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1. Multiplexed Nucleic Acid Hybridization Assays Using Single‐FRET‐Pair Distance‐Tuning 2017

   https://ncsu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1fS8MwED9EX_TB_2h1SgTBp7I1adcOhjDUsgenovO5pEnKJnPK5sC9-RH8jH4S79I_OHwQpNA2tKVt7i73S-7yC8CpQp-bNZqpa3wKM4bCdyPl-W6mvQg9ThhkRi4O5uQDbjQXJueHqAbcyDJse00GLtNpEdfn9enziAIHxCaOCB6bYA-Vj_DR7UXZEAt0XXZtFfRYLtFulZyNvx5f9Em_gOYibrWOJ96Ap_KTbb4JrXLwM_G-bskOLcNFSez4_9_bhPUCnrJOrk9bsGTG27D2g7RwB2SvyEF8N5q1B-c3xIg8VKyjhpp15zQDrJjb2a4PzhnKX86nzKYmsAfcjczXx2d8f9XHw50cTtglQVjUPSz3ZzRMswuP8VX_ousWCzW4SiDccgWCkMgLpE7TRlNnQsuQnH_IRTNV2hi0eT_zhGpJziUXAeIEP2v6Kcct0DwQ-8BCY4xoSBVJnWHjrVup7ytiu4s8kQYBd-CslFHymhNxJDnlMk-otpKqthyolSJMCoOcJtgtDSiW4TUcOKkuoylRfESOzcssvwc7WAjKHNjLRV-9ihMPIPZEHOBWan98Q_LQu76uSgf_eegQVuk8Tw2uwfLbZGaOYJkU7Njq-TGsdOL4rvcNrtsBsg

   Qiu, Xue; Guo, Jiajia; Jin, Zongwen; Petreto, Alexandra; Medintz, Igor L....

   Small (Weinheim An Der Bergstrasse, Germany), Vol. 13, Issue 25.

   Journal Article  |  Full Text Online

2. UNAFold 2008

   https://ncsu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1LSwMxEA5S6cWDT7TiowdPQjDvx1HE4kkF7Tkm2exJWrH24L_vJNuUFnrpcSFski_JTCYz8w1CdxF0bktUwElkN6PmAptIBW4bakDjaNkmv_mYs0oKK8Hu1SNZBHXNdeusHUU401jkkA0HNs9-tq9y3YKP97fVywo0ySzwVR5D_11pW1C-cJyEzOld5T9w81ZL1qf6bVfERFt73HYN3XShsqVmGh2ir5rfUwJSchmE9cj8h8KGWCgw1pgfd5r_ETrICRHDnKkAi3CM9tLkBPW7Ipb_p6g_fn0cTb-bMzQePX8-veBleQUcYeIUB2u1l43QJlpqdNCGJ6k1jSSGYFVsOA3MA2Ke2CiTUsS2JnpGbGjh3Ed-gYY6pcSJj8Y3LYjcxgYhYuaoM5QHKdkA3VbAHOzb7IzwkzSdz5yyQuTbywCddzi6n45ew8FYKGNWDdB9RcJli2PmKsUyYOGoK1g4wMIBFpe7NL5Cvb_febpGvbwaN2X7LAAfVbdw

   Markham, Nicholas R.; Zuker, Michael

   Bioinformatics, Vol. 453, pp. 3 - 31.

   The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is de... Read more

   The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is derived from “Unified Nucleic Acid Folding.” Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms that we have looked at, including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed using common formats. Similarly, a variety of melting profile plots is created when appropriate. These latter plots include experimental results if they are provided. The package is “command line” driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php. Read less

   Book Chapter  |  Full Text Online

3. Multiplexed Nucleic Acid Hybridization Assays Using Single‐FRET‐Pair Distance‐Tuning 2017

   https://ncsu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3JTsMwEB2xXODALghLZRASp6h1nDSJhJCqQtRDCxUt58hxHLWoLKIU0RufwDfyJcxkUysOSL0kcRIrjj3jefaMnwHOFdrcpFaPTG2Tm9EVtukpbptJzD20OK6TaDk_mZNNuNFamIwfopxwI81I-2tScBmNc7--VR0_jchxQOxyQlAXzFH4CB_dNYuOWKDpSvdWQYtlEu1Wwdn4J_ucTVoeUETkX7g5g15Fbn6CTXgsCp5GndBeB7Ph99WU8jDluSjoHRf_yS3YyEEqa2RStQ1L-nkH1meoC3dBdvJIxE8ds8vB1S3xIg8Va6hhzFpTWgeWr_C8rA6uGEqBnI5ZGqDAengY6Z-v7-D-po-nrhy-sWsCsiiBmO5PaLJmDx6Cm36zZebbNZiKWNZMxHqulonFVYzDdY0DT16XMqlZEdfcwWGjqzztRXYSWY6SboxIw6sJqVViR5q2OzsA5mqtRU0qT8YJduGxH9m2Is47j4vIcSwDLoqWCl8zOo4wI162QqqtsKwtA86wIcuXiEW71WiHdI_W83JX-B_cgOOincNcd8chjmAdcnv4jgGn5WPUOnKlyGf9MsF3PHLX-ggBDNjP5KP8FPEJIc4WBlhp0_5T0LDXabfL1OEimY5gja6zKOJjWHl_m-gTWCEprKQqUYHVRhB0O7-0ww9y

   Qiu, Xue; Guo, Jiajia; Jin, Zongwen; Petreto, Alexandra; Medintz, Igor L....

   Small (Weinheim An Der Bergstrasse, Germany), Vol. 13, Issue 25.

   Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time‐gated (TG) detection of a single terbium‐donor‐based Förster res... Read more

   Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time‐gated (TG) detection of a single terbium‐donor‐based Förster resonance energy transfer (FRET) pair can be used to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs in a single sample. This study demonstrates the applicability of single‐TG‐FRET‐pair multiplexing for molecular (Tb‐to‐dye) and nanoparticle (Tb‐to‐quantum‐dot) biosensing. Both systems use acceptor‐sensitization and donor‐quenching for quantifying biomolecular recognition and modification of the donor–acceptor distance for tuning the PL decays. TG intensity detection provides extremely low background noise and a quick and simple one‐step assay format. Single‐TG‐FRET‐pair multiplexing can be combined with spectral and spatial resolution, paving the way for biosensing with unprecedented high‐order multiplexing capabilities. Time‐gated photoluminescence detection of a single terbium‐donor‐based Förster resonance energy transfer (FRET) pair to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs from a single sample with a single measurement is shown. Both molecular (Tb‐to‐dye) and nanoparticle (Tb‐to‐quantum‐dot) FRET biosensing are demonstrated. Read less

   Journal Article  |  Full Text Online

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