Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primer-template junctions

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

Volumn 106, Issue 11, 2009, Pages 4231-4236

  Jose, Davis ^a   Datta, Kausiki ^a   Johnson, Neil P ^b,c   Von Hippel, Peter H ^a  

^a UNIVERSITY OF OREGON   (United States)

^b INSTITUT DE PHARMACOLOGIE ET DE BIOLOGIE STRUCTURALE   (France)

^c UNIVERSITÉ DE TOULOUSE   (France)

Author keywords

2 aminopurine |; Circular dichroism |; DNA unwinding |; Fluorescence forked DNA

Indexed keywords

2 AMINOPURINE; ACRYLAMIDE; ADENINE; DOUBLE STRANDED DNA; NUCLEIC ACID; PRIMER DNA; SINGLE STRANDED DNA;

ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; DNA CONFORMATION; DNA PROBE; DNA REPLICATION; DNA SEQUENCE; DNA TEMPLATE; FLUORESCENCE SPECTROSCOPY; GENE CONSTRUCT; PHOTOCHEMICAL QUENCHING; PRIORITY JOURNAL; PROTEIN ANALYSIS; SPECTRAL SENSITIVITY; SPECTROSCOPY;

DNA; DNA PRIMERS; DNA REPLICATION; DNA, SINGLE-STRANDED; NUCLEIC ACID CONFORMATION; SPECTRUM ANALYSIS; TEMPLATES, GENETIC; VIBRATION;

EID: 63149185297     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0900803106     Document Type: Article

References (24)

1. McConnell B, von Hippel PH (1970) Hydrogen exchange as a probe of the dynamic structure of DNA. I. General acid-base catalysis. J Mol Biol 50:297-316.
2. Gueron M, Leroy J (1992) Base-pair opening in double-stranded nucleic acids. Nucleic Acids and Molecular Biology (Springer, New York), pp 1-22.
3. Every AE, Russu IM (2007) Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA. Biopolymers 87:165-173.
4. McGhee JD, von Hippel PH (1977) Formaldehyde as a probe of DNA structure. III Mechanism of the initial reaction of formaldehyde with DNA. Biochemistry 16:3276-3293.
5. Delagoutte E,von Hippel PH (2002)Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases. Q Rev Biophys 35:431-478.
6. Hochstrasser RA, Carver TE, Sowers LC, Millar DP (1994) Melting of a DNA helix terminus within the active site of a DNA polymerase. Biochemistry33:11971-11979.
7. von Hippel PH, Delagoutte E (2001) Ageneral model for nucleic acid helicases and their "coupling" within macromolecular machines. Cell 104:177-190.
8. Wong CJ, Lucius AL, Lohman TM (2005) Energetics of DNA end binding by E.coli RecBC and RecBCD helicases indicate loop formation in the 3′-single-stranded DNA tail. J Mol Biol 352:765-782.
9. 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 low-energy CD and fluorescence spectroscopy. J Mol Biol 360:800-813.
10. 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 USA101:3426-3431.
11. Eritja R, et al. (1986) Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine. Nucleic Acids Res 14:5869-5884.
12. Guest CR, Hochstrasser RA, Sowers LC, Millar DP (1991) Dynamics of mismatched base pairs in DNA. Biochemistry30:3271-3279.
13. Jean JM, Hall KB (2001) 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking. Proc Natl Acad Sci USA 98:37-41.
14. Law SM, Eritja R, Goodman MF, Breslauer KJ (1996) Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry 35:12329-12337.
15. Johnson NP, Baase WA, von Hippel PH (2005) Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine. Proc Natl Acad Sci USA 102:7169-7173.
16. Lee BJ, Barch M, Castner EWJ, Völker J, Breslauer KJ (2007) Structure and dynamics in DNA looped domains: CAG triplet repeat sequence dynamics probed by 2-aminopurine fluorescence. Biochemistry 46:10756-10766.
17. Lakowicz JR (1999) Principles of Flourescence Spectroscopy (Kluwer/Plenum, New York), 2nd Ed.
18. Andreatta D, et al. (2006) Ultrafast dynamics in DNA: "Fraying" at the end of the helix. J Am Chem Soc 128:6885-6892.
19. Liu C, Martin CT (2002) Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence. J Biol Chem 277:2725-2731.
20. Cantor CR, Schimmel PR (1980) Biophysical Chemistry (Freeman, San Francisco).
21. Ballin JD, Shkel IA, Record MT, Jr. (2004) Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: Demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids Res 32:3271-3281.
22. Bommarito S, Peyret N, SantaLucia J Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28:1929-1934.
23. Liu JD, Zhao L, Xia T (2008) The dynamic structural basis of differential enhancement of conformational stability by 5′-and 3′-dangling ends in RNA. Biochemistry 47:5962-5975.
24. Baase WA, et al. (2009) DNA models of trinucleotide frameshift deletions: The formation of loops and bulges at the primer-template junction. Nucleic Acids Res, 10.1093/ nar/gkn1042.