Multi Stranded DNA

8/14/2019 Multi Stranded DNA

1/41

Multistranded DNA

for 10th Craiova International

Medical Students Conference


2/41

There are 28 possible base pairs thatinvolve at least two hydrogen bonds.

Base pairs


3/41

Watson-Crick,Reverse Watson-Crick,Hoogsteen,Reverse Hoogsteen,Wobble,Reverse Wobble

10 possible purine-pyrimidinebase pairs

Image: http://www.imb-jena.de/

Base pairs
http://www.imb-jena.de/ImgLibDoc/nana/IMAGE_NANA.htmlhttp://www.imb-jena.de/ImgLibDoc/nana/IMAGE_NANA.html


4/41

Homo purines

7 possible homo purine-purinebase pairs

Base pairs



5/41

Homo- and heteropyrimidines

7 possible pyrimidine-pyrimidinebase pairs

Base pairs



6/41

4 possible hetero purine-purinebase pairs

Base pairs

Hetero purines



7/41

The structure ofoligonucleotide

Source: Saenger,W., Principles of Nucleic Acid Structure, Springer Verlag New York


8/41Source: Saenger,W., Principles of Nucleic Acid Structure, Springer Verlag New York

The structure ofsugar


9/41

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


10/41

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


11/41

Co-ordinate

frame

Tip Inclination

movemen obases

Rotationmotions are co-

coordinated



12/41

Co-ordinate

frame

Opening

movemen obases

Rotationmotions are

opposed

Propeller Twist Buckle



13/41

Co-ordinate

frame

Twist

movemen obases

Rotationtwo-base pair step

Roll Tilt



14/41

Co-ordinate

frame

movemen obases

Translationmotions are co-coordinated

y displacement x

displacemeImage: http://www.imb-jena.de/


15/41

Co-ordinate

frame

movemen obases

Translationmotions areopposed

Stagger ShearStretch


mo emen o


16/41

Co-ordinate

frame

movemen obases

Translationtwo-base pair step

Rise ShiftSlide



17/41

mu s ran estructures

Triplex Quadruplex

Structure of a DNA quadruplex formed by telome


18/41

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


19/41

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.


20/41


21/41

Intramolecular triplex


22/41


23/41

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.


24/41

Intermolecular triplex

Py motif

Pu motif


25/41

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


26/41

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


27/41

DNA quadruplex/tetraplex


28/41

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


29/41

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.)


30/41

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


31/41

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


32/41

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


33/41

Parallel-strandintermoleculartetraplex(G4)

/ Tetramer

Image : Gene Structure I: DNA

and Chromatin Structures ;Losing Khan, Institute of


34/41

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


35/41

Image : Gene Structure I:DNA and Chromatin

Structures ; Losing Khan,Institute of Chemistry,

Dimeric hairpinquadruplex(G'2)


36/41


37/41

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


38/41

Quadruplex in a genepromoter

Pictures: European Molecular Biology Organization, 2007


39/41

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


40/41

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


41/41

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 :

Documents

Multi Stranded DNA