@article {65305, title = {A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition.}, journal = {Chembiochem}, volume = {21}, year = {2020}, month = {2019 May 17}, pages = {157-162}, abstract = {

As a ubiquitous second messenger, cyclic adenosine monophosphate (cAMP) mediates diverse biological processes such as cell growth, inflammation, and metabolism. The ability to probe these pathways would be significantly enhanced if we had a DNA-based sensor for cAMP. Herein, we describe a new, 31-base long single-stranded DNA aptamer for cAMP, denoted caDNApt-1, that was isolated by in vitro selection using systemic evolution of ligands after exponential enrichment (SELEX). caDNApt-1 has an approximately threefold higher affinity for cAMP than ATP, ADP, and AMP. Using non-denaturing gel electrophoresis and fluorescence spectroscopy, we characterized the structural changes caDNApt-1 undergoes upon binding to cAMP and revealed its potential as a cAMP sensor.

}, issn = {1439-7633}, doi = {10.1002/cbic.201900259}, author = {Sharma, Suruchi and Zajac, Matthew and Krishnan, Yamuna} } @article {24299, title = {A structural map of oncomiR-1 at single-nucleotide resolution.}, journal = {Nucleic Acids Res}, volume = {45}, year = {2017}, month = {2017 Sep 19}, pages = {9694-9705}, abstract = {

The miR-17-92a cluster, also known as {\textquoteright}oncomiR-1{\textquoteright}, is an RNA transcript that plays a pivotal regulatory role in cellular processes, including the cell cycle, proliferation and apoptosis. Its dysregulation underlies the development of several cancers. Oncomir-1 comprises six constituent miRNAs, each processed with different efficiencies as a function of both developmental time and tissue type. The structural mechanisms that regulate such differential processing are unknown, and this has impeded our understanding of the dysregulation of oncomiR-1 in pathophysiology. By probing the sensitivity of each nucleotide in oncomiR-1 to reactive small molecules, we present a secondary structural map of this RNA at single-nucleotide resolution. The secondary structure and solvent accessible regions of oncomiR-1 reveal that most of its primary microRNA domains are suboptimal substrates for Drosha-DGCR8, and therefore resistant to microprocessing. The structure indicates that the binding of trans-acting factors is required to remodel the tertiary organization and unmask cryptic primary microRNA domains to facilitate their processing into pre-microRNAs.

}, issn = {1362-4962}, doi = {10.1093/nar/gkx613}, author = {Chakraborty, Saikat and Krishnan, Yamuna} } @article {7080, title = {Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways.}, journal = {Nat Nanotechnol}, year = {2016}, month = {2016 Aug 22}, abstract = {

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

}, issn = {1748-3395}, doi = {10.1038/nnano.2016.150}, author = {Bhatia, Dhiraj and Arumugam, Senthil and Nasilowski, Michel and Joshi, Himanshu and Wunder, Christian and Chambon, Val{\'e}rie and Prakash, Ved and Grazon, Chlo{\'e} and Nadal, Brice and Maiti, Prabal K and Johannes, Ludger and Dubertret, Benoit and Krishnan, Yamuna} } @article {3575, title = {Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter}, journal = {Chemical Science }, volume = {7}, year = {2016}, pages = {1946-1953}, abstract = {

Chloride plays a major role in cellular homeostasis by regulating the lumenal pH of intracellular organelles. We have described a pH-independent, fluorescent chloride reporter called Clensor that has successfully measured resting chloride in organelles of living cells. Here, we describe the rational design of Clensor. Clensor integrates a chloride sensitive fluorophore called 10,10'-bis[3-carboxypropyl]-9,9'-biacridinium dinitrate (BAC) with the programmability, modularity and targetability available to nucleic acid scaffolds. We show that simple conjugation of BAC to a DNA backbone fails to yield a viable chloride-sensitive reporter. Fluorescence intensity and lifetime investigations on a series of BAC-functionalized structural variants yielded molecular insights that guided the rational design and successful realization of the chloride sensitive fluorescent reporter, Clensor. This study provides some general design principles that would aid the realization of diverse ion-sensitive nucleic acid reporters based on the sensing strategy of Clensor.

}, doi = {10.1039/C5SC04002G }, author = {Prakash, Ved and Saha, Sonali and Chakraborty, Kasturi and Krishnan, Yamuna} } @article {915, title = {Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices.}, journal = {Nanoscale}, volume = {7}, year = {2015}, month = {2015 Jun 14}, pages = {10008-12}, abstract = {

Here we tune the pH sensitivity of a DNA-based conformational switch, called the I-switch, to yield a set of fluorescent pH sensitive nanodevices with a collective, expanded pH sensing regime from 5.3 to 7.5. The expanded pH regime of this new family of I-switches originates from a dramatic improvement in the overall percentage signal change in response to pH of these nanodevices.

}, issn = {2040-3372}, doi = {10.1039/c5nr01158b}, author = {Halder, Saheli and Krishnan, Yamuna} } @article {1035, title = {Designing DNA nanodevices for compatibility with the immune system of higher organisms.}, journal = {Nat Nanotechnol}, volume = {10}, year = {2015}, month = {2015 Sep}, pages = {741-7}, abstract = {

DNA is proving to be a powerful scaffold to construct molecularly precise designer DNA devices. Recent trends reveal their ever-increasing deployment within living systems as delivery devices that not only probe but also program and re-program a cell, or even whole organisms. Given that DNA is highly immunogenic, we outline the molecular, cellular and organismal response pathways that designer nucleic acid nanodevices are likely to elicit in living systems. We address safety issues applicable when such designer DNA nanodevices interact with the immune system. In light of this, we discuss possible molecular programming strategies that could be integrated with such designer nucleic acid scaffolds to either evade or stimulate the host response with a view to optimizing and widening their applications in higher organisms.

}, issn = {1748-3395}, doi = {10.1038/nnano.2015.180}, author = {Surana, Sunaina and Shenoy, Avinash R and Krishnan, Yamuna} } @article {916, title = {Fast, Efficient, and Stable Conjugation of Multiple DNA Strands on Colloidal Quantum Dots.}, journal = {Bioconjug Chem}, volume = {26}, year = {2015}, month = {2015 Aug 19}, pages = {1582-9}, abstract = {

A novel method for covalent conjugation of DNA to polymer coated quantum dots (QDs) is investigated in detail. This method is fast and efficient: up to 12 DNA strands can be covalently conjugated per QD in optimized reaction conditions. The QD-DNA conjugates can be purified using size exclusion chromatography and the QDs retain high quantum yield and excellent stability after DNA coupling. We explored single-stranded and double-stranded DNA coupling, as well as various lengths. We show that the DNA coupling is most efficient for short (15 mer) single-stranded DNA. The DNA coupling has been performed on QDs emitting at four different wavelengths, as well as on gold nanoparticles, suggesting that this technique can be generalized to a wide range of nanoparticles.

}, issn = {1520-4812}, doi = {10.1021/acs.bioconjchem.5b00221}, author = {Banerjee, Anusuya and Grazon, Chlo{\'e} and Nadal, Brice and Pons, Thomas and Krishnan, Yamuna and Dubertret, Benoit} } @article {912, title = {A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells.}, journal = {Nat Nanotechnol}, volume = {10}, year = {2015}, month = {2015 Jul}, pages = {645-51}, abstract = {

The concentration of chloride ions in the cytoplasm and subcellular organelles of living cells spans a wide range (5-130 mM), and is tightly regulated by intracellular chloride channels or transporters. Chloride-sensitive protein reporters have been used to study the role of these chloride regulators, but they are limited to a small range of chloride concentrations and are pH-sensitive. Here, we show that a DNA nanodevice can precisely measure the activity and location of subcellular chloride channels and transporters in living cells in a pH-independent manner. The DNA nanodevice, called Clensor, is composed of sensing, normalizing and targeting modules, and is designed to localize within organelles along the endolysosomal pathway. It allows fluorescent, ratiometric sensing of chloride ions across the entire physiological regime. We used Clensor to quantitate the resting chloride concentration in the lumen of acidic organelles in Drosophila melanogaster. We showed that lumenal lysosomal chloride, which is implicated in various lysosomal storage diseases, is regulated by the intracellular chloride transporter DmClC-b.

}, issn = {1748-3395}, doi = {10.1038/nnano.2015.130}, author = {Saha, Sonali and Prakash, Ved and Halder, Saheli and Chakraborty, Kasturi and Krishnan, Yamuna} } @article {913, title = {Tuning the pH Response of i-Motif DNA Oligonucleotides.}, journal = {Chembiochem}, volume = {16}, year = {2015}, month = {2015 Jul 27}, pages = {1647-56}, abstract = {

Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.

}, issn = {1439-7633}, doi = {10.1002/cbic.201500182}, author = {Lannes, Laurie and Halder, Saheli and Krishnan, Yamuna and Schwalbe, Harald} }