Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence - PubMed (original) (raw)
. 1991 Nov 5;30(44):10606-13.
doi: 10.1021/bi00108a002.
Affiliations
- PMID: 1931983
- DOI: 10.1021/bi00108a002
Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence
K B Hall et al. Biochemistry. 1991.
Abstract
Four pentamers with the general sequence 5'CU(T)GU(T)G/5'CACAG have been prepared by chemical synthesis in order to generate duplex structures with common sequences. The four duplexes studied include the DNA.DNA duplex (5'dCACAG/5'dCTGTG) and the RNA.RNA duplex (5'rCUGUG/5'rCACAG) as well as the two corresponding DNA.RNA heteroduplexes (5'rCUGUG/5'dCACAG and 5'CACAG/5'dCTGTG). The measured entropy, enthalpy, and free energy changes upon melting are reported for each pentamer and compared to the predicted values where possible. Results show that the two DNA.RNA heteroduplexes are destabilized (delta G degrees 25 = -4.2 +/- 0.4 kcal/mol) relative to either the DNA.DNA duplex (delta G degrees 25 = -4.8 +/- 0.5 kcal/mol) or the RNA.RNA duplex (delta G degrees 25 = -5.8 +/- 0.6 kcal/mol). Circular dichroism spectra indicate that the RNA and the two heteroduplexes adopt an A-form conformation, while the DNA conformation is B-form. Imino proton NMR spectra also show that the heteroduplex structures resemble the RNA.RNA duplex.
Similar articles
- The contribution of DNA single-stranded order to the thermodynamics of duplex formation.
Vesnaver G, Breslauer KJ. Vesnaver G, et al. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3569-73. doi: 10.1073/pnas.88.9.3569. Proc Natl Acad Sci U S A. 1991. PMID: 2023903 Free PMC article. - Sequence specific thermodynamic and structural properties for DNA.RNA duplexes.
Ratmeyer L, Vinayak R, Zhong YY, Zon G, Wilson WD. Ratmeyer L, et al. Biochemistry. 1994 May 3;33(17):5298-304. doi: 10.1021/bi00183a037. Biochemistry. 1994. PMID: 7513557 - Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in four 40 base pair deoxyoligonucleotides.
Vallone PM, Benight AS. Vallone PM, et al. Biochemistry. 2000 Jul 4;39(26):7835-46. doi: 10.1021/bi000326k. Biochemistry. 2000. PMID: 10869190 - Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr.
Krause NM, Bains JK, Blechar J, Richter C, Bessi I, Grote P, Leisegang MS, Brandes RP, Schwalbe H. Krause NM, et al. Chembiochem. 2024 May 17;25(10):e202400049. doi: 10.1002/cbic.202400049. Epub 2024 Apr 29. Chembiochem. 2024. PMID: 38456652 Review. - Gel electrophoresis and the structure of RNA molecules.
Lilley DM, Bhattacharyya A, McAteer S. Lilley DM, et al. Biotechnol Genet Eng Rev. 1992;10:379-401. doi: 10.1080/02648725.1992.10647893. Biotechnol Genet Eng Rev. 1992. PMID: 1284511 Review. No abstract available.
Cited by
- Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids.
Huang KW, Wu CY, Toh SI, Liu TC, Tu CI, Lin YH, Cheng AJ, Kao YT, Chu JW, Hsiao YY. Huang KW, et al. Nucleic Acids Res. 2023 Nov 27;51(21):11927-11940. doi: 10.1093/nar/gkad910. Nucleic Acids Res. 2023. PMID: 37870446 Free PMC article. - Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.
Zuber J, Schroeder SJ, Sun H, Turner DH, Mathews DH. Zuber J, et al. Nucleic Acids Res. 2022 May 20;50(9):5251-5262. doi: 10.1093/nar/gkac261. Nucleic Acids Res. 2022. PMID: 35524574 Free PMC article. - Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids.
Zhang J, Fakharzadeh A, Pan F, Roland C, Sagui C. Zhang J, et al. Nucleic Acids Res. 2020 Sep 25;48(17):9899-9917. doi: 10.1093/nar/gkaa665. Nucleic Acids Res. 2020. PMID: 32821947 Free PMC article. - Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts.
Steffen FD, Khier M, Kowerko D, Cunha RA, Börner R, Sigel RKO. Steffen FD, et al. Nat Commun. 2020 Jan 8;11(1):104. doi: 10.1038/s41467-019-13683-4. Nat Commun. 2020. PMID: 31913262 Free PMC article. - The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers.
Zhang C, Fu H, Yang Y, Zhou E, Tan Z, You H, Zhang X. Zhang C, et al. Biophys J. 2019 Jan 22;116(2):196-204. doi: 10.1016/j.bpj.2018.12.005. Epub 2018 Dec 13. Biophys J. 2019. PMID: 30635125 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources