Aptamer

Nucleic acid aptamers are nucleic acid species (next-gen antibody mimics) having selectivity at par of antibodies for a given target generated via in-vitro selection or equivalently, SELEX (systematic evolution of ligands by exponential enrichment) ranging from small entities such as heavy metal ions to large entities like cells.[1] On the molecular level, aptamers bind to its cognate target through various non-covalent interactions viz., electrostatic interactions, hydrophobic interactions, and induced fitting. Aptamers are useful in biotechnological and therapeutic applications as they offer molecular recognition properties that rival that of the commonly used biomolecule, antibodies. In addition to their discriminate recognition, aptamers offer advantages over antibodies as they can be engineered completely in a test tube, are readily produced by chemical synthesis, possess desirable storage properties, and elicit little or no immunogenicity in therapeutic applications.[2]

In 1990, two labs independently developed the technique of selection: the Gold lab, using the term SELEX for their process of selecting RNA ligands against T4 DNA polymerase; and the Szostak lab, coining the term in vitro selection, selecting RNA ligands against various organic dyes. The Szostak lab also coined the term aptamer (from the Latin, apto, meaning 'to fit') for these nucleic acid-based ligands. Two years later, the Szostak lab and Gilead Sciences, independent of one another, used in vitro selection schemes to evolve single stranded DNA ligands for organic dyes and human coagulant, thrombin (see anti-thrombin aptamers), respectively. There does not appear to be any systematic differences between RNA and DNA aptamers, save the greater intrinsic chemical stability of DNA.

The notion of selection in vitro was preceded twenty-plus years prior when Sol Spiegelman used a Qbeta replication system as a way to evolve a self-replicating molecule.[3] In addition, a year before the publishing of in vitro selection and SELEX, Gerald Joyce used a system that he termed 'directed evolution' to alter the cleavage activity of a ribozyme.

Since the discovery of aptamers, many researchers have used aptamer selection as a means for application and discovery. In 2001, the process of in vitro selection was automated[4][5][6] by J. Colin Cox in the Ellington lab at the University of Texas at Austin, reducing the duration of a selection experiment from six weeks to three days.

While the process of artificial engineering of nucleic acid ligands is highly interesting to biology and biotechnology, the notion of aptamers in the natural world had yet to be uncovered until 2002 when two groups led by Ronald Breaker and Evgeny Nudler discovered a nucleic acid-based genetic regulatory element (which was named riboswitch) that possesses similar molecular recognition properties to the artificially made aptamers. In addition to the discovery of a new mode of genetic regulation, this adds further credence to the notion of an 'RNA World', a postulated stage in time in the origins of life on Earth.

Both DNA and RNA aptamers show robust binding affinities for various targets.[7][8][9] DNA and RNA aptamers have been selected for the same target. These targets include lysozyme,[10] thrombin,[11] human immunodeficiency virus trans-acting responsive element (HIV TAR),[12] hemin,[13] interferon γ,[14] vascular endothelial growth factor (VEGF),[15] prostate specific antigen (PSA),[16][17] dopamine,[18] and the non-classical oncogene, heat shock factor 1 (HSF1).[19] In the case of lysozyme, HIV TAR, VEGF and dopamine the DNA aptamer is the analog of the RNA aptamer, with thymine replacing uracil. The hemin, thrombin, and interferon γ, DNA and RNA aptamers were selected through independent selections and have unique sequences. Considering that not all DNA analogs of RNA aptamers show functionality, the correlation between DNA and RNA sequence and their structure and function requires further investigation.

Lately, a concept of smart aptamers, and smart ligands in general, has been introduced. It describes aptamers that are selected with pre-defined equilibrium (${\displaystyle K_{\mathrm {d} }}$), rate (${\displaystyle k_{\mathrm {off} }}$, ${\displaystyle k_{\mathrm {on} }}$) constants and thermodynamic (ΔH, ΔS) parameters of aptamer-target interaction. Kinetic capillary electrophoresis is the technology used for the selection of smart aptamers. It obtains aptamers in a few rounds of selection.

Recent developments in aptamer-based therapeutics have been rewarded in the form of the first aptamer-based drug approved by the U.S. Food and Drug Administration (FDA) in treatment for age-related macular degeneration (AMD), called Macugen offered by OSI Pharmaceuticals. In addition, the company NeoVentures Biotechnology Inc.[20] has successfully commercialized the first aptamer based diagnostic platform for analysis of mycotoxins in grain. Many contract companies develop aptamers and aptabodies to replace antibodies in research, diagnostic platforms, drug discovery, and therapeutics.

