Method of probe design for nucleic acid analysis by...

Details Method of probe design for nucleic acid analysis by... Method of probe design for nucleic acid analysis by...

2004-05-07

2010-12-28

Strzelecka, Teresa E (Department: 1637)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C536S023100, C536S024300

Reexamination Certificate

active

07858301

ABSTRACT:
Disclosed is an analysis method useful in multiplexed hybridization-mediated analysis of polymorphisms, i.e., wherein a labeled nucleic acid of interest (“target”) interacts with two or more pairs of immobilized degenerate capture probes. In one embodiment, one member of each pair has a sequence that is complementary to the normal (“wild-type”) sequence in a designated location of the target, while the other member of each pair has a sequence that is complementary to an anticipated variant (“mutant” or “polymorph”) sequence in that location of the target. These methods permit selection of two or more probe pairs such that, for each pair of probes interacting with a given target strand, interaction of the target with a preferred member of the probe pair is optimized. Also interpreting results obtained by multiplexed hybridization of the target to two or more pairs of probes under conditions permitting competitive hybridization is disclosed.

REFERENCES:
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patent: 7060431 (2006-06-01), Chee et al.
patent: 7132239 (2006-11-01), Livak et al.
SantaLucia, J. Jr., PNAS USA, vol. 95, pp. 1460-1465 (1998).
Breslauer, K.J. et al., PNAS USA, vol. 83, pp. 3746-3750 (1986).
Relogio, A. et al., Nucl. Acids Res., vol. 30,e51, pp. 1-10 (2002).
Chee, M. et al., Science, vol. 274, pp. 610-613 (1996).
Cherepinsky, Vera, “On mathematical aspects of genomic analysis”, Ph.D. Thesis, published Mar. 2004.
Thesis Chapter: “Competitive Hybridization: Physical Model” by V. Cherepinsky; Mar. 26, 2004.

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