Biomedical subjects

H T Allawi

Publications and source records attributed to H T Allawi.

7 recordsLinked to original sources

PubMed1999

Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches.

Thermodynamic measurements are reported for 51 DNA duplexes with A.A, C.C, G.G, and T.T single mismatches in all possible Watson-Crick contexts. These measurements were used to test the applicability of the nearest-neighbor model and to calculate the 16 unique nearest-neighbor parameters for the 4 single like with like base mismatches next to a Watson-Crick pair. The observed trend in stabilities of mismatches at 37 degrees C is G.G > T.T approximately A.A > C.C. The observed stability trend for the closing Watson-Crick pair on the 5' side of the mismatch is G.C >/= C.G >/= A.T >/= T.A. The mismatch contribution to duplex stability ranges from -2.22 kcal/mol for GGC.GGC to +2.66 kcal/mol for ACT.ACT. The mismatch nearest-neighbor parameters predict the measured thermodynamics with average deviations of DeltaG degrees 37 = 3.3%, DeltaH degrees = 7. 4%, DeltaS degrees = 8.1%, and TM = 1.1 degrees C. The imino proton region of 1-D NMR spectra shows that G.G and T.T mismatches form hydrogen-bonded structures that vary depending on the Watson-Crick context. The data reported here combined with our previous work provide for the first time a complete set of thermodynamic parameters for molecular recognition of DNA by DNA with or without single internal mismatches. The results are useful for primer design and understanding the mechanism of triplet repeat diseases.

Base Pair Mismatch↗

PubMed1998

NMR solution structure of a DNA dodecamer containing single G.T mismatches.

The three-dimensional solution structure of the self-complementary DNA dodecamer (CGT_GACGT_TACG above GCAT_TGCAG_TGC] which contains the thermodynamically destabilizing [TG_A above AT_T] motif was determined using two-dimensional NMR spectroscopy and simulated annealing protocols. Relaxation matrix analysis methods were used to yield accurate NOE derived distance restraints. Scalar coupling constants for the sugar protons were determined by quantitative simulations of DQF-COSY cross-peaks and used to determine sugar pucker populations. Twenty refined structures starting from random geometries converged to an average pairwise root mean square deviation of 0.49 A. Back calculated NOEs give Rc and Rx factors of 0.38 and 0.088, respectively. The final structure shows that each of the single G@T mismatches form a wobble pair with two hydrogen bonds where the guanine projects into the minor groove and the thymine projects into the major groove. The incorporation of the destabilizing [TG_A above AT_T] motif has little effect on the backbone torsion angles and helical parameters compared to standard B-form duplexes, which may explain why G.T mismatches are among the most commonly observed in DNA. The structure shows that perturbations caused by a G.T mismatch extend only to its neighboring Watson-Crick base pair, thus providing a structural basis for the applicability of the nearest-neighbor model to the thermodynamics of internal G.T mismatches.

Base Pair Mismatch↗

PubMed1998

Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects.

Thermodynamics of 27 oligonucleotides with internal A.C mismatches at two different pHs were determined from UV absorbance versus temperature melting profiles. The data were combined with four literature values and used to derive nearest-neighbor parameters for all 16 trimer sequences with internal A.C mismatches at pH 7.0 and 5. 0. The results indicate that the contribution of single A.C mismatches to duplex stability is strongly dependent on the solution pH and the nearest-neighbor context. On average, the protonation of an internal A.C mismatch stabilizes the duplex by 1.39 kcal/mol for DeltaG degrees37 and 7.0 degreesC for the TM. The nearest-neighbor parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM of oligonucleotides presented in this study with average deviations of 6.3%, 11.0%, 12.2%, and 1.8 degreesC, respectively, at pH 7.0 and 4.7%, 5.9%, 6.1%, and 1.3 degreesC, respectively, at pH 5. 0. At pH 7.0, the contribution of single A.C mismatches to helix stability ranges from 2.25 kcal/mol for TCA/AAT to 1.22 kcal/mol for GCG/CAC. At pH 5.0, however, the contribution of A+.C mismatches ranges from 1.09 kcal/mol for TCT/AAA to -0.43 kcal/mol for GCC/CAG. Implications of the results for replication fidelity and mismatch repair are discussed.

Adenine↗

PubMed1998

Thermodynamics of internal C.T mismatches in DNA.

Thermodynamics of 23 oligonucleotides with internal single C.T mismatches were obtained by measuring UV absorbance as a function of temperature. Results from these 23 duplexes were combined with three measurements from the literature to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal C.T mismatches. The data show that the nearest-neighbor model is adequate for predicting thermodynamics of oligonucleotides with internal C.T with average deviations for Delta G degrees37, Delta H degrees, Delta S degrees and T m of 6.4%, 9.9%, 10.6%, and 1.9 degreesC respectively. C.T mismatches destabilize the duplex in all sequence contexts. The thermodynamic contribution of C. T mismatches to duplex stability varies weakly depending on the orientation of the mismatch and its context and ranges from +1.02 kcal/mol for GCG/CTC and CCG/GTC to +1.95 kcal/mol for TCC/ATG.

Cytidine↗

PubMed1998

Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA.

Thermodynamics of 22 oligonucleotides with internal single G.A mismatches dissolved in 1 M NaCl were determined from absorbance versus temperature melting curves. These data, combined with five literature sequences, were used to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal G.A mismatches and Watson-Crick flanking base pairs. The G.A mismatch parameters predict DeltaG degrees 37, DeltaH degrees, DeltaS degrees, and TM with average deviations of 4.4%, 7.4%, 8.0%, and 1.5 degrees C, respectively. The nearest-neighbor parameters show that G.A mismatch stability is strongly context dependent, and DeltaG degrees 37 ranges from +1.16 kcal/mol for TGA/AAT to -0.78 kcal/mol for GGC/CAG. In addition, one-dimensional 1H NMR spectra show that the G.A pairing geometry is pH and context dependent.

Base Composition↗

PubMed1997

Thermodynamics and NMR of internal G.T mismatches in DNA.

Thermodynamics of 39 oligonucleotides with internal G.T mismatches dissolved in 1 M NaCl were determined from UV absorbance versus temperature profiles. These data were combined with literature values of six sequences to derive parameters for 10 linearly independent trimer and tetramer sequences with G.T mismatches and Watson-Crick base pairs. The G.T mismatch parameters predict DeltaG degrees 37, DeltaH degrees , DeltaS degrees , and TM with average deviations of 5.1%, 7.5%, 8.0%, and 1.4 degrees C, respectively. These predictions are within the limits of what can be expected for a nearest-neighbor model. The data show that the contribution of a single G.T mismatch to helix stability is context dependent and ranges from +1.05 kcal/mol for AGA/TTT to -1.05 kcal/mol for CGC/GTG. Several tests of the applicability of the nearest-neighbor model to G.T mismatches are described. Analysis of imino proton chemical shifts show that structural perturbations from the G.T mismatches are highly localized. One-dimensional NOE difference spectra demonstrate that G.T mismatches form stable hydrogen-bonded wobble pairs in diverse contexts. Refined nearest-neighbor parameters for Watson-Crick base pairs are also presented.

Base Composition↗

PubMed1996

Improved nearest-neighbor parameters for predicting DNA duplex stability.

Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson-Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 degrees C is GC > CG > GG > GA approximately GT approximately CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict deltaG degrees(37), deltaH degrees, deltaS degrees, and T(m) within 4%, 7%, 8%, and 2 degrees C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaC1.

Base Sequence↗