NMR STUDY OF MODIFIED DNA DUPLEXES

随着2D-核磁共振方法的发展，生物大分子的结构研究已成为常规工作。最近，药物分子与寡核苷酸或多肽的相互作用、DNA与蛋白质的相互作用揭示了寡核苷酸的底物-受体结合、药物识别图谱和结构异常的精细结构细节，并强调了它们在设计有效的生物动力学药物方面的意义。关于含有基本位点的寡核苷酸序列的个别结构研究已经发表，但还没有详细的解释解码基本位点的侧翼碱基对对DNA整体结构的贡献。提供这样一项研究变得至关重要，它将破译包含致癌基本部位损伤的DNA中侧翼碱基对的作用。一项完整的2D-核磁共振研究，通过分子动力学策略产生结构精炼所需的结构参数，将提供这样的解释，这将有助于设计更有效的癌症治疗药物。最近，几个研究小组开发了一种全新的方法，通过设计共价连接到微小沟槽结合药物的寡核苷酸，并估计它们与其他DNA和RNA序列的杂交能力。这种强结合的DNA偶联物具有反义药物的潜力，它选择性地与特定的序列结合，从而在癌症和艾滋病的治疗中阻止它们的进一步复制/转录。这种方法预示着在处理艾滋病病毒或突变细胞的核蛋白的同时，处理突变的DNA/RNA序列将进入一个新的领域。我们在Epoch制药公司的合作者已经设计并制备了一种包含CDPI3部分和两个等构鸟嘌呤(Ppg)残基的DNA结合物，将通过2D-核磁共振方法对其结构细节进行评估。这项研究将有助于开发更有效的反义/抗基因药物。已经与佛罗里达州奥兰多华特迪士尼纪念癌症研究所的巴里·施韦策博士建立了合作关系，他将在提案的各个方面提供协助，特别是在结构优化方案方面。

With the advancement in 2D-NMR methodologies, the structural investigatiOn of biological macromolecules has become routine. In recent past, interaction of drug molecules with Oligonucleotides or polypeptides, DNA-protein interaction have revealed fine structural details that illustrate the substrate-receptor binding, drug recognition profile, and structural abnormalities of oligonucleotides, and underline their implications in the design of potent biodynamic agents. Individual structural studies on oligonucleotide sequences containing abasic sites have been published, but a detailed account decoding the contribution of flanking base pairs of an abasic site on the overall structure of a DNA has not been accomplished. It becomes essential to furnish such a study, which would decipher the role of flanking base pairs in a DNA containing a carcinogenic abasic site lesion. A complete 2D-NMR study generating structural parameters required for the structure refinement by molecular dynamics strategies would furnish such account, which will aid in designing more potent drugs in the treatment of cancers. A whole new approach has been developed recently by few research groups, by designing oligonucleotides covalently linked to a minor groove binding drug and estimating their hybridization capability with other DNA and RNA sequences. Such strongly binding DNA conjugates have a potential of antisense agents, which selectively bind to specific sequences, thus blocking their further replication/transcription in the management of cancer and AIDS. This approach is heralding a new horizon in handling the mutant DNA/RNA sequences, while dealing with nucleoproteins of AIDS virus or mutagenic cells. A DNA conjugate containing a CDPI3 moiety, and two isoteric guanine, ppG residues, has been designed and prepared by our collaborators at Epoch Pharmaceuticals, which will be evaluated by 2D-NMR methods for structural details. This study will help developing more potent antisense/antigene agents. A collaboration with Dr. Barry Schweitzer of Walt Disney Memorial Cancer Institute, Orlando, FL/Molecular Staging, Inc., New Haven, CT has been established, who will assist in various aspects of the proposal, specially in structure refinement protocols.