NMR STUDY OF MODIFIED DNA DUPLEXES

随着二维核磁共振技术的发展，生物大分子的结构研究已成为常规。近年来，药物分子与寡核苷酸或多肽的相互作用、dna -蛋白质相互作用揭示了底物-受体结合、药物识别谱和寡核苷酸结构异常的精细结构细节，并强调了它们在有效生物动力药物设计中的意义。包含基本位点的寡核苷酸序列的个别结构研究已经发表，但解码基本位点的侧翼碱基对对DNA整体结构的贡献的详细说明尚未完成。提供这样的研究变得至关重要，它将破译DNA中含有致癌基本部位病变的侧翼碱基对的作用。一项完整的二维核磁共振研究将产生分子动力学策略所需的结构参数，这将有助于设计更有效的治疗癌症的药物。最近，一些研究小组开发了一种全新的方法，通过设计与小凹槽结合药物共价连接的寡核苷酸并估计其与其他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，可以选择性地结合特定序列，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。这种方法在处理艾滋病病毒或致突变细胞的核蛋白时，预示着处理突变DNA/RNA序列的新领域。我们在Epoch Pharmaceuticals的合作者设计并制备了一种含有CDPI3片段和两个等肠鸟嘌呤ppG残基的DNA偶联物，该偶联物将通过2D-NMR方法进行结构细节评估。这项研究将有助于开发更有效的反义/抗原药物。与佛罗里达州奥兰多华特迪士尼纪念癌症研究所/康涅狄格州纽黑文分子分期公司的Barry Schweitzer博士已经建立了合作关系，他将在提案的各个方面提供协助，特别是在结构优化协议方面。

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.