Dataset Information

Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders.

ABSTRACT: Recently, the utility of triptycene as a scaffold for targeting nucleic acid three-way junctions was demonstrated. A rapid, efficient route for the synthesis of bridgehead-substituted triptycenes is reported, in addition to solid-phase diversification to a new class of triptycene peptides. The triptycene peptides were evaluated for binding to a d(CAG)·(CTG) repeat DNA junction exhibiting potent affinities. The bridgehead-substituted triptycenes provide new building blocks for rapid access to diverse triptycene ligands with novel architectures.

SUBMITTER: Barros SA

PROVIDER: S-EPMC5107256 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders.

Barros Stephanie A SA Yoon Ina I Suh Sung-Eun SE Chenoweth David M DM

Organic letters 20160512 10

Recently, the utility of triptycene as a scaffold for targeting nucleic acid three-way junctions was demonstrated. A rapid, efficient route for the synthesis of bridgehead-substituted triptycenes is reported, in addition to solid-phase diversification to a new class of triptycene peptides. The triptycene peptides were evaluated for binding to a d(CAG)·(CTG) repeat DNA junction exhibiting potent affinities. The bridgehead-substituted triptycenes provide new building blocks for rapid access to div ...[more]

PMID: 27172288

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Project description:BackgroundConserved nucleic acid sequences play an essential role in transcriptional regulation. The motifs/templates derived from nucleic acid sequence datasets are usually used as biomarkers to predict biochemical properties such as protein binding sites or to identify specific non-coding RNAs. In many cases, template-based nucleic acid sequence classification performs better than some feature extraction methods, such as N-gram and k-spaced pairs classification. The availability of large-scale experimental data provides an unprecedented opportunity to improve motif extraction methods. The process for pattern extraction from large-scale data is crucial for the creation of predictive models.MethodsIn this article, a Teiresias-like feature extraction algorithm to discover frequent sub-sequences (CFSP) is proposed. Although gaps are allowed in some motif discovery algorithms, the distance and number of gaps are limited. The proposed algorithm can find frequent sequence pairs with a larger gap. The combinations of frequent sub-sequences in given protracted sequences capture the long-distance correlation, which implies a specific molecular biological property. Hence, the proposed algorithm intends to discover the combinations. A set of frequent sub-sequences derived from nucleic acid sequences with order is used as a base frequent sub-sequence array. The mutation information is attached to each sub-sequence array to implement fuzzy matching. Thus, a mutate records a single nucleotide variant or nucleotides insertion/deletion (indel) to encode a slight difference between frequent sequences and a matched subsequence of a sequence under investigation.ConclusionsThe proposed algorithm has been validated with several nucleic acid sequence prediction case studies. These data demonstrate better results than the recently available feature descriptors based methods based on experimental data sets such as miRNA, piRNA, and Sigma 54 promoters. CFSP is implemented in C++ and shell script; the source code and related data are available at https://github.com/HePeng2016/CFSP.

Dataset Information

Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders.

Publications

Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders.

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