메뉴 건너뛰기




Volumn 37, Issue 2, 2004, Pages 226-231

AutoDimer: A screening tool for primer-dimer and hairpin structures

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; DNA; GENES; MELTING; NUCLEIC ACIDS;

EID: 3943088401     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/04372st03     Document Type: Article
Times cited : (410)

References (40)
  • 2
    • 0036772248 scopus 로고    scopus 로고
    • Selecting signature oligonucleotides to identify organisms using DNA arrays
    • Kaderali, L. and A. Schliep. 2002. Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics 18:1340-1349.
    • (2002) Bioinformatics , vol.18 , pp. 1340-1349
    • Kaderali, L.1    Schliep, A.2
  • 5
    • 33947165692 scopus 로고    scopus 로고
    • A greedy algorithm for minimizing the number of primers in multiple per experiments
    • Doi, K. and H. Imai. 1999. A greedy algorithm for minimizing the number of primers in multiple per experiments. Genome Inform. Ser. Workshop Genome Inform. 10:73-82.
    • (1999) Genome Inform. Ser. Workshop Genome Inform. , vol.10 , pp. 73-82
    • Doi, K.1    Imai, H.2
  • 7
    • 0031608937 scopus 로고    scopus 로고
    • An introduction to PCR primer design and optimization of amplification reactions
    • Robertson, J.M. and J. Walsh-Weller. 1998. An introduction to PCR primer design and optimization of amplification reactions. Methods Mol. Biol. 98:121-154.
    • (1998) Methods Mol. Biol. , vol.98 , pp. 121-154
    • Robertson, J.M.1    Walsh-Weller, J.2
  • 8
    • 0029281784 scopus 로고
    • Selection of primers for polymerase chain reaction
    • Rychlik, W. 1995. Selection of primers for polymerase chain reaction. Mol. Biotechnol. 3:129-134.
    • (1995) Mol. Biotechnol. , vol.3 , pp. 129-134
    • Rychlik, W.1
  • 9
    • 0036276987 scopus 로고    scopus 로고
    • Primer design for PCR and sequencing in high-throughput analysis of SNPs
    • Vieux, E.F., P.Y. Kwok, and R.D. Miller. 2002. Primer design for PCR and sequencing in high-throughput analysis of SNPs. BioTechniques (Suppl):28-32.
    • (2002) BioTechniques , Issue.SUPPL. , pp. 28-32
    • Vieux, E.F.1    Kwok, P.Y.2    Miller, R.D.3
  • 10
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen, S. and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132:365-386.
    • (2000) Methods Mol. Biol. , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 11
    • 0024438993 scopus 로고
    • A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA
    • Rychlik, W. and R.E. Rhoads. 1989. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 17:8543-8551.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 8543-8551
    • Rychlik, W.1    Rhoads, R.E.2
  • 12
    • 0043122991 scopus 로고    scopus 로고
    • Primer Design Assistant (PDA): A web-based primer design tool
    • Chen, S.H., C.Y. Lin, C.S. Cho, C.Z. Lo, and C.A. Hsiung. 2003. Primer Design Assistant (PDA): a web-based primer design tool. Nucleic Acids Res. 31:3751-3754.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3751-3754
    • Chen, S.H.1    Lin, C.Y.2    Cho, C.S.3    Lo, C.Z.4    Hsiung, C.A.5
  • 13
    • 1842835760 scopus 로고    scopus 로고
    • Computer programs for PCR primer design and analysis
    • Chen, B.Y., H.W. Janes, and S. Chen. 2002. Computer programs for PCR primer design and analysis. Methods Mol. Biol. 192:19-29.
    • (2002) Methods Mol. Biol. , vol.192 , pp. 19-29
    • Chen, B.Y.1    Janes, H.W.2    Chen, S.3
  • 16
    • 1842844023 scopus 로고    scopus 로고
    • PRIMEGENS: Robust and efficient design of gene-specific probes for microarray analysis
    • Xu, D., G. Li, L. Wu, J. Zhou, and Y. Xu. 2002. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics 18:1432-1437.
    • (2002) Bioinformatics , vol.18 , pp. 1432-1437
    • Xu, D.1    Li, G.2    Wu, L.3    Zhou, J.4    Xu, Y.5
  • 17
    • 0024295554 scopus 로고
