1. New Weight Encoding Method -FRET-
MEC seminar
By Hee-Woong Lim

2. Model x3 Expression level (concentration) x2 x1 Classification
(+)
(-)
Expression level
(concentration)
Classification
with threshold 0
Gene1: x1
Gene2: x2
Weighted sum
sum no
yes
Gene3: x3
t1, t2, t3 are predetermined constants from training samples

3. Preprocessing and Input Data Generation
RNA1
RNA1
Probe1
Probe2
Probe3
RNA1
RNA2
RNA2 +
hybridization
RNA3
RNA4
Expressed RNA
Probes

4. S1 Input generation for Computing Expression level  concentration
RNA1
Probe1
RNA1
RNA1
Probe1
RNA1
RNA1
Probe1
Probe1
RNA1
Probe1
Probe1
RNA2
Probe2
RNA2
RNA2
Probe2 S1
exonuclease
RNA2
Probe2
Probe2
RNA3
Probe3
RNA3
Probe3
RNA4
Input generation for Computing
Expression level  concentration
Probe1
Probe2
Probe3
Probe2
Probe3
Probe3
Hybridization Product

5. DNAC Algorithm Basic Framework Weight Encoding Method
Preprocessing by hybridization of probes and expressed RNAs.
Detailed algorithm is determined by probe (DNA, PNA, molecular beacon) and modification.
Weight  probe, modification
Weight Encoding Method
SYBR
CyX-nucleotide
Molecular beacon

6. New Method for Weight Encoding
Fluorescence Resonance Energy Transfer (FRET)
Dye-Dye pair  frequency variation of output signal
Dye-Quencher pair  weak signal
Use signal intensity vs. distance between dye and quencher
Weight  signal intensity  distance  probe length
Sensitivity?
Dependency of fluorescence signal on the distance
E: energy transfer efficiency, R: distance, R0: Förster distance
Too sensitive and too short range (R0: 10~100 Å)
Reference
“Fluorescence Resonance Energy Transfer Between Donor-Acceptor Pair on Two Oligonucleotides Hybridized Adjacently to DNA Template”, L. Wang, et al. 2003
“The estimation of distances between specific backbone-labeled sites in DNA using fluorescence resonance energy transfer”, H. Ozaki, et al. 1992

7. FRET in M-DNA M-DNA FRET in M-DNA
Complex of duplex DNA (B-DNA) with certain divalent cations. (Zn2+)
At high pH (8.5) in the presence of Zn2+
Conductivity and self-assembly
Jeremy S. Lee, et al. Analytical Sciences, vol. 19, pp23
FRET in M-DNA
Jeremy S. Lee, et al. “Long range molecular wire behaviour in a metal complex of DNA”, J. of Biomol. Struct. Dyn. 2002
“Upon formation of M-DNA significant quenching of the fluorescence of the donor fluorophore was observed in duplexes up to 500 base pairs in length. The amount of quenching decreased with increasing length of the duplexes with a shallow distance dependence.”
Waiting for full version of the paper. -_-;