Revisiting the Central Dogma One Molecule at a Time

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2011 Feb 22

PMID 21335233

Citations 72

Authors

Carlos Bustamante

Wei Cheng

Yara X Mejia

Yara X Meija

Affiliations

Soon will be listed here.

Abstract

The faithful relay and timely expression of genetic information depend on specialized molecular machines, many of which function as nucleic acid translocases. The emergence over the last decade of single-molecule fluorescence detection and manipulation techniques with nm and Å resolution and their application to the study of nucleic acid translocases are painting an increasingly sharp picture of the inner workings of these machines, the dynamics and coordination of their moving parts, their thermodynamic efficiency, and the nature of their transient intermediates. Here we present an overview of the main results arrived at by the application of single-molecule methods to the study of the main machines of the central dogma.

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References

Galburt E, Grill S, Wiedmann A, Lubkowska L, Choy J, Nogales E . Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature. 2007; 446(7137):820-3. DOI: 10.1038/nature05701. View

Hohng S, Zhou R, Nahas M, Yu J, Schulten K, Lilley D . Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction. Science. 2007; 318(5848):279-83. PMC: 3558530. DOI: 10.1126/science.1146113. View

Lang M, Fordyce P, Engh A, Neuman K, Block S . Simultaneous, coincident optical trapping and single-molecule fluorescence. Nat Methods. 2005; 1(2):133-9. PMC: 1483847. DOI: 10.1038/nmeth714. View

Cornish P, Ermolenko D, Noller H, Ha T . Spontaneous intersubunit rotation in single ribosomes. Mol Cell. 2008; 30(5):578-88. PMC: 2491453. DOI: 10.1016/j.molcel.2008.05.004. View

Betterton M, Julicher F . Opening of nucleic-acid double strands by helicases: active versus passive opening. Phys Rev E Stat Nonlin Soft Matter Phys. 2005; 71(1 Pt 1):011904. DOI: 10.1103/PhysRevE.71.011904. View

Wen J, Lancaster L, Hodges C, Zeri A, Yoshimura S, Noller H . Following translation by single ribosomes one codon at a time. Nature. 2008; 452(7187):598-603. PMC: 2556548. DOI: 10.1038/nature06716. View

Jin J, Bai L, Johnson D, Fulbright R, Kireeva M, Kashlev M . Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol. 2010; 17(6):745-52. PMC: 2938954. DOI: 10.1038/nsmb.1798. View

Mackintosh S, Raney K . DNA unwinding and protein displacement by superfamily 1 and superfamily 2 helicases. Nucleic Acids Res. 2006; 34(15):4154-9. PMC: 1616963. DOI: 10.1093/nar/gkl501. View

Burroughs A, Iyer L, Aravind L . Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems. Genome Dyn. 2008; 3:48-65. DOI: 10.1159/000107603. View

10.

Chemla Y, Aathavan K, Michaelis J, Grimes S, Jardine P, Anderson D . Mechanism of force generation of a viral DNA packaging motor. Cell. 2005; 122(5):683-92. DOI: 10.1016/j.cell.2005.06.024. View

11.

Turnquist S, Simon M, Egelman E, Anderson D . Supercoiled DNA wraps around the bacteriophage phi 29 head-tail connector. Proc Natl Acad Sci U S A. 1992; 89(21):10479-83. PMC: 50362. DOI: 10.1073/pnas.89.21.10479. View

12.

Lohman T, Tomko E, Wu C . Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol. 2008; 9(5):391-401. DOI: 10.1038/nrm2394. View

13.

Ha T, Rasnik I, Cheng W, Babcock H, Gauss G, Lohman T . Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature. 2002; 419(6907):638-41. DOI: 10.1038/nature01083. View

14.

Wuite G, Smith S, Young M, Keller D, Bustamante C . Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature. 2000; 404(6773):103-6. DOI: 10.1038/35003614. View

15.

Korolev S, Yao N, Lohman T, Weber P, Waksman G . Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super-families of helicases. Protein Sci. 1998; 7(3):605-10. PMC: 2143965. DOI: 10.1002/pro.5560070309. View

16.

Park J, Myong S, Niedziela-Majka A, Lee K, Yu J, Lohman T . PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps. Cell. 2010; 142(4):544-55. PMC: 2943210. DOI: 10.1016/j.cell.2010.07.016. View

17.

Iyer L, Leipe D, Koonin E, Aravind L . Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 2004; 146(1-2):11-31. DOI: 10.1016/j.jsb.2003.10.010. View

18.

Bessman M, Lehman I, Simms E, Kornberg A . Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction. J Biol Chem. 1958; 233(1):171-7. View

19.

Mitchell M, Matsuzaki S, Imai S, Rao V . Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Res. 2002; 30(18):4009-21. PMC: 137109. DOI: 10.1093/nar/gkf524. View

20.

Grimes S, Jardine P, Anderson D . Bacteriophage phi 29 DNA packaging. Adv Virus Res. 2002; 58:255-94. DOI: 10.1016/s0065-3527(02)58007-6. View