Templating efficiency of naked DNA

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

Volumn 107, Issue 27, 2010, Pages 12074-12079

  Kervio, Eric ^a   Hochgesand, Annette ^b   Steiner, Ulrich E ^c   Richert, Clemens ^a,b  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF KARLSRUHE   (Germany)

^c UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MONOMER; NAKED DNA; NUCLEIC ACID BASE; PRIMER DNA;

ARTICLE; DNA BINDING; DNA FLANKING REGION; DNA REPLICATION; DNA SEQUENCE; DNA TEMPLATE; PRIORITY JOURNAL; PROTON TRANSPORT;

BASE SEQUENCE; DNA; DNA PRIMERS; DNA REPLICATION; MODELS, CHEMICAL; MODELS, GENETIC; MOLECULAR STRUCTURE; TEMPLATES, GENETIC;

EID: 77955452076     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0914872107     Document Type: Article

References (45)

1. Joyce C-M, Benkovic S-J (2004) DNA polymerase fidelity: Kinetics structure and checkpoints. Biochemistry 43:14317-14324. (Pubitemid 39491965)
2. Nudler E (2009) RNA Polymerase active center: The molecular engine of transcription. Annu Rev Biochem 78:335-361.
3. Berdis A-J (2009) Mechanisms of DNA polymerases. Chem Rev 109:2862-2879.
4. Kunkel T-A, Bebenek K (2000) DNA replication fidelity. Annu Rev Biochem 69:497-529.
5. Yang J, Zhuang Z, Roccasecca R-M, Trakselis M-A, Benkovic S-J (2004) The dynamic processivity of the T4 DNA polymerase during replication. Proc Natl Acad Sci USA 101:8289-8294. (Pubitemid 38736568)
6. Kuchta R-D, Benkovic P, Benkovic S-J (1988) Kinetic mechanism whereby DNA-polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 27:6716-6725.
7. Mendelman L-V, Boosalis M-S, Petruska J, Goodman M-F (1989) Nearest neighbor influences on DNA polymerase insertion fidelity. J Biol Chem 264:14415-14423. (Pubitemid 19214276)
8. Patel S-S, Wong I, Johnson K-A (1991) Pre-steady-state kinetic-analysis of processive DNA-replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 30:511-525.
9. Minetti C-A-S-A, et al. (2003) The thermodynamics of template-directed DNA synthesis: Base insertion and extension enthalpies. Proc Natl Acad Sci USA 100:14719-14724.
10. Joyce G-F, Orgel L-E (2006) The RNA World, eds R-F Gesteland, T-R Cech, and J-F Atkins (Cold Spring Harbor Laboratory Press, Plainview, NY), pp 23-56.
11. Sulston J, Lohrmann R, Orgel L-E, Miles H-T (1968) Nonenzymatic synthesis of oligoadenylates on a polyuridylic acid template. Proc Natl Acad Sci USA 59:726-733.
12. Kozlov I-A, Orgel L-E (2000) Nonenzymatic template-directed synthesis of RNA from monomers. Mol Biol 34:781-789. (Pubitemid 33214739)
13. Kanavarioti A, Bernasconi C-F, Baird E-E (1998) Effects of monomer and template concentration on the kinetics of nonenzymatic template-directed oligoguanylate synthesis. J Am Chem Soc 120:8575-8581. (Pubitemid 28442893)
14. Sievers D, von Kiedrowski G (1994) Self-Replication of complementary nucleotide-based oligonucleotides. Nature 369:221-224.
15. Luther A, Brandsch R, von Kiedrowski G (1998) Surface-promoted replication and exponential amplification of DNA analogues. Nature 396:245-248. (Pubitemid 28541384)
16. Inoue T, Orgel L-E (1983) A nonenzymatic RNA polymerase model. Science 219:859-862.
17. Wu T, Orgel L-E (1992) Non enzymatic template-directed synthesis on hairpin oligonucleotides. 3. Incorporation of adenosine and uridine residues. J Am Chem Soc 114:7963-7969.
18. Hill A-R, Orgel L-E, Wu T (1993) The limits of template-directed synthesis with 5′-phosphoro-(2-methyl)imidazolides. Origins Life Evol B 23:285-290.
19. Lohrmann R, Orgel L-E (1976) Template-directed synthesis of high molecular weight polynucleotide analogues. Nature 261:342-344.
20. Chen J-J, Cai X, Szostak J-W (2009) N2′ → P3′ Phosphoramidate glycerol nucleic acid as a potential alternative genetic system. J Am Chem Soc 131:2119-2121.
