Solvent-Modulated Energetics of Tetrameric DNA Polymorphism

我们建议继续我们的研究，以表征溶剂在调节生物聚合物的结合亲和力和构象偏好中的作用的热力学含量。在之前的预算期间，我们的研究主要集中在研究水和水溶性共溶剂在蛋白质和核酸转化以及配体-蛋白质结合的能量学中的作用。同时，我们已经开始建立一个程序，在这个程序中，我们表征了溶剂和单个溶剂组分对DNA g -四联体和i-基序的能量学的影响。g -四聚体和i-基序是一类重要的非典型四聚体DNA结构，具有重要的生物学意义。富含鸟嘌呤的DNA链容易折叠成各种g -四重结构，其中鸟嘌呤碱基以稳定的氢键排列相互结合，即g -四重结构。富含胞嘧啶的链在微酸性到接近中性的ph值时表现出折叠成i基序构象的倾向。后者代表了一种DNA构象，具有两股平行双链以反平行方向相互插入的四联体排列。****** g -四萜和i-基序在拓扑和结构上表现出很大的多样性，这被认为是生物学上的相关性。核苷酸序列、稳定反离子类型和环境条件（例如，渗透物或聚物的存在）的细微变化会导致g -四重体拓扑结构的剧烈变化。在要求的预算期内，我们建议探索水和水混溶的共溶剂（如尿素和甘氨酸甜菜碱）以及各种阳离子的浓度和pH值在指导非典型四联体DNA基序的多态性倾向中的作用。我们设计了一种实验策略，旨在开发一种预测算法，该算法可用于探索富鸟嘌呤序列的构象偏好作为环境因素的函数及其互补的富胞嘧啶链的存在。我们将采用差示扫描量热法、紫外/可见分光光度法、CD光谱法、超声波测速法和高精度密度法。我们已经论证了这些实验方法的可行性和信息量。******我们的长期目标是开发预测算法，以评估自然存在的核酸中功能重要域的序列特异性、结构特异性和溶剂特异性构象偏好。随着基因组序列在越来越多的生物体中产生的成功，这种能力正变得非常需要。最后，人们想要评估基因组中有利于特定结构基序的局部序列域是否与生物作用或控制的功能位点相对应

We propose to continue our studies to characterize the thermodynamic content of the role of solvent in modulating the binding affinity and conformational preferences of biopolymers. During the previous budget period, our studies were focussed on investigating the role of water and water-soluble cosolvents in the energetics of protein and nucleic acid transitions and ligand-protein binding. In parallel, we have begun to establish a program in which we characterize the influence of solvent and individual solvent components on the energetics of DNA G-quadruplexes and i-motifs. G-quadruplexes and i-motifs form an important class of noncanonical tetrameric DNA structures of biological importance. Guanine-rich DNA strands are prone to fold into various G-quadruplex structures in which guanine bases associate with each other in stable hydrogen-bonded arrangements, G-quartets. Cytosine-rich strands exhibit a propensity to fold into the i-motif conformation at slightly acidic to near neutral pH. The latter represents a DNA conformation with a tetraplex arrangement of two parallel-stranded duplexes intercalated into each other in an antiparallel orientation.******G-quadruplexes and i-motifs exhibit a great deal of diversity in topology and structure which is believed to be of biological relevance. Subtle changes in nucleotide sequence, type of the stabilizing counterion, and the environmental conditions (e. g., presence of osmolytes or crowders) results in dramatic changes in the topology of a G-quadruplex. During the requested budget period, we propose to explore the role of water and water-miscible cosolvents (such as urea and glycine betaine) and the concentration of various cations and pH in guiding the polymorphic tendencies of noncanonical tetraplex DNA motifs. We have designed an experimental strategy aimed at developing a predictive algorithm that can be used to explore the conformational preferences of guanine-rich sequences as a function of environmental factors and the presence of their complementary cytosine-rich strands. We will employ differential scanning calorimetry, UV/Vis spectrophotometry, CD spectroscopy, ultrasonic velocimetry, and high precision densimetry. We already have demonstrated the feasibility and information content of these experimental methods.******Our long-term objective is to develop predictive algorithms needed to evaluate sequence-specific, structure-specific, and solvent-specific conformational preferences of functionally important domains within naturally occurring nucleic acids. With the success in genomic sequence generation in an increasingly large number of organisms, such a capacity is becoming highly desirable. Ultimately, one would like to assess if local sequence domains in the genome that favor particular structural motifs correspond to functional sites of biological action or control.**