Thermodynamic stability and solution conformation of tandem G · A mismatches in RNA and RNA · DNA hybrid duplexes

Ebel, Susanne; Brown, Tom; Lane, Andrew N.

doi:10.1111/j.1432-1033.1994.tb18671.x

Cited by 28 publications

(18 citation statements)

References 44 publications

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“…one G and one A are on the same strand. Mismatches of GA type in DNA and RNA helices have been the subject of several studies in the past [14][15][16][17][18][19][20][21]. In the RNA folding, it is known that GA pairs contribute substantially to the RNA helix stability.…”

Section: Thermodynamic Outliersmentioning

confidence: 99%

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond

Hadiwikarta

Walter

Hooyberghs

et al. 2012

Nucleic Acids Research

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In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.

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Section: Thermodynamic Outliersmentioning

confidence: 99%

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond

Hadiwikarta

Walter

Hooyberghs

et al. 2012

Nucleic Acids Research

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“…4C, EC7ϩ2 Mismatched NDS). It is difficult to predict, however, which conformation is thermodynamically favored: although the dA:dG pair is stronger (30,31), rA is located at the end of the RNA oligonucleotide, and therefore, the rA:dG interaction in this context is less structurally constrained. The shift in the equilibrium between the two states of the 5Ј-end of the RNA toward the abnormally paired state determines the higher stability of the complex with mismatches in both the RNA and nontemplate DNA strands (Fig.…”

Section: Fig 2 Structural Analysis Of Pol II Ecs Obtained By Promotmentioning

confidence: 99%

The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex

Kireeva

Комиссарова

Waugh

et al. 2000

Journal of Biological Chemistry

207

188

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The sliding clamp model of transcription processivity, based on extensive studies of Escherichia coli RNA polymerase, suggests that formation of a stable elongation complex requires two distinct nucleic acid components: an 8 -9-nt transcript-template hybrid, and a DNA duplex immediately downstream from the hybrid. Here, we address the minimal composition of the processive elongation complex in the eukaryotes by developing a method for promoter-independent assembly of functional elongation complex of S. cerevisiae RNA polymerase II from synthetic DNA and RNA oligonucleotides. We show that only one of the nucleic acid components, the 8-nt RNA: DNA hybrid, is necessary for the formation of a stable elongation complex with RNA polymerase II. The double-strand DNA upstream and downstream of the hybrid does not affect stability of the elongation complex. This finding reveals a significant difference in processivity determinants of RNA polymerase II and E. coli RNA polymerase. In addition, using the imperfect RNA:DNA hybrid disturbed by the mismatches in the RNA, we show that nontemplate DNA strand may reduce the elongation complex stability via the reduction of the RNA:DNA hybrid length. The structure of a "minimal stable" elongation complex suggests a key role of the RNA:DNA hybrid in RNA polymerase II processivity.Characterization of the processivity determinants in yeast RNA polymerase II (Pol II) 1 is crucial for understanding the mechanisms controlling eukaryotic gene expression at the levels of promoter escape, pausing, arrest, and release of the RNA from transcription terminators (1, 2). The polymerase proceeds through the nucleosomal structure of the template and survives a prolonged pausing or arrest in the genes without dissociating from the template. Therefore, the formation of a highly stable elongation complex (EC), in which RNA polymerase is tightly bound to the nascent transcript and template, is absolutely required for the enzyme processivity (3). The mechanism that reconciles the strong stable binding of Pol II to the DNA with the high speed of forward translocation is unknown.Elongation of a promoter-initiated transcript occurs in the absence of general initiation factors, which dissociate from the enzyme during promoter escape (4). Processive elongation by eukaryotic Pol II can also be achieved using purified polymerase in a promoter-and factor-independent transcription system (5). Therefore, it is likely that the basic processivity function belongs to the core Pol II enzyme. Although it was shown that substantial changes in the nucleic acid array accompany the switch to a processive RNA synthesis (6), the role of DNA and RNA in the Pol II EC stability remains speculative (7). The elucidation of this role has been hampered by the extreme complexity of the native eukaryotic EC, which contains multiple transcription elongation factors (8). Differentiation between the effect of elongation factors on EC stability and activity and the role of the Pol II core enzyme interaction with RNA and DNA requires a...

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“…GÁA mismatches in the socalled sheared base-pair con®guration, in which both nucleotides are in the anti conformation, and in which hydrogen bonds are formed between the guanine 2-amino to the adenine N7 and the guanine N3 to the adenine 6-amino were originally found in a DNA duplex (Li et al, 1991) and an RNA hairpin loop (Heus & Pardi, 1991), and have been observed in RNA at loop helix junctions (Szewczak et al, 1993;Szewczak & Moore, 1995;Biou et al, 1994;Pley et al, 1994a,b;Scott et al, 1995;Cate et al, 1996;Huang et al, 1996;Fountain et al, 1996;Jucker et al, 1996), within internal loops in RNA (SantaLucia & Turner, 1993;Katahari et al, 1994;Szewczak et al, 1993;Szewczak & Moore, 1995) as well as in DNA (Chou et al, 192;Lane et al, 1992;Katahari et al, 1993;Ebel et al, 1994;Maskos et al, 1993). Thermodynamic studies have revealed that the stabilities of tandem GÁA basepairs in RNA can range over almost 5 kcal mol À1 , depending on the closing base-pair (Walter et al, 1994).…”

Section: Introductionmentioning

confidence: 95%

The detailed structure of tandem G·A mismatched base-pair motifs in RNA duplexes is context dependent

Heus

Wijmenga

Hoppe

et al. 1997

Journal of Molecular Biology

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Thermodynamic stability and solution conformation of tandem G · A mismatches in RNA and RNA · DNA hybrid duplexes

Cited by 28 publications

References 44 publications

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond

The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex

The detailed structure of tandem G·A mismatched base-pair motifs in RNA duplexes is context dependent

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