Publications by authors named "Niyati Jain"

6 Publications

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Nanoparticle based simple electrochemical biosensor platform for profiling of protein-nucleic acid interactions.

Talanta 2019 Apr 6;195:46-54. Epub 2018 Nov 6.

Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; Electronics Design Center, Case Western Reserve University, Cleveland, OH 44106, USA. Electronic address:

The analysis of protein-nucleic acid interactions is essential for biophysics related research. However, simple, rapid, and accurate methods for quantitative analysis of biomolecular interactions are lacking. We herein establish an electrochemical biosensor approach for protein-nucleic acid binding analysis. Nanoparticle based sensors are fabricated by highly-controlled inkjet printing followed by plasma conversion. A novel bioconjugation method is demonstrated as a simple and rapid approach for protein-based biosensor fabrication. As a proof of concept, we analyzed the binding interaction between unwinding protein 1 (UP1) and SL3 RNA, confirming the accuracy of this nanoparticle based electrochemical biosensor approach with traditional biophysical methods. We further accurately profiled and differentiated a unique binding interaction pattern of multiple G-tract nucleic acid sequences with heterogeneous nuclear ribonucleoprotein H1. Our study provides insights into a potentially universal platform for in vitro biomolecule interaction analysis using a nanoparticle based electrochemical biosensor approach.
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http://dx.doi.org/10.1016/j.talanta.2018.11.021DOI Listing
April 2019

Conserved structures formed by heterogeneous RNA sequences drive silencing of an inflammation responsive post-transcriptional operon.

Nucleic Acids Res 2017 Dec;45(22):12987-13003

Center for Gene Regulation in Health & Disease, Department of Biology, Geology and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA.

RNA-protein interactions with physiological outcomes usually rely on conserved sequences within the RNA element. By contrast, activity of the diverse gamma-interferon-activated inhibitor of translation (GAIT)-elements relies on the conserved RNA folding motifs rather than the conserved sequence motifs. These elements drive the translational silencing of a group of chemokine (CC/CXC) and chemokine receptor (CCR) mRNAs, thereby helping to resolve physiological inflammation. Despite sequence dissimilarity, these RNA elements adopt common secondary structures (as revealed by 2D-1H NMR spectroscopy), providing a basis for their interaction with the RNA-binding GAIT complex. However, many of these elements (e.g. those derived from CCL22, CXCL13, CCR4 and ceruloplasmin (Cp) mRNAs) have substantially different affinities for GAIT complex binding. Toeprinting analysis shows that different positions within the overall conserved GAIT element structure contribute to differential affinities of the GAIT protein complex towards the elements. Thus, heterogeneity of GAIT elements may provide hierarchical fine-tuning of the resolution of inflammation.
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http://dx.doi.org/10.1093/nar/gkx979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727460PMC
December 2017

Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution.

Proc Natl Acad Sci U S A 2017 02 13;114(9):2206-2211. Epub 2017 Feb 13.

Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106;

Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants ( = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo.
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http://dx.doi.org/10.1073/pnas.1616371114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338530PMC
February 2017

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1.

J Biol Chem 2016 Jan 24;291(5):2331-44. Epub 2015 Nov 24.

From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and

Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.
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http://dx.doi.org/10.1074/jbc.M115.674564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732216PMC
January 2016

Regio-selective chemical-enzymatic synthesis of pyrimidine nucleotides facilitates RNA structure and dynamics studies.

Chembiochem 2014 Jul 20;15(11):1573-7. Epub 2014 Jun 20.

Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, 1115 Biomolecular Sciences Building, College Park, MD 20782 (USA).

Isotope labeling has revolutionized NMR studies of small nucleic acids, but to extend this technology to larger RNAs, site-specific labeling tools to expedite NMR structural and dynamics studies are required. Using enzymes from the pentose phosphate pathway, we coupled chemically synthesized uracil nucleobase with specifically (13) C-labeled ribose to synthesize both UTP and CTP in nearly quantitative yields. This chemoenzymatic method affords a cost-effective preparation of labels that are unattainable by current methods. The methodology generates versatile (13) C and (15) N labeling patterns which, when employed with relaxation-optimized NMR spectroscopy, effectively mitigate problems of rapid relaxation that result in low resolution and sensitivity. The methodology is demonstrated with RNAs of various sizes, complexity, and function: the exon splicing silencer 3 (27 nt), iron responsive element (29 nt), Pro-tRNA (76 nt), and HIV-1 core encapsidation signal (155 nt).
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http://dx.doi.org/10.1002/cbic.201402130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127085PMC
July 2014

Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches.

Biochemistry 2010 May;49(17):3703-14

Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080-3021, USA.

High-resolution crystal structures and biophysical analyses of purine-sensing riboswitches have revealed that a network of hydrogen bonding interactions appear to be largey responsible for discrimination of cognate ligands against structurally related compounds. Here we report that by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand, we have detected the presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches. All three riboswitches have similar conformational distributions of the ligand-bound state. The known crystal structures represent the global minimum that accounts for 50-60% of the population, where there is no significant stacking interaction between the ligand and bases of the binding pocket, but the hydrogen-bonding cage collectively provides an electronic environment that promotes an ultrafast ( approximately 1 ps) charge transfer pathway. The ligand also samples multiple conformations in which it significantly stacks with either the adenine or the uracil bases of the A21-U75 and A52-U22 base pairs that form the ceiling and floor of the binding pocket, respectively, but favors the larger adenine bases. These alternative conformations with well-defined base stacking interactions are approximately 1-1.5 kcal/mol higher in DeltaG degrees than the global minimum and have distinct charge transfer dynamics within the picosecond to nanosecond time regime. Inside the pocket, the purine ligand undergoes dynamic motion on the low nanosecond time scale, sampling the multiple conformations based on time-resolved anisotropy decay dynamics. These results allowed a description of the energy landscape of the bound ligand with intricate details and demonstrated the elastic nature of the ligand recognition mode by the purine-sensing riboswitches, where there is a dynamic balance between hydrogen bonding and base stacking interactions, yielding the high affinity and specificity by the aptamer domain.
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http://dx.doi.org/10.1021/bi1000036DOI Listing
May 2010