Optimal hepatitis B virus primer sequence design for isothermal amplification

Biomedical Engineering - Applications, Basis and Communications

Volumn 19, Issue 3, 2007, Pages 137-144

  Lee, Szu Yuan ^a   Lee, Chun Nan ^a   Mark, Holl ^b,c   Meldrum, Deirdre R ^b,c   Lee, Chih Kung ^d   Lin, Chii Wann ^a,e  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b Arizona State University   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^e NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Hepatitis B virus; Isothermal; LAMP; Primer design

Indexed keywords

ELECTRIC LAMPS; ISOTHERMS;

DIAGNOSTIC APPLICATIONS; HEPATITIS B VIRUS; ISOTHERMAL; ISOTHERMAL AMPLIFICATIONS; LITERATURE REVIEWS; LOOP MEDIATED ISOTHERMAL AMPLIFICATIONS; OPTIMAL PERFORMANCE; PRIMER DESIGN;

VIRUSES;

BETAINE; BUFFER; VIRUS DNA;

ARTICLE; CONCENTRATION RESPONSE; CRYSTALLIZATION; DIAGNOSTIC VALUE; DNA SEQUENCE; EARLY DIAGNOSIS; ELECTRONICS; GENE AMPLIFICATION; GENE SEQUENCE; HEPATITIS B VIRUS; LOOP MEDIATED ISOTHERMAL AMPLIFICATION; MATHEMATICAL COMPUTING; MELTING POINT; NONHUMAN; REACTOR DESIGN; SENSITIVITY AND SPECIFICITY;

HEPATITIS B VIRUS;

EID: 46349083762     PISSN: 10162372     EISSN: None     Source Type: Journal    
DOI: 10.4015/S1016237207000215     Document Type: Article

References (28)

1. McMahon BJ, Epidemiology and natural history of hepatitis B, Semin Liver Dis 25(Suppl. 1):3-8, 2005.
2. Lee CZ et al., Correlation of HBV DNA levels in serum and liver of chronic hepatitis B patients with cirrhosis, Liver 22(2):130-135, 2002.
3. Chen CJ et al., Risk of hepatocellular carcinoma across a biological gradient of serum hepatitis B virus DNA level, J Am Med Assoc 295(1):65-73, 2006.
4. Iloeje UH et al., Predicting cirrhosis risk based on the level of circulating hepatitis B viral load, Gastroenterology 130(3):678- 686, 2006.
5. Lee SJ, Lee SY, Micro total analysis system (micro-TAS) in biotechnology, Appl Microbiol Biot 64(3):289-299, 2004.
6. Compton J, Nucleic acid sequence-based amplification, Nature 350(6313):91-92, 1991.
7. Walker GT et al., Strand displacement amplification - an isothermal, in vitro DNA amplification technique, Nucleic Acids Res 20(7):1691-1696, 1992.
8. Lizardi PM et al., Mutation detection and single-molecule counting using isothermal rolling-circle amplification, Nat Genet 19(3):225-232, 1998.
9. Vrana KE, Advancing technologies in gene amplification, Trends Biotechnol 14(11):413-415, 1996.
10. Notomi T et al., Loop-mediated isothermal amplification of DNA, Nucleic Acids Res 28(12):E63, 2000.
11. Nagamine K, Hase T, Notomi T, Accelerated reaction by loop-mediated isothermal amplification using loop primers, Mol Cell Probe 16(3):223-229, 2002.
12. Kampke T, Kieninger M, Mecklenburg M, Efficient primer design algorithms, Bioinformatics 17(3):214-215, 2001.
13. Dong F et al., Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA, Nucleic Acids Res 29(15):3248-3257, 2001.
14. Chavali S et al., Oligonucleotide properties determination and primer designing: A critical examination of predictions, Bioinformatics 21(20):3918-3925, 2005.
15. Marmur J, Doty P, Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature, J Mol Biol 5:109-118, 1962
16. Wallace RB et al., Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: The effect of single base pair mismatch, Nucleic Acids Res 6(11):3543-3557, 1979
17. Howley PM et al., A rapid method for detecting and mapping homology between heterologous DNAs, Evaluation of polyomavirus genomes, J Biol Chem 254(11):4876-4883, 1979.
18. Rychlik W, Rhoads RE, A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA, Nucleic Acids Res 17(21):8543-8551, 1989.
19. Breslauer KJ et al., Predicting DNA duplex stability from the base sequence, Proc Natl Acad Sci USA 83(11):3746-3750, 1986.
20. SantaLucia J Jr, Hicks D, The thermodynamics of DNA structural motifs, Annu Rev Bioph Biom 33:415-440, 2004.
21. SantaLucia J Jr, Allawi HT, Seneviratne PA, Improved nearest-neighbor parameters for predicting DNA duplex stability, Biochemistry 35(11):3555-3562, 1996.
22. Sugimoto N et al., Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes, Nucleic Acids Res 24(22):4501-4505, 1996.
23. SantaLucia J Jr, A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proc Natl Acad Sci USA 95(4):1460-1465, 1998.
24. Allawi HT, SantaLucia J Jr, Thermodynamics and NMR of internal GT mismatches in DNA, Biochemistry 36(34):10581-10594, 1997.
25. Lee SY et al., Miniature isothermal amplification reactor with an integrated optical detection unit, in World Congress on Medical Physics and Biomedical Engineering 2006 (WC2006). 2006: COEX conventional center, Seoul, Republic of Korea.
26. Lee SY et al., Efficient, specific, compact hepatitis B diagnostic device: Optical detection of the hepatitis B virus by isothermal amplification, Sens Actuat B-Chem 2007 (in press).
27. Baskaran N et al., Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content, Genome Res 6(7):633-638, 1996.
28. von Ahsen N et al., Application of a thermodynamic nearest-neighbor model to estimate nucleic acid stability and optimize probe design: Prediction of melting points of multiple mutations of apolipoprotein B-3500 and factor V with a hybridization probe genotyping assay on the LightCycler, Clin Chem 45(12):2094-2101, 1999.