Single molecule measurement of the 'speed limit' of DNA polymerase (Proceedings of the National Academy of Sciences of the United States of America (2009) 106, 48, (20294-20299) DOI:10.1073/pnas.0907404106);Single molecule measurement of the "speed limit" of DNA polymerase

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 48, 2009, Pages 20294-20299

  Schwartz, Jerrod J ^a   Quake, Stephen R ^a  

^a Stanford University   (United States)

Author keywords

DNA hairpin; DNA replication; FRET; Pausing

Indexed keywords

DNA POLYMERASE; NUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; CONTROLLED STUDY; DNA REPLICATION; DNA SYNTHESIS; ESCHERICHIA COLI; MOLECULE; NONHUMAN; OPTICAL RESOLUTION; PRIORITY JOURNAL; STOCHASTIC MODEL;

ESCHERICHIA COLI;

EID: 73949097615     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0913884107     Document Type: Erratum

References (34)

1. Smolina IV, Demidov VV, Frank-Kamenetskii MD (2003) Pausing of DNA Polymerases on duplex DNA templates due to ligand binding in vitro. J Mol Biol 326:1113-1125.
2. Deshpande AM, Newlon CS (1996) DNA replication fork pause sites dependent on transcription. Science 272:1030-1033.
3. Krasilnikova MM, Samadashwily GM, Krasilnikov AS, Mirkin SM (1998) Transcription through a simple DNA repeat blocks replication elongation. EMBO J 17:5095-5102.
4. Dalgaard JZ, Klar AJS (2000) swi1 and swi3 perform imprinting, pausing, and termination of DNA replication in S. pombe. Cell 102:745-751.
5. Takeuchi Y, Horiuchi T, Kobayashi T (2003) Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev 17:1497-1506.
6. Bedinger P, Munn M, AlbertsBM(1989) Sequence-specific pausing during in vitro DNA replication on double- stranded DNA templates. J Biol Chem 264:16880-16886.
7. LaDuca RJ, Fay PJ, Chuang C, McHenry CS, Bambara RA (1983) Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by 4 forms of Escherichia coli DNA polymerase III. Biochemistry 22:5177-5188.
8. Lemoine FJ, Degtyareva NP, Lobachev K, Petes TD (2005) Chromosomal translocations in yeast induced by low levels of DNA polymerase: A model for chromosome fragile sites. Cell 120:587-598.
9. Cha RS, KlecknerN(2002)ATRhomologMec1promotes fork progression, thus averting breaks in replication slow zones. Science 297:602-606.
10. Kang S, Ohshima K, Shimizu M, Amirhaeri S, Wells RD (1995) Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes. J Biol Chem 270:27014-27021.
11. Samadashwily GM, Raca G, Mirkin SM (1997) Trinucleotide repeats affect DNA replication in vivo. Nat Genet 17:298-304.
12. Tasara T, et al. (2003) Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. II. High-density labeling of natural DNA. Nucl Acids Res 31:2636-2646.
13. Maier B, Bensimon D, Croquette V (2000) Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc Natl Acad Sci USA 97:12002-12007.
14. Wuite GJL, Smith SB, Young M, Keller D, Bustamante C (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404:103-106.
15. Mytelka DS, ChamberlinMJ(1996) Analysis and suppression ofDNApolymerase pauses associated with a trinucleotide consensus. Nucl Acids Res 24:2774-2781.
16. Astatke M, Grindley NDF, Joyce CM (1998) How E. coli DNA polymerase I (klenow fragment) distinguishes between deoxy- and dideoxynucleotides. J Mol Biol 278:147-165.
17. Dahlberg ME, Benkovic SJ (1991) Kinetic mechanism of DNA polymerase I(Klenow fragment): Identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry 30:4835-4843.
18. Kuchta RD, Mizrahi V, Benkovic PA, Johnson KA, Benkovic SJ (1987) Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 26:8410-8417.
19. Purohit V, Grindley NDF, Joyce CM (2003) Use of 2-Aminopurine Fluorescence To Examine Conformational Changes during Nucleotide Incorporation by DNA Polymerase I (Klenow Fragment)†. Biochemistry 42:10200-10211.
20. Singh K, Srivastava A, Patel SS,ModakMJ(2007) Participation of the fingers subdomain of Escherichia coliDNApolymerase I in the strand displacement synthesis of DNA. J Biol Chem 282:10594-10604.
21. Weiss S (2000) Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat Struct Mol Biol 7:724-729.
22. Rees WA, Yager TD, Korte J, Von Hippel PH (1993) Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry 32:137-144.
23. Henke W, Herdel K, Jung K, Schnorr D, Loening SA (1997) Betaine improves the PCR amplification of GC-rich DNA sequences. Nucl Acids Res 25:3957-3958.
24. Baskaran N, et al. (1996) Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. Genome Res 6:633-638.
25. Joyce CM, et al. (2008) Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry 47:6103-6116.
26. Lee J-B, et al. (2006) DNA primase acts as a molecular brake in DNA replication. Nature 439:621-624.
27. Tanner NA, et al. (2008) Single-molecule studies of fork dynamics in Escherichia coli DNA replication. Nat Struct Mol Biol 15:170-176.
28. Eid J, et al. (2008) Real-time DNA sequencing from single polymerase molecules. Science 323:133-138.
29. Soengas MS, Gutiérrez C, Salas M (1995) Helix-destabilizing activity of φ29 single-stranded DNA binding protein: Effect on the elongation rate during strand displacement DNA replication. J Mol Biol 253:517-529.
30. Rasnik I, McKinney SA, Ha T (2006) Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Meth 3:891-893.
31. Chandran RS, John SE, Amit M (2005) Long time scale blinking kinetics of cyanine fluorophores conjugated to DNA and its effect on F[o-umlaut]rster resonance energy transfer. J Chem Phys 123:224708.
32. Aitken CE, Marshall RA, Puglisi JD (2008) An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J 94(5):1826-1835.
33. Crocker JC, Grier DG (1996) Methods of digital video microscopy for colloidal studies. J Colloid Interface Sci 179:298-310.
34. Kerssemakers JWJ, et al. (2006) Assembly dynamics of microtubules at molecular resolution. Nature 442:709-712.