Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids

Biochemistry

Volumn 48, Issue 18, 2009, Pages 3988-3997

  Huang, Yuegao ^a   Chen, Congju ^a,b   Russu, Irina M ^a  

^a WESLEYAN UNIVERSITY   (United States)

^b NewYork Presbyterian Hospital   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRS; BASE SEQUENCES; CHEMICAL NATURE; CONCENTRATION OF; DNA STRANDS; FREE ENERGY CHANGE; HYBRID STRUCTURE; IMINO PROTONS; OPENING REACTIONS; PROTON ACCEPTORS; PROTON EXCHANGE; RNA-DNA HYBRIDS; SUGAR MOIETY;

CHEMICAL STABILITY; DNA; DYNAMICS; GENES; MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POSITIVE IONS; PROTONS; REACTION RATES; RNA; STABILITY; SUGAR (SUCROSE); SUGARS;

NUCLEIC ACIDS;

AMMONIA; DNA; GUANINE; RNA;

ARTICLE; BACTERIOPHAGE LAMBDA; BASE PAIRING; CONCENTRATION (PARAMETERS); DNA RNA HYBRIDIZATION; DNA STRAND; ENERGY; GC RICH SEQUENCE; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTON TRANSPORT; TRANSCRIPTION TERMINATION;

BASE SEQUENCE; DNA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID HYBRIDIZATION; RNA;

ENTEROBACTERIA PHAGE LAMBDA;

EID: 66149094661     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi900070f     Document Type: Article

References (35)

