Consecutive terminal GU pairs stabilize RNA helices

Biochemistry

Volumn 49, Issue 49, 2010, Pages 10574-10581

  Nguyen, Mai Thao ^a   Schroeder, Susan J ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING CONSTANT; IMINO PROTONS; ORDERS OF MAGNITUDE; PHYSICAL FORCE; PREDICTION MODEL; RNA SECONDARY STRUCTURE PREDICTION; RNA STRUCTURES; STACKING ORIENTATION; TARGET SEQUENCES;

FORECASTING; MATHEMATICAL MODELS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; RNA; THERMODYNAMIC STABILITY;

THERMODYNAMICS;

MICRORNA;

ARTICLE; BASE PAIRING; ENERGY TRANSFER; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; RNA STRUCTURE; THERMOSTABILITY;

BASE PAIRING; DINUCLEOSIDE PHOSPHATES; HETERODUPLEX ANALYSIS; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; PREDICTIVE VALUE OF TESTS; RNA STABILITY; SEQUENCE ANALYSIS, RNA; THERMODYNAMICS;

EID: 78650103315     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101521p     Document Type: Article

References (46)

1. Castanotto, D. and Rossi, J. J. (2009) The promises and pitfalls of RNA-interference-based therapeutics Nature 457, 426-433
2. Carthew, R. W. and Sontheimer, E. J. (2009) Origins and Mechanisms of miRNAs and siRNAs Cell 136, 642-655
3. Haley, B. and Zamore, P. D. (2004) Kinetic Analysis of the RNAi Enzyme Complex Nat. Struct. Biol. 11, 599-606
4. Doench, J. G. and Sharp, P. A. (2004) Specificity of microRNA Target Selection in Translational Repression Genes Dev. 18, 504-511
5. Ameres, S. L., Martinez, J., and Schroeder, R. (2007) Molecular Basis for Target RNA Recognition and Cleavage by Human RISC Cell 130, 101-112
6. Ding, Y. and Lawrence, C. E. (2001) Statistical Prediction of Single-Stranded Regions in RNA Secondary Structure and Application to Predicting Effective Antisense Target Sites and Beyond Nucleic Acids Res. 29, 1034-1046
7. Tafer, H., Ameres, S. L., Obernosterer, G., Gebeshuber, C. A., Schroeder, R., Martinez, J., and Hofacker, I. L. (2008) The impact of target accessibility on the design of effective siRNAs Nat. Biotechnol. 26, 578-583
8. Clanton-Arrowood, K., McGurk, J., and Schroeder, S. J. (2008) 3′ Terminal Nucleotides Determine Thermodynamic Stabilities of Mismatches at the Ends of RNA Helices Biochemistry 47, 13418-13427
9. Freier, S. M., Kierzek, R., Caruthers, M. H., Neilson, T., and Turner, D. H. (1986) Free energy of GU contributions and other terminal mismatches to helix stability Biochemistry 25, 3209-3213
10. Sugimoto, N., Kierkek, R., Freier, S. M., and Turner, D. H. (1986) Energetics of Internal GU Mismatches in Ribonucleotide Helixes Biochemistry 25, 5755-5759
11. He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A. E., and Turner, D. H. (1991) Nearest-neighbor parameters for GU mismatches Biochemistry 30, 11124-11132
12. 2 by two-dimensional NMR and simulated annealing Biochemistry 35, 14077-14089
13. 2 Biochemistry 36, 8030-8038
14. 2 Biochemistry 39, 8970-8982
15. Schroeder, S. J. and Turner, D. H. (2001) Thermodynamic stabilities of internal loops with GU closing pairs in RNA Biochemistry 40, 11509-11517
16. 2: Probing the structural features that shape the thermodynamic stability of GA pairs Biochemistry 46, 1511-1522
17. Schroeder, S. J., Fountain, M. A., Kennedy, S. D., Lukavsky, P. J., Puglisi, J. D., Krugh, T. R., and Turner, D. H. (2003) Thermodynamic Stability and Structural Feautures of the J4/5 Loops in a Pneumocystis carini Group I Intron Biochemistry 42, 14184-14196
18. Stombaugh, J., Zirbel, C. L., and Leontis, N. B. (2009) Frequency and Isostericity of RNA Base Pairs Nucleic Acids Res. 37, 2294-2312
19. Petersheim, M. and Turner, D. H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp Biochemistry 22, 256-263
20. Borer, P. N., Dengler, B., Tinoco, I., Jr., and Uhlenbeck, O. C. (1974) Stability of ribonucleic double-stranded helices J. Mol. Biol. 86, 843-853
21. Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., and Turner, D. H. (1986) Improved free-energy parameters for predictions of RNA duplex stability Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377
