Multi Stranded Dna

Multistranded DNA for 10th Craiova International Medical Students Conference

Base pairs

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

Base pairs

10 possible purine-pyrimidine base pairs

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

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Base pairs

7 possible homo purine-purine base pairs

Homo purines

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Base pairs

7 possible pyrimidine-pyrimidine base pairs

Homo- and hetero pyrimidines

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Base pairs

4 possible hetero purine-purine base pairs

Hetero purines

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The structure of oligonucleotide

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

The structure of sugar

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

Chi angle anti and syn conformational ranges for glycosydic bonds in pyrimidine (left) and purine (right) nucleosides

Source: Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University

movement of bases • • • •

moving in concert moving in opposition steps between two base-pairs translocational movement of base-pairs relative to the helix axis

movements of bases in sequencedependent structures : Tip

Inclination

Opening

Propeller

Buckle

Twist

Roll

Tilt

Slide

Rise

Shift

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http://www.imb-jena.de/ImgLibDoc/nana/IMAGE_NASP.html

movement of bases Co-ordinate frame

Rotation motions are cocoordinated

Tip

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

movement of bases Co-ordinate frame

Rotation motions are opposed

Opening

Propeller Twist

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

movement of bases Co-ordinate frame

Rotation two-base pair step

Twist

Roll

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

movement of bases Co-ordinate frame

Translat motions are coion coordinated

y displacement

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

movement of bases Co-ordinate frame

Translat motions are ion opposed

Stagger

Stretch

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

movement of bases Co-ordinate frame

Translat two-base pair step ion

Rise

Slide

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

DNA multistranded structures  Triplex

 Quadruplex

Structure of a DNA quadruplex formed by telome

DNA triplex

 Intramolecular  H-DNA (Py triplexes)  *H-DNA (Pu triplexes)  Intermolecular  Pu motif  Py motif

Image : http://www.cryst.bbk.ac.uk/ Classification according to : Do DNA Triple Helices or Quadruplexes Have a Role in Transcription ; DNA Conformation and Transcription edited by Takashi Ohyama. ©2005

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 Commonwealth University School of Medicine.

 Intramolecular triplex

4 Isomers of Intramolecular Triplexes

Do DNA Triple Helices or Quadruplexes Have a Role in Transcription ; DNA Conformation and Transcription edited by Takashi Ohyama. ©2005 Eurekah.com and Springer Science+Business Media.

 Intermolecular triplex

 Py motif

 Pu motif

Occurrence & biologic roles of triplexes: Triple helix formation is sensitive to :  the length of the third strand  single base mismatches  cation concentration and valence  pH backbone composition (DNA or RNA) of the three strands  Negative super-coiling tension Functions :  Inhibit gene expression in-vivo (including a case demonstrating the inhibition of HIV-1 transcription in infected human cells) Involved in promoter-enhancer transaction  Protection against UV-induced pyrimidine dimerization in DNA  DNA repair and recombination (RAD51, * According to the article “The potential for gene repair via triple helix formation”, by Michael M. Seidman and Peter M. Glazer © 2003, American RecASociety , etc.)* for Clinical Investigation (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=171401)

Methods of noticing triplexes in vivo :  Immunodetection using triplex antibodies  Immunodetection by triplex-specific antibodies was combined with fluorescence in situ non-denaturating hybridization (N-FISH)  Nuclease S1 (nuclease-hypersensitive elements, which are indicative of unusual DNA structures, and triplexes)  Identification of triplex-specific and single strand-specific proteins

DNA quadruplex/tetraplex

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 structure contains three layers of G-tetrads. The hydrogen bonds in these layers are represented

Classification: (According to: Paula Bates, Jean-Louis Mergny & Danzhou Yang, The First International Meeting on Quadruplex DNA, 21-24 April 2007, in Louisville, Kentucky, USA.)

Tetramer

Dimer

Monomer

Strand Connectivity Alternatives for Monomers

Strand Connectivity Alternatives for Dimers

According to : G-quadruplex DNA structures - Variations on a theme ,

Quadruplex polymorphism

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 diversity suggests 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-2 reprinted with permission from Dai et al (2006b); hTel-1 reprinted with permission from Dai et al (2007b); hTel-2 reprinted with permission from Dai et al (2007a).

Human telomere

A schematic model of DNA secondary structure composed of compact-stacking multimers of the hybrid-type quadruplex structures (top and middle) in human telomeres. The model of the compact-stacking multimers of the parallelstranded structures is also shown (bottom). (According to: Paula Bates, Jean-Louis Mergny & Danzhou Yang, The First International Meeting on Quadruplex DNA, 21-24 April 2007, in

Parallel-strand intermolecular tetraplex (G4) / Tetramer

©Image : Gene Structure I: DNA and Chromatin Structures ; Losing Khan, Institute of

Chemical structure of a Hoogsteen hydrogen-bonded G-quartet , from a telomere.

©Image : Gene Structure I: DNA and Chromatin Structures ; Losing Khan, Institute of

Dimeric hairpin quadruplex (G'2)

©Image : Gene Structure I: DNA and Chromatin Structures ; Losing Khan, Institute of Chemistry,

Occurrence & biologic roles of quadruplexes: It is estimated that there might be more than 370,000 potential quadruplex-forming sequences in the human genome (Huppert & Balasubramanian, 2005; Todd et al, 2005).

Potential location in a genome: Genes: o Promoter region (oncogene promoter sequences) o Intron o Exon Telomeres Functions :  Ligands that stabilize the quadruplex might lead to cellular senescence by preventing telomere extension mediated by telomerase (TEL)  Able of rapid inducement of apoptosis by displacing telomerebinding proteins, for example, protection of telomeres 1 (POT1).

Quadruplex in a gene promoter

© Pictures: European Molecular Biology Organization, 2007

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 indicative of 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,

Image from : Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo; Katrin Paeschke, Tomas Simonsson,

Conclusion DNA Triplexes & Quadruplexes are :  Powerful gene-specific tools that can be employed in a wide range of applications in experimental biology and gene-based biotechnology and therapeutics.