1. Rich, A. (2006) Discovery of the Hybrid Helix and the First DNA-RNA Hybridization. J. Biol. Chem. 281, 7693-7696. (Pubitemid 43847382)
2. Hall, K. B. (1993) NMR spectroscopy of DNA/RNA hybrids. Curr. Opin. Struct. Biol. 3, 336-339. (Pubitemid 23207563)
3. Fedoroff, O. Y., Salazar, M., and Reid, B. R. (1993) Structure of a DNA:RNA Hybrid Duplex. Why RNase H Does Not Cleave Pure RNA. J. Mol. Biol. 233, 509-523.
4. Sanghani, S. R., and Lavery, R. (1994) Theoretical studies of DNA-RNA hybrid conformations. Nucleic Acids Res. 22, 1444-1449. (Pubitemid 24166845)
5. Horton, N. C., and Finzel, B. C. (1996) The Structure of an RNA/DNAHybrid: A Substrate of the Ribonuclease Activity of HIV-1 Reverse Transcriptase. J. Mol. Biol. 264, 521-533. (Pubitemid 27010742)
6. Fedoroff, O. Y., Ge, Y., and Reid, B. R. (1997) Solution Structure of r(gaggacug):d(CAGTCCTC) Hybrid: Implications for the Initiation of HIV-1 (+)-Strand Synthesis. J. Mol. Biol. 269, 225-239. (Pubitemid 27248287)
7. Gyi, J. I., Lane, A. N., Conn, G. L., and Brown, T. (1998) Solution Structures of DNA-RNA Hybrids with Purine-Rich and Pyrimidine-Rich Strands: Comparison with the Homologous DNA and RNA Duplexes. Biochemistry 37, 73-80. (Pubitemid 28049109)
8. Xiong, Y., and Sundaralingam, M. (2000) Crystal structure of a DNA-RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). Nucleic Acids Res. 28, 2171-2176. (Pubitemid 30255541)
9. Kopka, M. L., Leavelle, L., Won Han, G., Ng, H.-L., and Dickerson, R. E. (2003) An Unusual Sugar Conformation in the Structure of an RNA/DNA Decamer of the Polypurine Tract May Affect Recognition by RNase H. J. Mol. Biol. 334, 653-665. (Pubitemid 37433883)
10. Noy, A., Perez, A., Marquez, M., Luque, F. J., and Orozco, M. (2005) Structure, Recognition Properties, and Flexibility of the DNA3RNA Hybrid. J. Am. Chem. Soc. 127, 4910-4920. (Pubitemid 40489645)
11. Priyakumar, U. D., and MacKerell, A. D. Jr. (2008) Atomic Detail Investigation of the Structure and Dynamics of DNA·RNA Hybrids: A Molecular Dynamics Study. J. Phys. Chem. B 112, 1515-1524.
12. Hall, K. B., and McLaughlin, L. W. (1991) Thermodynamic and Structural Properties of Pentamer DNA3 DNA, RNA·RNA, and DNA·RNA Duplexes of Identical Sequence. Biochemistry 30, 10606-10613.
13. Ratmeyer, L., Vinayak, R., Zhong, Y. Y., Zon, G., and Wilson, W. D. (1994) Sequence Specific Thermodynamic and Structural Properties for DNA·RNA Duplexes. Biochemistry 33, 5298-5304. (Pubitemid 24150999)
14. Lesnik, E. A., and Freier, S. M. (1995) Relative Thermodynamic Stability of DNA, RNA, and DNA:RNA Hybrid Duplexes: Relationship with base Composition and Structure. Biochemistry 34, 10807-10815.
15. Martin, F. H., and Tinoco, I. J. (1980) RNA-DNA hybrid duplexes containing oligo (dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 8, 2295-2299.
16. Roberts, R. W., and Crothers, D. M. (1992) Stability and Properties of Double and Triple Helices: Dramatic Effects of RNA or DNA Backbone Composition. Science 258, 1463-1466. (Pubitemid 23011000)
17. Gyi, J. I., Conn, G. L., Lane, A. N., and Brown, T. (1996) Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA-RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes. Biochemistry 35, 12538-12548. (Pubitemid 26318051)
18. Wilson, K. S., and von Hippel, P. H. (1994) Stability of Escherichia coli Transcription Complexes Near an Intrinsic Terminator. J. Mol. Biol. 244, 36-51. (Pubitemid 24360080)
19. von Hippel, P. H. (1998) An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing. Science 281, 660-665.
20. Larson, M. H., Greenleaf, W. J., Landick, R., and Block, S. M. (2008) Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination. Cell 132, 971-982.
21. Datta, K., and von Hippel, P. H. (2008) Direct Spectroscopic Study of Reconstituted Transcription Complexes Reveals That Intrinsic Termination is Driven Primarily by Thermodynamic Destabilization of the Nucleic Acid Framework. J. Biol. Chem. 283, 3537-3549.
22. Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798.
23. Chen, C., and Russu, I. M. (2004) Sequence-Dependence of the Energetics of Opening of AT Base Pairs in DNA. Biophys. J. 87 1-7.
24. Russu, I. M. (2004) Probing Site-Specific Energetics in Proteins and Nucleic Acids by Hydrogen Exchange and NMR Spectroscopy. Methods Enzymol. 379, 152-175. (Pubitemid 38313471)
25. Plateau, P., and Gueron, M. (1982) Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104, 7310-7311.
26. Mori, S., Abeygunawardana, C., Johnson, M. O., and van Zijl, P. C. M. (1995) Improved Sensitivity of HSQC Spectra of Exchanging Protons at Short Interscan Delays Using a new Fast HSQC (FHSQC) Detection Scheme That Avoids Water Saturation. J. Magn. Reson., Ser. B 108, 94-98.
27. Chen, C., Jiang, L., Michalczyk, R., and Russu, I. M. (2006) Structural Energetics and Base-Pair Opening Dynamics in Sarcin-Ricin Domain RNA. Biochemistry 45, 13606-13613.
28. Lippens, G., Dhalluin, C., and Wieruszeski, J.-M. (1995) Use of a water flip-back pulse in the homonuclear NOESY experiment. J. Biomol. NMR 5, 327-331.
29. Gueron, M., and Leroy, J.-L. (1995) Studies of Base Pair Kinetics by NMR Measurement of Proton Exchange. Methods Enzymol. 261, 383-413.
30. Gueron, M., Charretier, E., Hagerhorst, J., Kochoyan, M., Leroy, J. L., and Moraillon, A. (1990) Applications of Imino Proton Exchange to Nucleic Acid Kinetics and Structures. In Structure & Methods (Sarma, R. H., and Sarma, M. H., Eds.) pp 113-137, Adenine Press, Albany, NY.
31. Benight, A. S., Schurr, J. M., Flynn, P. F., Reid, B. R., and Wemmer, D. E. (1988) Melting of a Self-complementary DNA Minicircle. Comparison of Optical Melting Theory with Exchange Broadening of the Nuclear Magnetic Resonance Spectrum. J. Mol. Biol. 200, 377-399.
32. Weast, R. C. (1987) CRC Handbook of Chemistry and Physics, 67th ed., CRC Press, Boca Raton, FL.
33. Ts'o, P. O. P. (1974) Basic Principles in Nucleic Acid Chemistry, Vol.I, Academic Press, New York.
34. Wang, S., and Kool, E. T. (1995) Origins of the Large Differences in Stability of DNA and RNA Helices: C-5 Methyl and 2′-Hydroxyl Effects. Biochemistry 34, 4125-4132.
35. Wu, P., Nakano, S., and Sugimoto, N. (2002) Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. Eur. J. Biochem. 269, 2821-2830. (Pubitemid 34754009)