21. Schrum J-P, Ricardo A, Krishnamurthy M, Blain J-C, Szostak J-W (2009) Efficient and rapid template-directed nucleic acid copying using 2′-amino-2′,3′-dideoxyribonucleoside-5′- phosphorimidazolide monomers. J Am Chem Soc 131:14560-14570.
22. Mansy S-S, et al. (2008) Template-directed synthesis of a genetic polymer in a model protocell. Nature 454:122-125.
23. Wuite G-J, Smith S-B, 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. (Pubitemid 30143142)
24. Eid J, et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133-138.
25. Griesang N, Giessler K, Lommel T, Richert C (2006) Four color enzyme-free interrogation of DNA sequences with chemically activated 3′-fluorophore- labeled nucleotides. Angew Chem Int Edit 45:6144-6148. (Pubitemid 44453059)
26. Hagenbuch P, Kervio E, Hochgesand A, Plutowski U, Richert C (2005) Chemical primer extension: Efficiently determining single nucleotides in DNA. Angew Chem Int Edit 44:6588-6592. (Pubitemid 41502806)
27. Eisenhuth R, Richert C (2009) Convenient syntheses of 3′-amino-2′3′-dideoxynucleosides their 5′-monophosphates and 3′-aminoterminal oligodeoxynucleotide primers. J Org Chem 74:26-37.
28. Sarracino D, Richert C (1996) Quantitative MALDI-TOF spectrometry of oligonucleotides and a nuclease assay. Bioorg Med Chem Lett 6:2543-2548. (Pubitemid 26375265)
29. Rojas Stütz J-A, Richert C (2001) A steroid cap adjusts the selectivity and accelerates the rates of nonenzymatic single nucleotide extensions of an oligonucleotide. J Am Chem Soc 123:12718-12719.
30. Fersht A (1999) Structure and Mechanism in Protein Science (Freeman, New York), pp 259-266.
31. Kanavarioti A, Stronach M-W, Ketner R-J, Hurley T-B (1995) Large steric effect in the substitution reaction of amines with phosphoimidazolide-activated nucleosides. J Org Chem 60:632-637.
32. Loeb L-A, Kunkel T-A (1982) Fidelity of DNA-synthesis. Annu Rev Biochem 51:429-457.
33. Goodman M-F, Fygenson K-D (1998) DNA polymerase fidelity: From genetics toward a biochemical understanding. Genetics 148:1475-1482.
34. Lincoln T-A, Joyce G-F (2009) Self-sustained replication of an RNA enzyme. Science 323:1229-1232.
35. Zielinski M, Kozlov I-A, Orgel L-E (2000) A comparison of RNA with DNA in template-directed synthesis. Helv Chim Acta 83:1678-1684. (Pubitemid 30662518)
36. Orgel L-E (1992) Molecular replication. Nature 358:203-209.
37. Hartel C, Göbel M-W (2000) Substitution of adenine by purine-2,6-diamine improves the nonenzymatic oligomerization of ribonucleotides on templates containing thymidine. Helv Chim Acta 83:2541-2549.
38. Beier M, Reck F, Wagner T, Krishnamurthy R, Eschenmoser A (1999) Chemical etiology of nucleic acid structure: Comparing pentopyranosyl (2′-4′) oligonucleotides with RNA. Science 283:699-703. (Pubitemid 129506241)
39. JohnstonW-K, Unrau P-J, Lawrence M-S, Glasner M-E, Bartel D-P (2001) RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 292:1319-1325.
40. Vogel S-R, Richert C (2007) Adenosine residues in the template do not block spontaneaous replication steps of RNA. Chem Commun 1896-1898.
41. Kyogoku Y, Lord R-C, Rich A (1969) An infrared study of hydrogen-bonding specificity of hypoxanthine and other nucleic acid derivatives. Biochim Biophys Acta 179:10-17.
42. Lawrence M-S, Bartel D-P (2003) Processivity of ribozyme catalyzed RNA polymerization. Biochemistry 42:8748-8755.
43. Bartel D-P, Doudna J-A, Usman N, Szostak J-W (1991) Template-directed primer extension catalyzed by the Tetrahymena ribozyme. Mol Cell Biol 11:3390-3394.
44. Switzer C, Moroney S-E, Benner S-A (1989) Enzymatic incorporation of a new base pair into DNA and RNA. J Am Chem Soc 111:8322-8323. (Pubitemid 19255518)
45. Krueger A-T, Kool E-T (2007) Model systems for understanding DNA base pairing. Curr Opin Chem Biol 11:588-594.