New Weight Encoding Method -FRET- 2004.3.2 MEC seminar By Hee-Woong Lim

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

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

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

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

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 http://www.idtdna.com/program/techbulletins/techbulletins.asp

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. -_-;