3.6.6 References for 3.6

Turner, Douglas H.; Sugimoto, Naoki; Freier, Susan M.

doi:10.1007/10361369_57

Cited by 2 publications

(5 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This estimated value is also in good agreement with the measured value. The number of nucleus base pairs analyzed by the nearest-neighbor parameters is the same as the previous typical data . Thus, these results suggest that the activation energies can be understood by an analysis of the enthalpy based on the nearest-neighbor parameters.…”

Section: Resultssupporting

confidence: 80%

“…The equilibrium constants for the double helix formation can be predicted using the nearest-neighbor parameters because K = exp (−Δ G °/ RT ) and Δ G °= Δ H ° − T Δ S °. The forward rates, k on , are about 10 5 −10 7 M -1 s -1 . Thus, the value of k off can be predicted because K = k on / k off .…”

Section: Discussionmentioning

confidence: 98%

“…The light source was a D2 lamp and all relaxations were measured at 260 nm with a 14-nm band-pass. The range of the temperature jump was determined to be 3.2 °C for a capacitor charged at 12.5 kV in a solution containing 1 M NaCl by calibration of a test sample using the phenolphthalein-β-cyclodextrin inclusion reaction . The reaction temperature was controlled by setting the initial sample temperature at 3.2 °C lower than the final sample temperature.…”

Section: Methodsmentioning

confidence: 99%

“…From a kinetic standpoint, typical data exist for the kinetic properties of the Watson−Crick base pairs. − The forward rates, k on , of the duplex formation of nucleic acids are about 10 5 −10 7 M -1 s -1 , and depend on the sequence and salt conditions. The activation energy for k on is negative or zero . The dissociation rates significantly depend on the size, sequence, condition, and complementarity of the nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Kinetic Property of Bulged Helix Formation: Analysis of Kinetic Behavior Using Nearest-Neighbor Parameters

et al. 2000

View full text Add to dashboard Cite

Bulge structure is one of the well-known and important nucleic acid secondary structures containing unpaired nucleotides. Although the thermodynamic property has been thoroughly investigated, the detailed kinetic property of the bulged helix formation is still unknown. We now investigated the helix formation mechanism for bulged helices using temperature-jump experiments. The activation energy for the duplex association (E a+1 ) obtained from the temperature dependence of the rate constants showed that the E a+1 value depended on both the bulged nucleotide and its flanking base pairs. The activation energy for duplex dissociation (E a-1 ), however, did not always depend on the bulged nucleotide. In the case of d(TAGCGTTATAA)/ d(ATCCAATATT) with one C bulge (GCG-bulge helix) and d(TAGAGTTATAA)/d(ATCCAATATT) with one A bulge (GAG-bulge helix), that had different bulged nucleotides and the same flanking base-pairs, the E a+1 value of -13.5 kcal/mol for the GCG-bulge helix was 11.9 kcal/mol more negative than the value of -1.6 kcal/mol for the GAG-bulge helix. The E a-1 value of 50.9 kcal/mol for the GCG-bulge helix was, however, close to 48.7 kcal/mol of the GAG-bulge helix. These data indicate that the rate-limiting steps for both the GCG-bulge and GAG-bulge helices are likely to be the same step. Furthermore, since it was known that fully matched helix formations can be estimated using nearest-neighbor parameters [

show abstract

Section: Resultssupporting

confidence: 80%

Section: Discussionmentioning

confidence: 98%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Kinetic Property of Bulged Helix Formation: Analysis of Kinetic Behavior Using Nearest-Neighbor Parameters

et al. 2000

View full text Add to dashboard Cite

show abstract

“…We reasoned that application of this model to the duplexes containing a or F was appropriate on the basis of the following ground. If the melting of the duplexes is a two-state transition, eq 1 Tm_1 = [R ln(Ct/«) + AS°]AH°(1) can be applied (Turner et al, 1990). In eq 1, Tm is the melting temperature of a duplex, AH0 and AS°are calculated enthalpy and entropy changes for duplex formation, R is the gas constant, Ct is the total strand concentration, and n reflects the symmetry factor, which is 4 in the present study dealing with non-self-complementary strands.…”

Section: Resultsmentioning

confidence: 99%

Influence of .alpha.-Deoxyadenosine on the Stability and Structure of DNA. Thermodynamic and Molecular Mechanics Studies

Ide¹,

Shimizu²,

Kimura³

et al. 1995

Biochemistry

View full text Add to dashboard Cite

The alpha anomer of deoxyadenosine (alpha) and an abasic site (tetrahydrofuran, F), which are DNA lesions produced by free radicals, were site-specifically incorporated in 9-mer duplexes d(TGAGXGTAC).d-(GTACNCTCA), where X = alpha or F and N = A, G, C, or T. Their influence on thermodynamic stability and structure of DNA was assessed by UV-melting measurements and molecular mechanics calculations. UV-melting studies revealed that a duplex containing an alpha T pair was as stable as the parental duplex containing an AT pair at the same site. Furthermore, the stability of duplexes containing alpha varied depending on the base opposite this lesion, with the Tm decreasing in the following order: alpha T > alpha C approximately alpha A > alpha G. On the contrary, an abasic site introduced in the same site showed a significantly greater destabilizing effect than alpha, but variation of Tm with the bases opposite F was less evident. To delineate the molecular mechanism of thermodynamic effects of an alpha lesion, molecular mechanics calculations were performed for the same duplexes as used for UV-melting measurements. The results suggest that the structural perturbation introduced into DNA by an alpha N pair is alpha G> alpha A > alpha C > alpha T, showing a parallel correlation with the destabilizing effects of alpha N pairs. On the basis of these results, it is discussed how the perturbations introduced by these DNA lesions may influence the selection of nucleotides opposite the lesions by DNA polymerases and the interaction with DNA repair enzymes such as Escherichia coli endonuclease IV and exonuclease III.

show abstract

3.6.6 References for 3.6

Cited by 2 publications

References 84 publications

Kinetic Property of Bulged Helix Formation: Analysis of Kinetic Behavior Using Nearest-Neighbor Parameters

Kinetic Property of Bulged Helix Formation: Analysis of Kinetic Behavior Using Nearest-Neighbor Parameters

Influence of .alpha.-Deoxyadenosine on the Stability and Structure of DNA. Thermodynamic and Molecular Mechanics Studies

Contact Info

Product

Resources

About