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Marvin H. Caruthers Lincoln J. Mcbride Laurent P. Bracco John W. Dubendorff 《Nucleosides, nucleotides & nucleic acids》2013,32(1-2):95-105
Abstract An in situ method is described for synthesizing DNA which incorporates a new series of amidine protected deoxy-nucleosides and bis-dialkylaminophosphines as phosphitylating agents. These procedures were used to synthesize d(GGGAATTCCC) which was digested by EcoRI. 相似文献
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Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids 总被引:8,自引:0,他引:8
S M Freier N Sugimoto A Sinclair D Alkema T Neilson R Kierzek M H Caruthers D H Turner 《Biochemistry》1986,25(11):3214-3219
The stabilizing effects of dangling ends and terminal base pairs on the core helix GCGC are reported. Enthalpy and entropy changes of helix formation were measured spectrophotometrically for AGCGCU, UGCGCA, GGCGCCp, CGCGCGp, and the corresponding pentamers XGCGCp and GCGCYp containing the GCGC core plus a dangling end. Each 5' dangling end increases helix stability at 37 degrees C roughly 0.2 kcal/mol and each 3' end from 0.8 to 1.7 kcal/mol. The free energy increments for dangling ends on GCGC are similar to the corresponding increments reported for the GGCC core [Freier, S. M., Alkema, D., Sinclair, A., Neilson, T., & Turner, D. H. (1985) Biochemistry 24, 4533-4539], indicating a nearest-neighbor model is adequate for prediction of stabilization due to dangling ends. Nearest-neighbor parameters for prediction of the free energy effects of adding dangling ends and terminal base pairs next to G.C pairs are presented. Comparison of these free energy changes is used to partition the free energy of base pair formation into contributions of "stacking" and "pairing". If pairing contributions are due to hydrogen bonding, the results suggest stacking and hydrogen bonding make roughly comparable favorable contributions to the stability of a terminal base pair. The free energy increment associated with forming a hydrogen bond is estimated to be -1 kcal/mol of hydrogen bond. 相似文献
4.
Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability 总被引:19,自引:0,他引:19
R Kierzek M H Caruthers C E Longfellow D Swinton D H Turner S M Freier 《Biochemistry》1986,25(24):7840-7846
A solid-phase method using a phosphoramidite approach is described for synthesis of oligoribonucleotides. The method was used to synthesize pairs of oligomers with identical nearest neighbors but different sequences. Comparison of thermodynamic parameters for these pairs provides a test of the nearest-neighbor hypothesis for prediction of helix stability. In general, pairs of sequences with identical nearest neighbors have enthalpy and entropy changes for helix formation that differ by 8% on average, delta Go37 that differ by 6% on average, and melting temperatures within 0-5 degrees C of each other. These limits are typical of the accuracy that should be expected from nearest-neighbor predictions of RNA helix stability. UCAUGA and UGAUCA have the same nearest neighbors but melting temperatures that differ by 7 degrees C. This suggests some sequences will not be approximated well by the nearest-neighbor model. 相似文献
5.
Studies of gene control regions. III. Binding of synthetic and modified synthetic lac operator DNAs to lactose repressor. 总被引:10,自引:6,他引:4 下载免费PDF全文
Chemically synthesized lactose operator DNA was tested for binding with lactose repressor protein. These operator DNAs were found to (1) bind specifically to lactose SQ repressor as measured by release of binding with the inducing ligand isopropyl-beta-D-thiogalactoside, (2) have dissociation half-lives of 37 seconds (21 base-paired duplex) and 46 seconds (26 base-paired duplex) and (3) have dissociation half-lives with x86 repressor of 9 minutes (21 base-paired duplex) and 18 minutes (26 base paired duplex). Modified operators containing 5-bromodeoxyuridine and deoxyuridine at specific sites were also prepared. These analogs bound both repressors about as tightly as the wild type sequence. 相似文献
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Christopher I Keeling Macaire MS Yuen Nancy Y Liao T Roderick Docking Simon K Chan Greg A Taylor Diana L Palmquist Shaun D Jackman Anh Nguyen Maria Li Hannah Henderson Jasmine K Janes Yongjun Zhao Pawan Pandoh Richard Moore Felix AH Sperling Dezene P W Huber Inanc Birol Steven JM Jones Joerg Bohlmann 《Genome biology》2013,14(3):R27