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Interaction of Ruthenium II Polypyridyl Complexes with DNA

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... binding complexes;AFM limited to lower concentrations due to curling ... Ruthenium(II) polypyridyl complexes can be used to study DNA (photophysical/redox) ... – PowerPoint PPT presentation

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Title: Interaction of Ruthenium II Polypyridyl Complexes with DNA


1
Interaction of Ruthenium (II) Polypyridyl
Complexes with DNA
  • Japeck Tang
  • Ch221A
  • March 15, 2007

Mihailovic A, et al. Exploring the interaction of
ruthenium(II) polypyridyl complexes with DNA
using single-molecule techniques. LANGMUIR 22
(10) 4699-4709 MAY 9 2006.
2
Outline
  • Introduction
  • Theory
  • Overstretching B-DNA
  • Ruthenium Complexes
  • Experimental Setup
  • Results
  • Conclusion

3
Introduction
  • Binding of Ruthenium(II) Polypyridyl Complexes
  • Used to study DNA structure, small molecule
    binding
  • Noncovalent (electrostatic/van der Waals)
  • Intercalation
  • vs electrostatic/groove binding
  • Lengthens DNA (observe binding rate)
  • Stabilizes DNA (increased melting temperature)
  • Study binding via AFM optical tweezers

4
Theory (B-DNA)
  • Overstretching
  • Normal 3.4Å/bp
  • Overstretched 5.8Å/bp
  • Transition force 65pN
  • Max force 100pN

Smith SB, Cui YJ, Bustamante C. Overstretching
B-DNA The elastic response of individual
double-stranded and single-stranded DNA
molecules. SCIENCE 271 (5250) 795-799 FEB 9 1996.
5
(No Transcript)
6
Theory (Ruthenium)
  • Various Complexes
  • Photophysical/redox properties
  • Absorb visible light (changes when bound)
  • Dipyridophenazine (dppz) light switches
  • Oxidize guanine bases

7
Theory (Ruthenium)
8
Experimental Setup
  • Methods of Characterization
  • AFM Measurements
  • Immobile DNA on mica surface
  • Manually trace and measure lengths
  • Optical Tweezers
  • DNA stretching
  • Shift in force-extension curves

9
Experimental Fitting (AFM)
  • Binding equilibrium
  • Binding constant

10
Experimental Fitting (AFM)
  • Fit data using AFM measured DNA lengths
  • Gaussian fit ? average length
  • Assume 0.34nm lengthening/intercalation, 172pM
    DNA strands

11
Experimental Fitting (AFM)
  • Given initial Ru concentration Ru0
  • 750nM base pairs, neighbor exclusion (n)
  • Solve for Kb and n

12
Experimental Fitting (Optical)
  • McGhee-von Hippel model for binding
  • T fractional occupancy of Ru to DNA
  • b extension/bp n binding site size in bp c
    Ru
  • Solve for Kb, n given measured T

13
Results (AFM)
14
Results (AFM)
15
Results (Optical)
Ru-(phen)2dppz2
16
Results (Optical)
Ru-(phen)32
17
Results (Optical)
Ru-(bpy)32
18
Summary of Results
  • Kb lower for AFM due to Mg2
  • DNA stretching is better for weakly binding
    complexesAFM limited to lower concentrations due
    to curling
  • Ru(phen)32 binds 3 orders weaker than
    Ru(phen)2dppz2

19
Conclusion
  • Ruthenium(II) polypyridyl complexes can be used
    to study DNA (photophysical/redox)
  • Intercalation lengthens and stabilizes DNA
  • Intercalation can be observed, and binding
    constants determined via either AFM or optical
    tweezers measurements
  • Optical tweezers are better than AFM for weakly
    binding complexes
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