Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork

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

Volumn 109, Issue 36, 2012, Pages 14428-14433

  Jose, Davis ^a   Weitzel, Steven E ^a   Von Hippel, Peter H ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

2 aminopurine; DNA structure; Helicase mechanisms; T4 DNA replication complex

Indexed keywords

DOUBLE STRANDED DNA; GUANOSINE 5' O (3 THIOTRIPHOSPHATE); GUANOSINE TRIPHOSPHATE; HELICASE; SINGLE STRANDED DNA;

ARTICLE; BACTERIOPHAGE T4; BASE PAIRING; COMPLEX FORMATION; CONTROLLED STUDY; DNA REPLICATION FORK; DNA STRUCTURE; ENZYME REGULATION; FLUORESCENCE ANALYSIS; MOLECULAR PROBE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN SUBUNIT;

BACTERIOPHAGE T4; BASE PAIRING; CIRCULAR DICHROISM; DNA HELICASES; DNA REPLICATION; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SPECTROMETRY, FLUORESCENCE;

EID: 84865989446     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1212929109     Document Type: Article

References (16)

1. Jose D, Datta K, Johnson NP, von Hippel PH (2009) Spectroscopic studies of positionspecific DNA "breathing" fluctuations at replication forks and primer-template junctions. Proc Natl Acad Sci USA 106:4231-4236.
2. von Hippel PH, Delagoutte E (2001) A general model for nucleic acid helicases and their "coupling" within macromolecular machines. Cell 104:177-190.
3. Lohman TM (1992) Escherichia coli DNA helicases: Mechanisms of DNA unwinding. Mol Microbiol 6:5-14.
4. Lohman TM, Bjornson KP (1996) Mechanisms of helicase-catalyzed DNA unwinding. Annu Rev Biochem 65:169-214. (Pubitemid 26250608)
5. Donmez I, Patel SS (2006) Mechanisms of a ring shaped helicase. Nucleic Acids Res 34:4216-4224. (Pubitemid 44542201)
6. Young MC, Schultz DE, Ring D, von Hippel PH (1994) Kinetic parameters of the translocation of bacteriophage T4 gene 41 protein helicase on single-stranded DNA. J Mol Biol 235:1447-1458. (Pubitemid 24150398)
7. Delagoutte E, von Hippel PH (2001) Molecular mechanisms of the functional coupling of the helicase (gp41) and polymerase (gp43) of bacteriophage T4 within the DNA replication fork. Biochemistry 40:4459-4477. (Pubitemid 32319592)
8. Richardson RW, Nossal NG (1989) Characterization of the bacteriophage T4 gene 41 DNA helicase. J Biol Chem 264:4725-4731. (Pubitemid 19081383)
9. Dong F, von Hippel PH (1996) The ATP-activated hexameric helicase of bacteriophage T4 (gp41) forms a stable primosome with a single subunit of T4-coded primase (gp61). J Biol Chem 271:19625-19631. (Pubitemid 26271643)
10. Jose D,Weitzel SE, Jing D, von Hippel PH (2012) Assembly and subunit stoichiometry of the functional helicase-primase (primosome) complex of bacteriophage T4 DNA replication system. Proc Natl Acad Sci USA, 10.1073/pnas.1210040109.
11. Cha TA, Alberts BM (1986) Studies of the DNA helicase-RNA primase unit from bacteriophage T4. A trinucleotide sequence on the DNA template starts RNA primer synthesis. J Biol Chem 261:7001-7010.
12. Johnson NP, Baase WA, von Hippel PH (2004) Low-energy circular dichroism of 2-aminopurine dinucleotide as a probe of local conformation of DNA and RNA. Proc Natl Acad Sci USA 101:3426-3431. (Pubitemid 38338211)
13. Datta K, Johnson NP, von Hippel PH (2006) Mapping the conformation of the nucleic acid framework of the T7 RNA polymerase elongation complex in solution using lowenergy CD and fluorescence spectroscopy. J Mol Biol 360:800-813. (Pubitemid 43993923)
14. Lakowicz J (1999) Principles of Fluorescence Spectroscopy (Kluwer/Plenum, New York).
15. Bujalowski W, Jezewska MJ (1995) Interactions of Escherichia coli primary replicative helicase DnaB protein with single-stranded DNA. The nucleic acid does not wrap around the protein hexamer. Biochemistry 34:8513-8519.
16. Dong F, Gogol EP, von Hippel PH (1995) The phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate. J Biol Chem 270:7462-7473.