Method of preparing DNA sequences with known ligand binding char

Details Method of preparing DNA sequences with known ligand binding char Method of preparing DNA sequences with known ligand binding char

1995-04-26

1997-01-14

Elliott, George C.

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

435 911, 435 912, 435 5, 536 243, 536 2433, C12Q 168, C12Q 170, C12P 1934, C07H 2104

Patent

active

055938345

ABSTRACT:
A method for determining at least one DNA sequence that can be employed as a flanking sequence to a DNA binding site for a ligand, wherein the DNA binding site is located within a preselected DNA sequence, to provide a relative increase, decrease, or approximate equality in binding constant of the ligand for its DNA binding site, or relative composite reaction rate for the ligand and a DNA sequence. Also provided are applications of the method to determine DNA primers useful in conjunction with DNA amplification to detect the presence or absence of DNA sequences and to diagnose diseases related to viral DNA, such as human immunodeficiency virus.

REFERENCES:
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Lowe et al (1990) "A computer program for selection of oligonucleotide primers for polymerase chain reactions" Nucl. Acids Res. 18:1757-1761.
Breslauer et al (1986) "Predicting DNA duplex stability from the base sequence" Proc. Natl. Acad. Sci 83:3746-3750.
Rychlik (1993) "Selection of primers for polymerase chain reaction" in PCR protocols, v. 15 of Methods in Mol. Biol., White, ed. Totowa, N.J.: Humana Press, pp. 31-40.
Amaratunga, M. et al., "Studies of DNA Dumbbells. II. Construction and Characterization of DNA Dumbbells with a 16 Base-Pair Duplex Stem and T.sub.n End Loops (n=2,3,4,6,8,10,14)" Biopolymers, vol. 21, pp. 865-869 (1992).
Doktycz, M. et al., "Studies of DNA Dumbbells. I. Melting Curves of 17 DNA Dumbbells with Different Duplex Stem Sequences Linked by T.sub.4 Endloops: Evaluation of the Nearest-Neighbor Stacking Interactions in DNA" Biopolymers, vol. 32, pp. 849-864 (1992).
Goldstein, R. F. and A. S. Benight, "How Many Numbers Are Required to Specify Sequence-Dependent Properties of Polynucleotides?" Biopolymers, vol. 32, pp. 1679-1693 (1992).
Bishop, K. D. et al., "Actinomycin D induced DNase I hypersensitivity and asymmetric structure transmission in a DNA dodecamer" Nucleic Acids Research, vol. 19, pp. 871-875 (1991).
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