Premeltons in DNA

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• 作者：Henry M. Sobell
• 刊名：Journal of Structural and Functional Genomics
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：17
• 期：1
• 页码：17-31
• 全文大小：4,754 KB
• 刊物主题：Biochemistry, general; Animal Genetics and Genomics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Bioinformatics; Human Genetics;
• 出版者：Springer Netherlands
• ISSN：1570-0267
• 卷排序：17

文摘

Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B–B (or A–A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B–A (or A–B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible—and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5′ and 3′ ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions—all readily testable—as will be described in this review.KeywordsPremeltonsMeltonsIntercalationEthidium-DNA bindingActinomycin-DNA bindingB- to A- DNA structural phase-transitionDNA-melting and premeltingGene-regulationRNA-polymerase: promoter recognitionProtein: DNA allosterismDNA transcriptionInitiationElongationTermination of RNA-synthesis