Non-modified aptamers are cleared rapidly from the bloodstream, with a half-life of minutes to hours, mainly due to nuclease degradation and clearance from the body by the kidneys, a result of the aptamer's inherently low molecular weight. Unmodified aptamer applications currently focus on treating transient conditions such as blood clotting, or treating organs such as the eye where local delivery is possible. This rapid clearance can be an advantage in applications such as in vivo diagnostic imaging. An example is a tenascin-binding aptamer under development by Schering AG for cancer imaging. Several modifications, such as 2'-fluorine-substituted pyrimidines, polyethylene glycol (PEG) linkage, etc. (both of which are used in Macugen, an FDA-approved aptamer) are available to scientists with which to increase the serum half-life of aptamers easily to the day or even week time scale.

Another approach to increase the nuclease resistance of aptamers is to develop Spiegelmers, which are composed entirely of an unnatural L-ribonucleic acid backbone. A Spiegelmer of the same sequence has the same binding properties of the corresponding RNA aptamer, except it binds to the mirror image of its target molecule.

In addition to the development of aptamer-based therapeutics, many researchers such as the Ellington lab have been developing diagnostic techniques for aptamer based plasma protein profiling called aptamer plasma proteomics. This technology will enable future multi-biomarker protein measurements that can aid diagnostic distinction of disease versus healthy states.

Furthermore, the Hirao lab applied a genetic alphabet expansion using an unnatural base pair[21][22] to SELEX and achieved the generation of high affinity DNA aptamers.[23] Only few hydrophobic unnatural base as a fifth base significantly augment the aptamer affinity to target proteins.

As a resource for all in vitro selection and SELEX experiments, the Ellington lab has developed the Aptamer Database cataloging all published experiments.

Peptide aptamers [24] are artificial proteins selected or engineered to bind specific target molecules. These proteins consist of one or more peptide loops of variable sequence displayed by a protein scaffold. They are typically isolated from combinatorial libraries and often subsequently improved by directed mutation or rounds of variable region mutagenesis and selection. In vivo, peptide aptamers can bind cellular protein targets and exert biological effects, including interference with the normal protein interactions of their targeted molecules with other proteins. Libraries of peptide aptamers have been used as "mutagens", in studies in which an investigator introduces a library that expresses different peptide aptamers into a cell population, selects for a desired phenotype, and identifies those aptamers that cause the phenotype. The investigator then uses those aptamers as baits, for example in yeast two-hybrid screens to identify the cellular proteins targeted by those aptamers. Such experiments identify particular proteins bound by the aptamers, and protein interactions that the aptamers disrupt, to cause the phenotype.[25][26] In addition, peptide aptamers derivatized with appropriate functional moieties can cause specific postranslational modification of their target proteins, or change the subcellular localization of the targets.[27]

Peptide aptamers can also recognize targets in vitro. They have found use in lieu of antibodies in biosensors [28][29] and used to detect active isoforms of proteins from populations containing both inactive and active protein forms.[30] Derivatives known as tadpoles, in which peptide aptamer "heads" are covalently linked to unique sequence double-stranded DNA "tails", allow quantification of scarce target molecules in mixtures by PCR (using, for example, the quantitative real-time polymerase chain reaction) of their DNA tails.[31]

The peptides that form the aptamer variable regions are synthesized as part of the same polypeptide chain as the scaffold and are constrained at their N and C termini by linkage to it. This double structural constraint decreases the diversity of the conformations that the variable regions can adopt,[32] and this reduction in conformational diversity lowers the entropic cost of molecular binding when interaction with the target causes the variable regions to adopt a single conformation. As a consequence, peptide aptamers can bind their targets tightly, with binding affinities comparable to those shown by antibodies (nanomolar range).

Peptide aptamer scaffolds are typically small, ordered, soluble proteins. The first scaffold,[24] which is still widely used,[33] is Escherichia coli thioredoxin, the trxA gene product (TrxA). In these molecules, a single peptide of variable sequence is displayed instead of the Gly-Pro motif in the TrxA -Cys-Gly-Pro-Cys- active site loop. Improvements to TrxA include substitution of serines for the flanking cysteines, which prevents possible formation of a disulfide bond at the base of the loop, introduction of a D26A substitution to reduce oligomerization, and optimization of codons for expression in human cells,.[33][34] Reviews in 2015 have reported studies using 12 [33] and 20 [35] other scaffolds.

