Calorimetric and spectroscopic investigation of the helix-to-coil transition of the self-complementary deoxyribonucleotide ATGCAT

Marky, Luis A.; Canuel, Lita L.; Jones, R. A. C.; Breslauer, Kenneth J.

doi:10.1016/0301-4622(81)80013-0

Cited by 35 publications

(32 citation statements)

References 27 publications

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“…1A). Het-10 would require the unlikely fraying of 2 base pairs to expose the −12/−11 junction (see Marky et al 1981). Het-11 is analogous to that used previously.…”

Section: Premelted Templates Can Be Transcribed By 54 Holoenzyme Alonmentioning

confidence: 99%

“…The tightest binding was to the −12/−11 location, which was proposed to be important for transcriptional silencing in the absence of activator. The prior heteroduplex experiments (Wedel and Kustu 1995) had the −11 position as a terminal A:T base pair, which would be interconvertible with the −12/−11 junction by the fraying of the base pair (favored at 37°C; see Marky et al 1981). The lack of unregulated transcription could have resulted from the use of a template with a junction that maintained proper regulation.…”

Section: Premelted Templates Can Be Transcribed By 54 Holoenzyme Alonmentioning

confidence: 99%

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Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Guo

Lew²,

Gralla³

2000

Genes Dev.

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Transcription control at the melting step is not yet understood. Here, band shift, cross-linking, and transcription experiments on diverse DNA probes were used with two bacterial RNA polymerase holoenzymes that differ in how they regulate melting. Data indicated that both 54 and 70 holoenzymes assume a default closed form that cannot establish single-strand binding. Upon activation the enzymes are converted to an open form that can bind simultaneously to the upstream fork junction and to the melted transcription start site. The key difference is that 54 imposes tighter regulation by creating a complex molecular switch at −12/−11; the current data show that this switch can be thrown by activator. In this case an ATP-bound enhancer protein causes 54 to alter its cross-linking pattern near −11 and also causes a reorganization of holoenzyme: DNA interactions, detected by electrophoretic mobility-shift assay. At a temperature-dependent 70 promoter, elevated temperature alone can assist in triggering conformational changes that enhance the engagement of single-strand DNA. Thus, the two factors modify the same intrinsic opening pathway to create quite different mechanisms of transcriptional regulation.

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“…1A). Het-10 would require the unlikely fraying of 2 base pairs to expose the −12/−11 junction (see Marky et al 1981). Het-11 is analogous to that used previously.…”

Section: Premelted Templates Can Be Transcribed By 54 Holoenzyme Alonmentioning

confidence: 99%

Section: Premelted Templates Can Be Transcribed By 54 Holoenzyme Alonmentioning

confidence: 99%

Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Guo

Lew²,

Gralla³

2000

Genes Dev.

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“…Tm is defined as the temperature at which a, the fraction of strands in the duplex state, is equal to 0.5 [6].…”

Section: Methodsmentioning

confidence: 99%

“…1 is correct and if this process is cooperative. Thus, by measuring these two enthalpies separately, it is possible to determine whether there are any intermediate base-pairing states involved in the melting process, or whether the melting is a "none or all" transition [6,7].…”

Section: Methodsmentioning

confidence: 99%

Base sequence effects on interactions of aromatic mutagens with DNA

Geacintov¹

1992

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“…The purities were verified by hplc. The hexamer d(ATGAT) was synthesized by a modified diester method as previously described (12). The hexamer d(GCGCGC) and octamer d(GGAATTCC) were synthesized by Collaborative Research Waltham, MA and were kind gifts from Drs.…”

Section: Methodsmentioning

confidence: 99%

Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: resolution of a salt effect into specific and non-specific components

Marky¹,

Blumenfeld²,

Breslauer³

1988

Can. J. Chem.

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. 66, 836 (1988). Temperature-dependent uv spectroscopy has been used to determine the differential salt effect of tetramethylammonium chloride (Me4NC1) and sodium chloride (NaCl) on the thermal stabilities of a series of deoxyoligonucleotide duplexes that sy'stematically differ in base composition and sequence. This approach has allowed us to resolve the AT-specific effect of Me4N+ from the more general, non-specific cation effects of Me4Nf versus Na'. Our results reveal that in the absence of AT-specific effects, Me4N' (relative to Na') significantly reduces the thermal stability of duplex structures. We offer an interpretation of this differential salt effect in terms of the influence of the condensed cation on water structure at the surface of the duplex. We also observe an AT-specific effect of Me4N+ which results in an increased thermal stability for AT-containing duplexes in Me4NC1 relative to NaC1. This specific effect which is governed by mass action is found to be uninfluenced by base sequence and to be a linear function of the percent AT base pairs in the duplex.Luis A. MARKY, KENNETH S. BLUMENFELD et KENNETH J. BRESLAUER. Can. J. Chem. 66, 836 (1988). On a utilise la spectroscopie uv a tempkrature variable pour determiner l'effet diffkrentiel de sel des chlorures de tetramCthylammonium (Me4NC1) et de sodium (NaCl) sur les stabilites thermiques d'une skrie de duplex de d~soxyoligonuclko-tides qui diffkrent d'une f a~o n systematique dans la composition de la base ainsi que dans la skquence. Cette approche nous a permis de differencier entre l'effet spkcifique au AT du cation Me4N+ des effets cationiques plus gknkral mais non specifiques du Me4N' vs Na'. Nos resultats revklent que, en l'absence d'effets spkcifiques au AT, le Me4N' (par rapportau Na') reduit d'une f a~o n importante la stabilite thermique des structures des duplex. On offre une interprktation de cet effet differentiel de sel en fonction de l'influence du cation condense sur la structure de l'eau la surface du duplex. On a aussi observe un effet du Me4N+ qui est specifique au AT et qui provient d'une augmentation, dans le Me4NC1 par rapport au NaCL, de la stabilitk thermique des duplex contenant du AT. On a trouve que ces effet specifique, qui est soumis a la loi d'action de masse, n'est pas influence par la sequence de la base et qu'il est une fonction liniaire du pourcentage des paires de bases AT dans le duplex.[Traduit par la revue] Introduction Experimental The effect of added salt on the stability of helical polynucleotides is well documented and generally depends on the nature of the cationic species (1-4). Cation: can exert their stabilizing or destabilizing influences through specific and/or non-specific interactions with the polymer. Examples of non-specific interactions include general electrostatic effects (e.g. cation condensation and screening) as well as the resulting perturbation of local water structure surrounding the polymer. Essentially all cations in aqueous solution manifest such non-specific effects to varying degr...

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Calorimetric and spectroscopic investigation of the helix-to-coil transition of the self-complementary deoxyribonucleotide ATGCAT

Cited by 35 publications

References 27 publications

Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Base sequence effects on interactions of aromatic mutagens with DNA

Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: resolution of a salt effect into specific and non-specific components

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Calorimetric and spectroscopic investigation of the helix-to-coil transition of the self-complementary deoxyribonucleotide ATGCAT

Cited by 35 publications

References 27 publications

Promoter opening by ς54 and ς70 RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Promoter opening by ς54 and ς70 RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Base sequence effects on interactions of aromatic mutagens with DNA

Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: resolution of a salt effect into specific and non-specific components

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Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control