    • Characterization of RNA hairpin loop stability
    • Groebe, D.R. and O.C. Uhlenbeck. 1988. Characterization of RNA hairpin loop stability. Nucleic Acids Res. 16:11725-11735.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 11725-11735
    • Groebe, D.R.1    Uhlenbeck, O.C.2
  • 18
    • 0026593806 scopus 로고
    • Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
    • Antao, V.P. and I. Tinoco, Jr. 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res. 20:819-824.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 819-824
    • Antao, V.P.1    Tinoco Jr., I.2
  • 20
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, Jr., J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95:1460-1465.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 1460-1465
    • SantaLucia Jr., J.1
  • 21
    • 0034663473 scopus 로고    scopus 로고
    • Discrimination of primer 3′-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction
    • Ayyadevara, S., J.J. Thaden, and R.J. Shmookler Reis. 2000. Discrimination of primer 3′-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction. Anal. Biochem. 284:11-18.
    • (2000) Anal. Biochem. , vol.284 , pp. 11-18
    • Ayyadevara, S.1    Thaden, J.J.2    Shmookler Reis, R.J.3
  • 22
    • 0034929692 scopus 로고    scopus 로고
    • Capillary electrophoresis as a tool for optimization of multiplex PCR reactions
    • Butler, J.M., C.M. Ruitberg, and P.M. Vallone. 2001. Capillary electrophoresis as a tool for optimization of multiplex PCR reactions. Fresenius J. Anal. Chem. 369:200-205.
    • (2001) Fresenius J. Anal. Chem. , vol.369 , pp. 200-205
    • Butler, J.M.1    Ruitberg, C.M.2    Vallone, P.M.3
  • 24
    • 0026899849 scopus 로고
    • Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest-neighbor stacking interactions in DNA
    • Doktycz, M.J., R.F. Goldstein, T.M. Paner, F.J. Gallo, and A.S. Benight. 1992. Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: evaluation of the nearest-neighbor stacking interactions in DNA. Biopolymers 32:849-864.
    • (1992) Biopolymers , vol.32 , pp. 849-864
    • Doktycz, M.J.1    Goldstein, R.F.2    Paner, T.M.3    Gallo, F.J.4    Benight, A.S.5
  • 25
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto, N., S. Nakano, M. Yoneyama, and K. Honda. 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 24:4501-4505.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4
  • 26
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • SantaLucia, Jr., J., H.T. Allawi, and P.A. Seneviratne. 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555-3562.
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • SantaLucia Jr., J.1    Allawi, H.T.2    Seneviratne, P.A.3
  • 27
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal GT mismatches in DNA
    • Allawi, H.T. and J. SantaLucia, Jr. 1997. Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry 36:10581-10594.
    • (1997) Biochemistry , vol.36 , pp. 10581-10594
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 28
    • 0032581024 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics of internal AC mismatches in DNA: Sequence dependence and pH effects
    • Allawi, H.T. and J. SantaLucia, Jr. 1998. Nearest-neighbor thermodynamics of internal AC mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435-9444.
    • (1998) Biochemistry , vol.37 , pp. 9435-9444
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 29
    • 0032212134 scopus 로고    scopus 로고
    • NMR solution structure of a DNA dodecamer containing single GT mismatches
    • Allawi, H.T. and J. SantaLucia, Jr. 1998. NMR solution structure of a DNA dodecamer containing single GT mismatches. Nucleic Acids Res. 26:4925-4934.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4925-4934
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 30
    • 0032102940 scopus 로고    scopus 로고