Peptide aptamer selection can be made using different systems, but the most used is currently the yeast two-hybrid system. Peptide aptamers can also be selected from combinatorial peptide libraries constructed by phage display and other surface display technologies such as mRNA display, ribosome display, bacterial display and yeast display. These experimental procedures are also known as biopannings. Among peptides obtained from biopannings, mimotopes can be considered as a kind of peptide aptamers. All the peptides panned from combinatorial peptide libraries have been stored in a special database with the name MimoDB.[36][37]

Selection of Ligand Regulated Peptide Aptamers (LiRPAs) has been demonstrated. By displaying 7 amino acid peptides from a novel scaffold protein based on the trimeric FKBP-rapamycin-FRB structure, interaction between the randomized peptide and target molecule can be controlled by the small molecule Rapamycin or non-immunosuppressive analogs.

The Affimer protein, an evolution of peptide aptamers, is a small, highly stable protein engineered to display peptide loops which provides a high affinity binding surface for a specific target protein. It is a protein of low molecular weight, 12–14 kDa,[38] derived from the cysteine protease inhibitor family of cystatins.[39][40][41][42]

The Affimer scaffold is a stable protein based on the cystatin protein fold. It displays two peptide loops and an N-terminal sequence that can be randomised to bind different target proteins with high affinity and specificity similar to antibodies. Stabilisation of the peptide upon the protein scaffold constrains the possible conformations which the peptide may take, thus increasing the binding affinity and specificity compared to libraries of free peptides.

The Affimer protein scaffold was developed initially at the MRC Cancer Cell Unit in Cambridge then across two laboratories at the University of Leeds.[39][40][41][42] Affimer technology has been commercialised and developed by Avacta Life Sciences, who are developing it as reagents for research and therapeutic applications.

X-Aptamers are a new generation of aptamers designed to improve on the binding and versatility of regular DNA/RNA- based aptamers. X-Aptamers are engineered with a combination of natural and chemically-modified DNA or RNA nucleotides. Base modifications allow incorporation of various functional groups/small molecules into X-aptamers, opening a wide range of uses and a higher likelihood of binding success compared to standard aptamers. Thiophosphate backbone modifications at selected positions enhance nuclease stability and binding affinity without sacrificing specificity. [43] [44]

X-Aptamers are able to explore new features by utilizing a new selection process. Unlike SELEX, X-Aptamer selection does not rely on multiple repeated rounds of PCR amplification but rather involves a two-step bead-based discovery process. In the primary selection process, combinatorial libraries are created where each bead will carry approximately 10^12 copies of a single sequence. The beads operate as carriers, where the bound sequences will ultimately be detached into solution. In the secondary solution pull-down process, each target will be used to individually pull down the binding sequences from solution. The binding sequences are amplified, sequenced, and analyzed. Sequences that are enriched for each target can then be synthesized and characterized.[45]

AptaBiD or Aptamer-Facilitated Biomarker Discovery is a technology for biomarker discovery.[46] AptaBiD is based on multi-round generation of an aptamer or a pool of aptamers for differential molecular targets on the cells which facilitates exponential detection of biomarkers. It involves three major stages: (i) differential multi-round selection of aptamers for biomarker of target cells; (ii) aptamer-based isolation of biomarkers from target cells; and (iii) mass spectrometry identification of biomarkers. The important feature of the AptaBiD technology is that it produces synthetic affinity probes (aptamers) simultaneously with biomarker discovery. In AptaBiD, aptamers are developed for cell surface biomarkers in their native state and conformation. In addition to facilitating biomarker identification, such aptamers can be directly used for cell isolation, cell visualization, and tracking cells in vivo. They can also be used to modulate activities of cell receptors and deliver different agents (e.g., siRNA and drugs) into the cells.

Aptamers have an innate ability to bind to any molecule they're targeted at, including cancer cells and bacteria. Bound to a target, aptamers inhibit its activity. Aptamers suffer from two issues that limit their effectiveness. Firstly, the bonds they form with target molecules are usually too weak to be effective, and second, they're easily digested by enzymes.

Adding an unnatural base to a standard aptamer can increase its ability bind to target molecules. A second addition in the form of a "mini hairpin DNA" gives the aptamer a stable and compact structure that is resistant to digestion, extending its life from hours to days.

Aptamers are less likely to provoke undesirable immune responses than antibodies.

The ability of aptamers to reversibly bind molecules such as proteins has generated increasing interest in using them to facilitate controlled release of therapeutic biomolecules, such as growth factors. This can be accomplished by tuning the affinity strength to passively release the growth factors,[54] along with active release via mechanisms such as hybridization of the aptamer with complementary oligonucleotides[55] or unfolding of the aptamer due to cellular traction forces.[56]

Aptamers have been used to create hot start functions in PCR enzymes to prevent non-specific amplification during the setup and initial phases of PCR reactions.[57]