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Oligonucleotide Modifications for Structure–Activity Studies (SAR)

Custom DNA and RNA base analogs, lesions, fluorescent probes and sugar/linkage variants for mapping base pairing, stacking, kinetics, repair and protein–nucleic acid recognition.

2-AP • Pyrrolo-dC • BODIPY-TR-X 5-Br • 5-I • 5-F • 8-Br 7-Deaza • 8-Aza • 3-Deaza 8-oxo-dG • ε-dA • dX • Pyr UPLC/HPLC • LC-MS
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Overview Why SAR Oligos Design & Technology SAR Modification Guide Applications Related Services FAQ Contact
Overview

Map Structure–Activity Relationships with Site-Specific Oligo Modifications

Bio-Synthesis manufactures base-analog oligonucleotides for structure–activity relationship studies, including fluorescent base analogs, halogenated bases, deaza/aza purines, thio/amino substitutions, site-specific lesions, abasic mimics and sugar/linkage variants.

These modifications help researchers probe polymerase fidelity and bypass, BER/NER repair recognition, protein–DNA contacts, base flipping, stacking dynamics, backbone geometry and local sequence-context effects.

Available formats include tubes, duplexes and 96-well plates, with purification and analytical QC support from RUO to GMP-like supply paths.

Native Base → Analog Scan → Measurable SAR Readout
base analoglesion probepublication-ready controls
Why Use SAR Oligo Modifications?

Turn a Sequence into a Mechanistic Experiment

Structure–activity oligos let you change one chemical feature at a time while keeping the surrounding sequence constant.

Pair

Base Pairing

Alter H-bond donors, acceptors or ring nitrogens to test pairing rules, Hoogsteen contacts and enzyme readout.

Stack

Stacking & Dynamics

Use 2-AP, pyrrolo-dC or pyrene to monitor local stacking, base flipping and conformational changes.

Damage

Damage Recognition

Embed oxidative, hydroxy, deamination or abasic mimics to interrogate repair, bypass and recognition pathways.

Geo

Backbone Geometry

Probe sugar pucker, non-canonical linkages and local flexibility using araC, pseudouridine, 2′–5′ linkages and spacers.

Design & Technology

Choose the Analog by the Structural Question

The best SAR design starts with one measurable question: pairing, stacking, electronics, repair recognition, photochemistry or backbone geometry.

Need base flipping readout?

2-AP or pyrrolo-dC

Need photochemistry?

5-Br, 5-I or thio bases

Need H-bond perturbation?

Deaza / aza / thio / amino

Need repair or bypass model?

8-oxo, ε-dA, dX, 5-OH-dC

Need geometry control?

araC, ψ-dU, 2′–5′ linkage, Pyr

Scan

Position Scan

Start with −1 / 0 / +1 around the motif, then refine based on the first readout.

Ctrl

Control Set

Include native base, positional swap, scrambled strand and duplex vs single-strand controls.

Env

Buffer & Light

Control cations, oxygen, oxidants and UV exposure for halogenated, thio and fluorescent analogs.

QC

QC Readiness

Use HPLC/UPLC purification and LC-MS identity confirmation, especially for lesion and labile analogs.

Modification Guide

SAR Base Analog & Lesion Selector

Browse SAR oligonucleotide modifications in four practical categories. This keeps the guide easier to scan while preserving the specific modification names, codes and applications researchers search for.

Select a SAR category to view modification options

Fluorescent & Reporter Analogs — environment-sensitive reporters for stacking, base flipping, local polarity, binding and FRET-style readouts.

Best fordynamics
Readoutfluorescence / FRET
Design focusinternal placement
QC focusslight handling
CategoryModificationCode Primary Effect Typical Application
Fluorescent Analog 2-Aminopurine deoxyribose [2-AP-dR] Environment-sensitive adenine analog; stacking and base-flipping reporter Polymerase studies, local dynamics, base flipping
Fluorescent Analog 2-Aminopurine riboside [2-AP-r] RNA-compatible fluorescent adenine analog RNA folding, ribozyme and RNA-protein interaction studies
Fluorescent Analog Pyrrolo-2′-dC [Pyrrolo-dC] Environment-sensitive cytidine analog Binding, mismatch sensing, stacking and microenvironment studies
Reporter Dye BODIPY-TR-X [BODIPY-TR-X] Bright fluorescent reporter with spectral separation FRET, association assays and imaging-oriented probe designs
Intercalator 5′-Pyrene Cap [5′-Pyrene] π-stacking and hydrophobic intercalation Helix assembly, stacking and structural perturbation studies

Design note: Place 2-AP and pyrrolo-dC internally, avoid terminal quenching and benchmark against native-base controls at the same position.

