Increased amplification success from forensic samples with locked nucleic acids

Forensic Science International: Genetics

Volumn 5, Issue 4, 2011, Pages 276-280

  Ballantyne, Kaye N ^a,b   Van Oorschot, Roland A H ^a   Mitchell, R John ^b  

^a Victoria Police Forensic Services Department   (Australia)

^b LA TROBE UNIVERSITY   (Australia)

Author keywords

Amplification; Forensic; Locked nucleic acids; Trace DNA

Indexed keywords

LOCKED NUCLEIC ACID; PRIMER DNA;

ARTICLE; CAPILLARY ELECTROPHORESIS; GENOTYPE; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION;

BASE SEQUENCE; DNA PRIMERS; ELECTROPHORESIS, CAPILLARY; FORENSIC GENETICS; GENOTYPE; HUMANS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; TANDEM REPEAT SEQUENCES;

EID: 79953844554     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2010.04.001     Document Type: Article

References (26)

1. P. Gill, J. Whitaker, C. Flaxman, N. Brown, J. Buckleton, An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA, Forensic Sci. Int. 112 (2000) 17-40.
2. I. Findlay, R. Frazier, A. Taylor, P. Quirke, A. Urquhart, Single cell DNA fingerprinting for forensic applications, Nature 389 (1997) 355-356.
3. C.J. Fregeau, K.L. Bowen, B. Leclair, I. Trudel, L. Bishop, R.M. Fourney, AmpFlSTR Profiler Plus short tandem repeat DNA analysis of casework samples, mixture samples, and nonhuman DNA samples amplified under reduced PCR volume condition (25 ml), J. Forensic Sci. 48 (2003) 1014-1034. (Pubitemid 37102043)
4. J.M. Butler, Y. Shen, B.R. McCord, The development of reduced size STR amplicons as tools for analysis of degraded DNA, J. Forensic Sci. 48 (2003) 1054-1064. (Pubitemid 37107410)
5. J.M. Butler, Constructing STR Multiplex Assays, in: A. Carracedo (Ed.), Methods in Molecular Biology: Forensic DNA Typing Protocols, Humana Press, New Jersey, 2005, pp. 53-66.
6. L.A. Ugozzoli, D. Latorra, R. Pucket, K. Arar, K. Hamby, Real-time genotyping with oligonucleotide probes containing locked nucleic acids, Anal. Biochem. 324 (2004) 143-152.
7. A. Simenov, T.T. Nikiforov, Single nucleotide polymorphism genotyping using short, fluorescently labelled locked nucleic acid (LNA) probes and fluorescence polarization detection, Nucleic Acid Res. 30 (2002) e91.
8. B. Kennedy, K. Arar, V. Reja, R.J. Henry, Locked nucleic acids for optimising displacement probes for quantitative real-time PCR, Anal. Biochem. 348 (2006) 294-299.
9. J.S. Jepsen, M.D. Sørensen, J. Wengel, Locked nucleic acid: a potent nucleic acid analog in therapeutics and biotechnology, Oligonucleotides 14 (2004) 130-146. (Pubitemid 38987382)
10. B. Vester, J. Wengel, LNA (Locked Nucleic Acid): high-affinity targeting of complementary RNA and DNA, Biochemistry 43 (2004) 13233-13241. (Pubitemid 39391124)
11. M. Peterson, J. Wengel, LNA: a versatile tool for therapeutics and genomics, TRENDS Biotechnol. 21 (2003) 74-81. (Pubitemid 36165007)
12. M. Peterson, C.B. Nielsen, K.E. Nielsen, G.A. Jensen, K. Bondensgaard, S.K. Singh, V.K. Rajwanshi, A.A. Koshkin, B.M. Dahl, J. Wengel, J.P. Jacobsen, The conformations of locked nucleic acids, J. Mol. Recogn. 13 (2000) 44-53.
13. G.A. Jensen, S.K. Singh, R. Kumar, J. Wengel, J.P. Jacobsen, A comparison of the solution structures of an LNA:DNA duplex and the unmodified DNA:DNA duplex, J. Chem. Soc. Perkin Trans. 2 (2001) 224-1232.
14. Y. You, B.G. Moreira, M.A. Behlke, R. Owczarzy, Design of LNA probes that improve mismatch discrimination, Nucleic Acids Res. 34 (2006) e60.
15. J.D. Levin, D. Fiala, M.F. Samala, J.D. Kahn, R.J. Peterson, Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers, Nucleic Acids Res. 34 (2006) e142.
16. D.A. Braasch, D.R. Corey, Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA, Chem. Biol. 8 (2001) 1-7.
17. E. Reynisson, M.H. Josefsen, M. Krause, J. Hoorfar, Evaluation of probe chemistries and platforms to improve the limits of real-time PCR, J. Microbiol. Methods 66 (2006) 206-216. (Pubitemid 43903028)
18. K.N. Ballantyne, R.A.H. van Oorschot, R.J. Mitchell, Locked nucleic acids in PCR primers increase sensitivity and performance, Genomics 91 (2007) 301-305.
19. D. Latorra, K. Arar, J.M. Hurley, Design considerations and effects of LNA in PCR primers, Mol. Cell Probes 17 (2003) 253-259. (Pubitemid 37346175)
20. I. Koukoulas, F.E. O'Toole, P. Stringer, R.A. van Oorschot, Quantifiler observations of relevance to forensic casework, J. Forensic Sci. 53 (2008) 135-141. (Pubitemid 351239229)
21. K.N. Ballantyne, R.A.H. van Oorschot, R.J. Mitchell, Reduce optimisation time and effort: Taguchi experimental design methods, Forensic Sci. Int.: Genet. Suppl. Ser. 1 (2008) 7-8.
22. H. Kaur, A. Arora, J. Wengel, S. Maiti, Thermodynamic, counterion, and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes, Biochemistry 45 (2006) 7347-7355.
23. Y. Sasaki, D. Miyoshi, N. Sugimoto, Effect of molecular crowding on DNA polymerase activity, Biotechnol. J. 1 (2006) 440-446.
24. P.M. McTigue, R.J. Peterson, J.D. Kahn, Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA) - DNA duplex formation, Biochemistry 43 (2004) 5388-5405. (Pubitemid 38620931)
25. A. Ivanova, N. Rösch, The structure of LNA:DNA hybrids from molecular dynamics simulations: the effect of locked nucleotides, J. Phys. Chem. A 111 (2007) 9307-9319.
26. M.J. Brownstein, J.D. Carpen, J.R. Smith, Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping, Biotechniques 20 (1996) 1008-1010.