Design and synthesis of a photocleavable fluorescent nucleotide 3'-O-allyl-dGTP-PC-Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis

Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria

Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.

Design and synthesis of fluorescence-labeled nucleotide with a cleavable azo linker for DNA sequencing

A cleavable azo linker was synthesized and reacted with 5-(6)-carboxytetramethyl rhodamine succinimidyl ester, followed by further reactions with di(N-succinimidyl) carbonate and 5-(3-amino-1-propynyl)-2'-deoxyuridine 5'-triphosphate [dUTP(AP3)] to obtain the terminal product dUTP-azo linker-TAMRA as a potential reversible terminator for DNA sequencing by synthesis with no need for 3'-OH blocking.

Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing

An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.

New class of 8-aryl-7-deazaguanine cell permeable fluorescent probes

A one step synthesis of fluorescent 8-aryl-(7-deazaguanines) has been accomplished. Probes exhibit blue to green high quantum yield fluorescence in a variety of organic and aqueous solutions, high extinction coefficients, and large Stokes shifts often above 100 nm. The probes are highly cell permeable, and exhibit stable bright fluorescence once intracellular; therefore are suited to the design of biosensors.

Design and synthesis of new acid cleavable linkers for DNA sequencing by synthesis

A new kind of acid sensitive tetrahydrofuranyl (THF) linker was synthesized and then reacted with 5-(6)-carboxytetramethylrhodaminesuccinimidyl ester (5(6)-TAMRA, SE), followed by di(N-succinimidyl) carbonate (DSC) and modified 2'-deoxyuridine triphosphate (dUTP); the final product, as a reversible terminator for DNA sequencing by synthesis (DNA SBS), was given obtained and confirmed by 1H-NMR, 31P-NMR, and HRMS with purity of up to 99%. The synthesized dye-labeled terminator incorporated into DNA strand successfully, and the fluorophore was cleaved completely under acidic conditions. The preliminary results encourage us to explore more acid-sensitive linkers for DNA SBS to increase the cleavage efficiency under weakly acidic conditions.

2,4-Bis(4-aryl-1,2,3-triazol-1-yl)pyrrolo[2,3-d]pyrimidines: synthesis and tuning of optical properties by polar substituents

Novel D–π–A–π–D type chromophores – 2,4-bis(4-aryl-1,2,3-triazol-1-yl)pyrrolo[2,3-d]pyrimidines were prepared and their photophysical, electrochemical properties in conjunction with quantum chemical calculations were investigated.

Bis-naphthobipyrrolylmethene derived BODIPY complex: an intense near-infrared fluorescent dye

Synthesis of a novel π-extended BODIPY derived from naphthobipyrrole is presented. This dye molecule displays very intense near-infrared (NIR) absorption (ε > 400,000 M(-1) cm(-1)) and emission bands (>700 nm), accompanied by high quantum yield (φf = 0.65) owing to its extended π-conjugation along with imposed structural rigidification.

Caged nucleotides/nucleosides and their photochemical biology

Nucleotides and nucleosides are not only key units of DNA/RNA that store genetic information, but are also the regulators of many biological events of our lives. By caging the key functional groups or key residues of nucleotides with photosensitive moieties, it will be possible to trigger biological events of target nucleotides with spatiotemporal resolution and amplitude upon light activation or photomodulate polymerase reactions with the caged nucleotide analogues for next-generation sequencing (NGS) and bioorthogonal labeling. This review highlights three different caging strategies for nucleotides and demonstrates the photochemical biology of these caged nucleotides.

Toward the single-hour high-quality genome

Today, resequencing of a human genome can be performed in approximately a week using a single instrument. Thanks to a steady logarithmic rate of increase in performance for DNA sequencing platforms over the past seven years, DNA sequencing is one of the fastest developing technology fields. As the process becomes faster, it opens up possibilities within health care, diagnostics, and entirely new fields of research. Immediate genetic characterization of contagious outbreaks has been exemplified, and with such applications for the direct benefit of human health, expectations of future sensitive, rapid, high-throughput, and cost-effective technologies are steadily growing. Simultaneously, some of the limitations of a rapidly growing field have become apparent, and questions regarding the quality of some of the data deposited into databases have been raised. A human genome sequenced in only an hour is likely to become a reality in the future, but its definition may not be as certain.

Perylene-fused BODIPY dye with near-IR absorption/emission and high photostability

A N-annulated perylene unit was successfully fused to the meso- and β-positions of a boron dipyrromethene (BODIPY) core. The newly synthesized BODIPY dye 1b exhibits intensified near-infrared (NIR) absorption and the longest emission maximum ever observed for all BODIPY derivatives. In addition, this dye possesses excellent solubility and photostability, beneficial to practical applications.