22. Lukavsky, P. and Puglisi, J. (2001) RNAPack: An integrated NMR approach to RNA structure determination Methods 25, 316-332
23. Sugimoto, N., Kierkek, R., and Turner, D. H. (1987) Sequence Dependence for the Energetics of Terminal Mismatches in Ribooligonucleotides Biochemistry 26, 4559-4562
24. Turner, D. H. (2000) Conformational Changes. In Nucleic Acids: Structures, Properties, and Functions (Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr., Eds.) pp 259 - 334, University Science Books, Sausalito, CA.
25. Johnson, S. M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K. L., Brown, D., and Slack, F. J. (2005) RAS is regulated by the let-7 microRNA family Cell 120, 635-647
26. Mayr, C., Hemann, M. T., and Bartel, D. P. (2007) Disrupting the pairing bewteen let-7 and Hmga2 enhances oncogenic transformation Science 315, 1576-1579
27. Shell, S., Park, S.-M., Radjabi, A. R., Schickel, R., Kistner, E. O., Jewell, D. A., Feig, C., Lengyel, E., and Peter, M. E. (2007) Let-7 expression defines two different stages of cancer Proc. Natl. Acad. Sci. U.S.A. 104, 11400-11405
28. Serra, M., Baird, J., Dale, T., Fey, B., Retatagos, K., and Westhof, E. (2002) Effects of magnesium ions on the stabilization of RNA oligomers of defined structures RNA 8, 307-323
29. Gonzalez, R. L., Jr. and Tinoco, I., Jr. (1999) Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot J. Mol. Biol. 289, 1267-1282
30. Keel, A., Rambo, R., Batey, R., and Kieft, J. (2007) A general strategy to solve the phase problem in RNA crystallography Structure 15, 761-772
31. 15N NMR Evaluation of GC, Tandem GU, and Tandem GA Sites Nucleosides, Nucleotides Nucleic Acids 28, 424-434
32. Williams, A., Longfellow, C., Freier, S., Kierzek, R., and Turner, D. (1989) Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC Biochemistry 28, 4283-4291
33. Seol, Y., Skinner, G. M., and Visscher, K. (2004) Elastic properties of single-stranded charged homopolymeric ribonucleotide Phys. Rev. Lett. 10, 118102
34. Seol, Y., Skinner, G. M., and Visscher, K. (2007) Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking Phys. Rev. Lett. 98, 158103-158107
35. Hyeon, C., Dima, R. I., and Thirumalai, D. (2006) Size, shape, and flexibility of RNA Structures J. Chem. Phys. 125, 194905-194915
36. Liu, J. D., Zhoa, L., and 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
37. Miyoshi, D., Nakamura, K., Tateishi-Karimata, H., Ohmichi, T., and Sugimoto, N. (2009) Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions J. Am. Chem. Soc. 131, 3522-3531
38. Schroeder, S. J. and Turner, D. H. (2000) Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA Biochemistry 39, 9257-9274
39. Walter, A. E., Wu, M., and Turner, D. H. (1994) The stability and structure of tandem GA mismatches in RNA depend on closing base pairs Biochemistry 33, 11349-11354
40. Ragan, C., Cloonan, N., Grimmond, S. M., Zuker, M., and Ragan, M. A. (2009) Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH PLoS One 4, e5745
41. Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292
42. Gruber, A., Lorenz, R., Bernhart, S., Neubock, R., and Hofacker, I. (2008) The Vienna RNA Websuite Nucleic Acids Res. 36, W70-W74
43. Zuker, M. (2003) Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction Nucleic Acids Res. 31, 3406-3415
44. Ding, Y., Chan, C. Y., and Lawrence, C. E. (2004) Sfold Web Server for Statistical Folding and Rational Design of Nucleic Acids Nucleic Acids Res. 32, W135-W141
45. Xia, T., Santa Lucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., and Turner, D. H. (1998) Thermodynamic Parameters for an Expanded Nearest-neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs Biochemistry 37, 14719-14735
46. Sugimoto, N., Kierzek, R., and Turner, D. H. (1987) Sequence Dependence for the Energetics of Dangling Ends and Terminal Base Pairs in Ribonucleic Acid Biochemistry 26, 4554-4558