molecular modeling of nanoscale bioassemblies for clinical laboratory diagnostics
DESCRIPTION
Molecular Modeling of Nanoscale Bioassemblies for Clinical Laboratory Diagnostics. City of Hope National Medical Center Scott F. Roalofs with Dr. Steven S. Smith. Overview. Purpose Introduction to Bionanotechnology FRET Modification of Bioassemblies Molecular Models Conclusions - PowerPoint PPT PresentationTRANSCRIPT
Molecular Modeling of Nanoscale Bioassemblies for Clinical Laboratory Diagnostics
City of Hope National Medical Center
Scott F. Roalofswith
Dr. Steven S. Smith
Overview
Purpose Introduction to Bionanotechnology FRET Modification of Bioassemblies Molecular Models Conclusions Acknowledgements
Purpose
To design and develop a tool that would allow rapid diagnose of tumor cells from a biopsy My specific part: Modeling of
bioassemblies using Insight II
Y-Junction
Ni Linker StructureFluorescent Molecules
Tumor Cell
Bionanotechnology
Uses molecular biology, chemistry and physics to link molecules into complex assemblies
Must be under 100nm in its largest dimension
Artificial and require some assembly outside of a living system
FRET
Förster resonance energy transfer Fluorescent donor is excited at its
specific excitation wavelength Dipole-dipole interactions:
Excited state is non-radioactively transferred to an acceptor
Acceptor returns to the electronic ground state
Changing Target Specificity DNA methyltransferase HhaI has
the ability to be targeted to specific recognition sites in the Y-Junction
Covalently trapped on duplex DNA using 5’-fluorocytosine
Bioassemblies can be modified with various targeting and detection chemistries
Y-Junction Structure
Fluorine
Fluorine
FluorineFluorine
Fluorine
Sulfur Linker Structure
3’
5’
oligomer
oligomerN
S
S O
O
O
P
HO
O
O
OHC
C
O-
O-
O
O
S
O
P O
O
O-
O P
HO
O
O-
HO
S
O
O
N
C
C
O-
O-
O
O
IDA
Sulfur Linker
17,234 kcal/mol
Previous work Horsey et al., Chem Comm, 2002,
1950-51. Compared chelated vs. non-
chelated Sulfur Linker complex 15°C difference in Tm: chelated vs.
non-chelated Sulfur Linker complex Smith lab has been unable to
reproduce these results
6 Linker Structure
N
(CH2)6
S O P
HO
O
O
OHC
C
O-
O-
O
O
3’
ologomer
5’
oligomer
(CH2)6
S
O
P O
O
O-
O P
HO
O
O-
HO
N
C
C
O-
O-
O
O
IDA
6 Linker
17,249 kcal/mol
Linker Modifications
Linker structures were modified Previous models identified possible
unwanted interactions with Ni Synthesis protocol was modified
Removed (CH2)3 OH Replaced with a Cytosine base
Modified Linker
Conclusions
Models are visually appealing for use in presenting one’s ideas
Molecular modeling provides 3D visual renderings of hand drawn structures Models may identify questionable
structure flaws that may not have be noticeable on a hand drawn structure
Acknowledgements
Dr. Steven S. Smith Jarrod Clark Katarzyna Lamparska-Kupsik SoCalBSI NIH
Questions ?
FRET
www.olympusfluoview.com/applications/fretinfo.html
IDA=iminodiacetic acid