Criteria

Aptamers

Antibody

Basic composition

Nucleotide (four members: A, G, T/U and C)

Amino acid (20 members)

Materials

Nucleic acid (single-stranded DNA or RNA)

• Protein (polymer peptide)

•Antibodies consist of two light chains and two heavy chains

Molecular weight and/or size

• 6–30kDa (20–100nt)

• ~2nm

• 150–180kDa

• ~15nm

Secondary structure

•Hairpin, stem, loop, bulge, G-quadruplex or kissing complex

• α-Helix and β-fold

Binding pattern and/or mechanism of action

• Surface recognition

• Three-dimensional interactions via van der Waals forces, hydrogen bonding and electrostatic interactions similar to the way antibodies bind to antigen

• Reversal of activity via complementary antidote oligonuclotides

• Binding pocket (key and lock model)

• Three-dimensional interaction; antibodies recognize epitopes located on the target antigen

Affinity

•High

• Multivalent aptamers can confer increasing affinity and additional functions

•High

•Affinity between antibody and antigen depends on the number of identical epitopes on the target antigen

Specificity

•High

• The aptamer is able to identify single point mutations and conformational isomers

•High

•Antigens may have multiple epitopes, which allow different antibodies to bind to the same antigen

Potential targets

•Wide range: ions, organic and inorganic molecules, nucleic acids, peptides, proteins, toxins, viral particles, whole cells, entire organs and live animals

• Limited to immunogenic molecules

•No toxins or other molecules that do not cause strong immune responses

Generation and discovery

• In vitro SELEX (2–15 selection rounds)

• ~2–8 weeks

•Aptamer can be selected in hours or days via high-throughput automated SELEX

• In vivo biological system

• ~6 months or longer

Manufacturing and costs

•Chemical solid-phase synthesis

•Controllable and completely in vitro procedure

• 2 days for milligrams; 2 weeks for grams

•No or low risk of contamination

• Facile regulatory affairs and cGMP

• Low cost for DNA; high cost for long RNA (>60nt) with special modifications

•Costs lowered with the development of new technology

• In vivo (animal-based production)

• Potential contamination due to cells or animal-based production

• 3 months for 5–20 grams

• From mammalian cells: high cost

• From transgenic plants or animals: low cost

Batch-to-batch variation

•None or low

• Significant

Physical and

thermal stability

•Very stable and long shelf-life

• Resistant to high temperature (even up to 95°C) and cycles of denaturation and renaturation

•Aptamers can be lyophilized for long-term storage and transport at room temperature

•Unstable and limited shelf-life

• Susceptible to temperature (even at room temperature or 37°C) and irreversible denaturation

• Requires refrigeration for storage and transport

Chemical modification and

conjugation

•Convenient and controllable

•Various types available, including sugar, backbone, base and other modifications

•Aptamers can be rationally modified without loss of binding affinity

• Restricted and uncontrollable

• Limited types and chemical reactions

• Stochastic modifications very likely to cause negative consequences, such as loss of activity

Tissue uptake and penetration

• Faster

• Slower

Immunogenicity

•None or low immunogenicity

•High immunogenicity

• Increased immune reaction with repeated dosing

Nuclease degradation

•Vulnerable

• Limited half-life in vivo (~10min for unmodified version)

• Resistant and not affected by nucleases in vivo

Kidney filtration

• Faster

• Short circulation time in vivo (~30min for unconjugated version)

• Slower

• Long circulation time (up to 1 month)

Patents and distribution

• Exclusive patents in SELEX technology

• Limited initial distribution

• Expired protection or no early patents

• More widespread distribution

Development and market

• The development pathway is less explored

• Insufficient education and investment (R&D support)

•Commercialization has focused on diagnostic-based aptamer products

•Well-developed infrastructure

•Abundant support from finance and education

• Rapid and sustained increase in drug market share