Carboxyl BODIPY dyes from bicarboxylic anhydrides: one-pot preparation, spectral properties, photostability, and biolabeling

New fluorescent dyes based on 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) and functionalized with a free carboxyl group have been conveniently synthesized from pyrroles and dicarboxylic anhydrides in one-pot reactions. Their spectral properties in different solvents showed little effect of solvatochromism (<10 nm). The methyl groups on the BODIPY skeleton benefit the fluorescence quantum yields (Phi(f) up to 0.80 in water) but affect the photostability of the dyes. Photooxidation and photodegradation experiments suggest that dyes 1a and 2a exhibit excellent photostability, especially in water, and several factors were taken into account to elucidate the experimental phenomena. Dyes 1c and 2c, derived from 1a and 2a via the esterification of NHS (N-hydroxysuccinimidyl ester), can be easily acquired in high yields (>90%). Single crystal X-ray structures of dyes 2c and 3a are also obtained and discussed. The fluorescence labeling of BSA and followed prestaining method for gel electrophoresis of BSA demonstrate that the protein can be directly observed by naked eyes at as low as 2 ng level under a normal UV fluorescence electrophorogram gel image system.

The removal of fluorescence in sequencing-by-synthesis

Fluorescent oligonucleotides provide useful way to study DNA during the sequencing-by-synthesis process. They allow researchers to determine the sequence of a short DNA strand. Fluorescence created by these chemicals must be removed after a few based pairs are read in order to continue reading the DNA sequence. Researchers have developed a variety of methods to solve this problem. This paper reviews the development of fluorescence removal in DNA sequencing and summarizes several methods of removing the fluorescence.

A facile synthetic approach to 7-deazaguanine nucleosides via a Boc protection strategy

An efficient route to the preparation of 5-substituted 2-amino-7-((2R,4R,5R)-tetrahydro-4-hydroxy-5-(hydroxymethyl)furan-2-yl)-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one compounds has been developed by the condensation of omega-substituted aldehydes with 2,6-diaminopyrimidin-4(3H)-one, followed by Boc protection to afford the corresponding N(2),N(2),N(7)-tris-Boc-O(4)-t-Bu-5-substituted 2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, which is amenable to direct condensation with 1-chloro-2-deoxy-3,5-di-O-p-toluoyl-alpha-D-erythro-pentofuranose. This route affords an efficient synthesis to 2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, 2-amino-5-alkyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, and guanine nucleosides.

A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis

Fluorescent 2′-deoxynucleotides containing a protecting group at the 3′-O-position are reversible terminators enabling array-based DNA sequencing by synthesis (SBS) approaches. Herein, we describe the synthesis of a new family of 3′-OH unprotected cleavable fluorescent 2′-deoxynucleotides and their evaluation as reversible terminators for high-throughput DNA SBS strategies. In this first version, all four modified nucleotides bearing a cleavable disulfide Alexa Fluor® 594 dye were assayed for their ability to act as a reversible stop for the incorporation of the next labeled base. Their use in SBS leaded to a signal–no signal output after successive addition of each labeled nucleotide during the sequencing process (binary read-out). Solid-phase immobilized synthetic DNA target sequences were used to optimize the method that has been applied to DNA polymerized colonies or clusters obtained by in situ solid-phase amplification of fragments of genomic DNA templates.

The fluoride cleavable 2-(cyanoethoxy)methyl (CEM) group as reversible 3'-O-terminator for DNA sequencing-by-synthesis - synthesis, incorporation, and cleavage

A new and promising sequencing technology called sequencing-by-synthesis (SBS) enables fast determination of DNA sequences. 2'-Deoxynucleotides containing the (2-cyanoethoxy)methyl (CEM) group at the 3'-O-position are potential reversible terminators for the SBS technology. Herein we describe the synthesis, the incorporation by several polymerases, and the cleavage of this 3'-O-blocking group using 3'-O-CEM-thymidinyl-5'-O-triphosphate 7 as an example.

Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators

DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction offers a paradigm to decipher DNA sequences. We report here the construction of such a DNA sequencing system using molecular engineering approaches. In this approach, four nucleotides (A, C, G, T) are modified as reversible terminators by attaching a cleavable fluorophore to the base and capping the 3'-OH group with a small chemically reversible moiety so that they are still recognized by DNA polymerase as substrates. We found that an allyl moiety can be used successfully as a linker to tether a fluorophore to 3'-O-allyl-modified nucleotides, forming chemically cleavable fluorescent nucleotide reversible terminators, 3'-O-allyl-dNTPs-allyl-fluorophore, for application in SBS. The fluorophore and the 3'-O-allyl group on a DNA extension product, which is generated by incorporating 3'-O-allyl-dNTPs-allyl-fluorophore in a polymerase reaction, are removed simultaneously in 30 s by Pd-catalyzed deallylation in aqueous buffer solution. This one-step dual-deallylation reaction thus allows the reinitiation of the polymerase reaction and increases the SBS efficiency. DNA templates consisting of homopolymer regions were accurately sequenced by using this class of fluorescent nucleotide analogues on a DNA chip and a four-color fluorescent scanner.