Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens

Abstract

High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.

Indel-correcting DNA barcodes for high-throughput sequencing

“…Current state-of-the art error-correcting DNA barcoding applications often use Hamming or Levenshtein error correction strategies ( 20 , 23 ). Hamming codes only correct substitutions, and are thus insufficient for any DNA barcode applications with indels ( 26 ).…”

“…Error-correcting barcodes must efficiently detect and correct all DNA sequencing and synthesis errors. Many current DNA barcode strategies repurpose error-correcting codes developed for computers ( 18 , 19 ), such as Hamming or Reed–Solomon codes, to DNA applications ( 20 , 21 ). Hamming distance (i.e., the number of substitutions between two sequences of equal length) is possibly the most used due to its simplicity.…”

Exploiting Molecular Barcodes in High-Throughput Cellular Assays

“…Among these are guanine-cytosine (GC) content, homopolymer length, and certain sequences that must be avoided because of their natural presence in a sample or their recognition by a restriction enzyme. 38 These limitations imply that most techniques based on random synthesis of a DNA barcode greatly overestimate the number of useful barcodes that can be generated when groups calculate the theoretical number as an exponential function (4 number of bases ). Taking into account these considerations, Lyons et al 38 provide a framework for generating billions of acceptable DNA barcodes.…”

Compound Collections at KU 1947-2017: Cheminformatic Analysis and Computational Protein Target Prediction

“…(Mayr and Bojanic, 2009) The size and possible structures attainable in small-molecule space endow them with unique features to study and modulate biology. (Lyons et al, 2017) Recently, these libraries are important trends for synthesized molecules over this time period. In their analysis, they found that average molecular weights increased by 100 Da from the 1950s to the 2000s, leading to so-called "molecular obesity."…”