    • Thermodynamics of internal CT mismatches in DNA
    • Allawi, H.T. and J. SantaLucia, Jr. 1998. Thermodynamics of internal CT mismatches in DNA. Nucleic Acids Res. 26:2694-2701.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2694-2701
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 31
    • 0032562140 scopus 로고    scopus 로고
    • Nearest neighbor thermodynamic parameters for internal GA mismatches in DNA
    • Allawi, H.T. and J. SantaLucia, Jr. 1998. Nearest neighbor thermodynamic parameters for internal GA mismatches in DNA. Biochemistry 37:2170-2179.
    • (1998) Biochemistry , vol.37 , pp. 2170-2179
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 32
    • 0033596964 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics and NMR of DNA sequences with internal AA, CC, GG, and TT mismatches
    • Peyret, N., P.A. Seneviratne, H.T. Allawi, and J. SantaLucia, Jr. 1999. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal AA, CC, GG, and TT mismatches. Biochemistry 38:3468-3477.
    • (1999) Biochemistry , vol.38 , pp. 3468-3477
    • Peyret, N.1    Seneviratne, P.A.2    Allawi, H.T.3    SantaLucia Jr., J.4
  • 33
    • 0035965696 scopus 로고    scopus 로고
    • Sequence context and thermodynamic stability of a single base pair mismatch in short deoxyoligonucleotide duplexes
    • Hall, T.S., P. Pancoska, P.V. Riccelli, K. Mandell, and A.S. Benight. 2001. Sequence context and thermodynamic stability of a single base pair mismatch in short deoxyoligonucleotide duplexes. J. Am. Chem. Soc. 123:11811-11812.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 11811-11812
    • Hall, T.S.1    Pancoska, P.2    Riccelli, P.V.3    Mandell, K.4    Benight, A.S.5
  • 34
    • 0037425541 scopus 로고    scopus 로고
    • DNA sequence context and multiplex hybridization reactions: Melting studies of heteromorphic duplex DNA complexes
    • Riccelli, P.V., T.S. Hall, P. Pancoska, K.E. Mandell, and A.S. Benight. 2003. DNA sequence context and multiplex hybridization reactions: melting studies of heteromorphic duplex DNA complexes. J. Am. Chem. Soc. 125:141-150.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 141-150
    • Riccelli, P.V.1    Hall, T.S.2    Pancoska, P.3    Mandell, K.E.4    Benight, A.S.5
  • 35
    • 0033527321 scopus 로고    scopus 로고
    • Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability
    • Vallone, P.M., T.M. Paner, J. Hilario, M.J. Lane, B.D. Faldasz, and A.S. Benight 1999. Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers 50:425-442.
    • (1999) Biopolymers , vol.50 , pp. 425-442
    • Vallone, P.M.1    Paner, T.M.2    Hilario, J.3    Lane, M.J.4    Faldasz, B.D.5    Benight, A.S.6
  • 37
    • 0037526212 scopus 로고    scopus 로고
    • Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci
    • Schoske, R., P.M. Vallone, C.M. Ruitberg, and J.M. Butler. 2003. Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal. Bioanal. Chem. 375:333-343.
    • (2003) Anal. Bioanal. Chem. , vol.375 , pp. 333-343
    • Schoske, R.1    Vallone, P.M.2    Ruitberg, C.M.3    Butler, J.M.4
  • 38
    • 3943071529 scopus 로고    scopus 로고
    • A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome
    • Vallone, P.M., R.S. Just, M.D. Coble, J.M. Butler, and T.J. Parsons. 2004. A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int. J. Legal Med. 118:147-157.
    • (2004) Int. J. Legal Med. , vol.118 , pp. 147-157
    • Vallone, P.M.1    Just, R.S.2    Coble, M.D.3    Butler, J.M.4    Parsons, T.J.5
  • 39
    • 85087602834 scopus 로고    scopus 로고
    • Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension
    • In press
    • Vallone, P.M. and J.M. Butler. Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J. Forensic Sci. (In press).
    • J. Forensic Sci.
    • Vallone, P.M.1    Butler, J.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.