HYBRIDIZATION

A strand finds its match

probe + target → duplex

A single-stranded DNA probe on the gate pairs, base by base, with its complementary target: A with T, and G with C. Once the strands zip together, the target's backbone puts its negative charge next to the surface.

Sequence sets specificity: only a matching strand binds well.

THE CHARGE

Every base brings a charge

≈ −1 per nucleotide

DNA's phosphate backbone carries about one negative charge per nucleotide. A 20-nucleotide target adds about 20 elementary charges when it hybridizes, so DNA gives a large, well-defined signal for each binding event.

Hybridization adds a burst of negative charge.

AN UPPER BOUND

Unscreened, the shift would be volts

2×10¹² e/cm² → 0.9 V

Suppose 10¹¹ probes per cm² each capture a 20-nucleotide target: 2×10¹² elementary charges per cm². With C_ox = 0.345 µF/cm², ΔVth ≈ −Q/C_ox comes out near 0.9 V. Real signals are tens of millivolts, because ions in the sample screen most of that charge.

Screening turns volts into millivolts.

SPECIFICITY

Telling a match from a near-miss

Mismatch One wrong base weakens the duplex and its binding

Temperature Warming a little melts loosely paired strands and keeps perfect matches

Salt Lower salt weakens all pairing, which raises stringency

Probe length Shorter probes notice a single mismatch more easily

Stringency, meaning temperature and salt, is the knob for specificity.

NEUTRAL PROBES

PNA as a probe

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PNA

Peptide nucleic acid has an uncharged backbone

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Low-salt pairing

With no charge on the probe repelling the target, it hybridizes well in low salt

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Cleaner signal

All the added charge comes from the target, not the probe

A neutral probe helps both binding and interpretation.

UNIT 22 STUDY COMPLETE

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Ready for the Fab Challenge?

You've covered how a probe strand captures its match, and why DNA is a natural charge signal.