases
Rotationmotions are
opposed
Propeller Twist Buckle
Image: http://www.imb-jena.de/
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Co-ordinate
frame
Twist
movemen obases
Rotationtwo-base pair step
Roll Tilt
Image: http://www.imb-jena.de/
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Co-ordinate
frame
movemen obases
Translationmotions are co-coordinated
y displacement x
displacemeImage: http://www.imb-jena.de/
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Co-ordinate
frame
movemen obases
Translationmotions areopposed
Stagger ShearStretch
Image: http://www.imb-jena.de/
mo emen o
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Co-ordinate
frame
movemen obases
Translationtwo-base pair step
Rise ShiftSlide
Image: http://www.imb-jena.de/
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mu s ran estructures
Triplex Quadruplex
Structure of a DNA quadruplex formed by telome
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DNA triplex
Intramolecular H-DNA (Pytriplexes)
*H-DNA (Putriplexes)
Intermolecular
Pu motif Py motif
Image : http://www.cryst.bbk.ac.uk/
Classification according to : Do DNA Triple Helices orQuadruplexes Have a Role in Transcription ; DNAConformation and Transcription edited by Takashi Ohyama. 2005
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Base triplets
Structure of a platinated DNA G.GC triplex. Molecular dynamics
calculations (AMBER 5) were performed by Evan Kransdorf,presently in the MD/PhD program at the Virginia CommonwealthUniversity School of Medicine.
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Intramolecular triplex
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4 Isomers ofIntramolecular
Triplexes
Do DNA Triple Helices or Quadruplexes Have a Role in Transcription ; DNA Conformation andTranscription edited by Takashi Ohyama. 2005 Eurekah.com and Springer Science+Business Media.
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Intermolecular triplex
Py motif
Pu motif
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Occurrence & biologic roles of triplexes:
Functions : Inhibit gene expression in-vivo (including acase demonstrating the inhibition of HIV-1transcription in infected human cells)Involved in promoter-enhancer transactionProtectionagainst UV-induced pyrimidine dimerization inDNA
DNA repair and recombination (RAD51,RecA , etc.)*
Triple helix formation is sensitive to : the length of the third strand single base mismatches cation concentration and valence pHbackbone composition (DNA or
RNA) of the three strandsNegative super-coiling tension
* According to the article The potential for gene repair via triple helix formation, by Michael M. Seidman and Peter M. Glazer2003, American Society for Clinical Investigation (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=171401)
http://www.nature.com/nature/journal/v344/n6266/abs/344568a0.htmlhttp://en.wikipedia.org/wiki/RAD51http://en.wikipedia.org/wiki/RAD51http://www.nature.com/nature/journal/v344/n6266/abs/344568a0.html -
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Methods of noticing triplexes in vivo :
Immunodetection using triplex antibodiesImmunodetection by triplex-specific antibodies was combined
with fluorescence in situ non-denaturating hybridization (N-FISH) Nuclease S1 (nuclease-hypersensitive elements, which are indicativeof unusual DNA structures, and triplexes) Identification of triplex-specific and single strand-specific proteins
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DNA quadruplex/tetraplex
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3D Structure of the intramolecular human telomeric G-quadruplex in potassium solution
(PDB ID 2HY9). The backbone is represented by a tube. The center of this structurecontains three layers of G-tetrads. The hydrogen bonds in these layers are represented
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Tetramer Dimer Monomer
Classification:
(According to: Paula Bates, Jean-Louis Mergny & Danzhou Yang, The First International Meeting on QuadruplexDNA, 21-24 April 2007, in Louisville, Kentucky, USA.)
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Strand Connectivity Alternatives for Dimers
Strand Connectivity Alternatives for Monomers
According to : G-quadruplex DNA structures - Variations on a theme ,
http://bio.lundberg.gu.se/simonsson/BC_2001.pdfhttp://bio.lundberg.gu.se/simonsson/BC_2001.pdfhttp://bio.lundberg.gu.se/simonsson/BC_2001.pdfhttp://bio.lundberg.gu.se/simonsson/BC_2001.pdfhttp://bio.lundberg.gu.se/simonsson/BC_2001.pdf -
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Quadruplex polymorphism. Examples of intramolecular G-quadruplexes with different folding and capping structures.Intramolecular G-quadruplex structures are all derived from a single-stranded DNA (top). The conformational diversitysuggests that these G-quadruplex structures might be specifically recognized by various proteins and small molecule
ligands. c-myc reprinted with permission from Ambrus et al (2005), copyright 2005 American Chemical Society; bcl-2reprinted with permission from Dai et al (2006b); hTel-1 reprinted with permission from Dai et al (2007b); hTel-2 reprintedwith permission from Dai et al (2007a).
Quadruplex polymorphism
H t l
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A schematic model of DNA secondary structurecomposed of compact-stacking multimers of thehybrid-type quadruplex structures (top andmiddle) in human telomeres. The model of thecompact-stacking multimers of the parallel-stranded structures is also shown (bottom).
Human telomere
(According to: Paula Bates, Jean-Louis Mergny & Danzhou Yang, The First International Meeting on Quadruplex DNA, 21-24 April 2007, in
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Parallel-strandintermoleculartetraplex(G4)
/ Tetramer
Image : Gene Structure I: DNA
and Chromatin Structures ;Losing Khan, Institute of
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Chemical structureof a Hoogsteenhydrogen-bondedG-quartet , from a
telomere.
Image : Gene Structure I: DNA
and Chromatin Structures ;Losing Khan, Institute of
Di i h i i
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Image : Gene Structure I:DNA and Chromatin
Structures ; Losing Khan,Institute of Chemistry,
Dimeric hairpinquadruplex(G'2)
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Occurrence & biologic roles ofquadruplexes:
Potential location in a genome:Genes:
o Promoter region (oncogene promotersequences)
o Introno Exon
Telomeres
Functions : Ligands that stabilize the quadruplex might lead to cellularsenescence by preventing telomere extension mediated by telomerase(TEL) Able of rapid inducement of apoptosis by displacing telomere-
binding proteins, for example, protection of telomeres 1 (POT1).
It is estimated that there might be more than
370,000 potential quadruplex-forming sequences inthe human genome
(Huppert & Balasubramanian, 2005;Todd et al, 2005).
http://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.htmlhttp://www.nature.com/embor/journal/v8/n11/full/7401073.html -
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Quadruplex in a genepromoter
Pictures: European Molecular Biology Organization, 2007
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Methods of noticing quadriplexes in vivo :
Specific antibodies for staining throughout the cell cycle (Sty49, Sty3) Quadruplex-binding proteins
Nuclease S1 (nuclease-hypersensitive elements, which are indicativeof unusual DNA structures, and quadruplex-forming potential) Covalently binding platinum derivatives Quadruplex ligands linked to a nuclease
Image from :Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo; Katrin Paeschke, Tomas Simonsson,an Postber Daniela Rhodes and Hans Li s 2005 .Nature Structural and Molecular Biolo 12 10 847-854.
http://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdf -
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Image from : Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo;Katrin Paeschke, Tomas Simonsson,
http://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdfhttp://bio.lundberg.gu.se/simonsson/NSMB_2005.pdf -
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Conclusion
Powerful gene-specific tools that can beemployed in a wide range of applications in
experimental biology and gene-basedbiotechnology and therapeutics.
DNA Triplexes & Quadruplexes are :