Base Pairing & Electronic Effects — halogenated, deaza/aza, thio and amino bases for testing H-bonding, electronics, photochemistry and enzyme readout.

Best forH-bond / electronic tests
ReadoutTm / kinetics / binding
Design focusnative control
QC focussanalog identity
Category Modification Code Primary Effect Typical Application
Halogenated Base 5-Bromo-dU [5-Br-dU] Photoreactive halogenated uracil; electronic and steric perturbation Photocrosslinking, Tm modulation and protein-contact mapping
Halogenated Base 5-Bromo-dC [5-Br-dC] Halogenated cytidine for stacking and electronic effects Base-pairing, helix stability and photochemical studies
Halogenated Base 5-Iodo-dU [5-I-dU] Heavy-atom effect and photoreactivity Cleavage mapping, crosslinking and structural probing
Halogenated Base 5-Iodo-dC [5-I-dC] Heavy-atom cytidine analog Photochemistry, stacking and recognition studies
Halogenated Base 5-Fluoro-dU [5-F-dU] Subtle electronic modulation with minimal size change Tm, H-bond and polymerase-fidelity studies
Halogenated Base 8-Bromo-2′-deoxyadenosine [8-Br-dA] C8 purine perturbation affecting stacking and conformation Polymerase, syn/anti and stacking studies
Halogenated Base 8-Bromo-2′-deoxyguanosine [8-Br-dG] C8 guanine perturbation affecting helix geometry Fidelity, repair and conformation studies
Deaza Base 7-Deaza-2′-deoxyadenosine [7-Deaza-dA] Removes N7 from adenine Hoogsteen, protein-contact, metal/cation and enzyme-readout studies
Deaza Base 7-Deaza-2′-deoxyguanosine [7-Deaza-dG] Removes N7 from guanine Protein recognition, polymerase readout and cation-contact studies
Deaza/Aza Base 7-Deaza-8-aza-deoxyadenosine [7-Deaza-8-aza-dA] Dual purine ring electronics change Hoogsteen, stacking and SAR mapping
Deaza/Aza Base 7-Deaza-8-aza-deoxyguanosine [7-Deaza-8-aza-dG] Dual purine ring electronics change in guanine Stacking, recognition and electronic-effect studies
Deaza Base 3-Deaza-deoxyadenosine [3-Deaza-dA] N3 perturbation of adenine H-bond network Base-pairing and enzyme-recognition studies
Adduct / Base Analog O6-Phenyl-2′-deoxyinosine [O6-Ph-dI] Bulky hydrophobic O6 adduct mimic Adduct recognition, polymerase bypass and stacking studies
Thio Base 4-Thio-dT [4-S-dT] Photoreactive sulfur substitution UV studies, photo-crosslinking and dynamics
Thio Base 4-Thio-dU [4-S-dU] Photoreactive sulfur-substituted uracil RNA/DNA dynamics and UV-reactivity studies
Thio Base 2-Thio-dT [2-S-dT] Alters donor/acceptor and wobble behavior Base-pairing, wobble and stacking studies
Thio Base 6-Thio-dG [6-S-dG] Electronic and photoreactive guanine analog Repair, photochemistry and H-bond perturbation studies
Amino Base 8-Amino-dA [8-NH2-dA] Adds donor group at C8 H-bond and stacking perturbation studies
Amino Base 8-Amino-dG [8-NH2-dG] Adds donor group at C8 of guanine Recognition, pairing and local electronics studies
Adduct N4-Ethyl-dC [N4-Et-dC] Exocyclic amine adduct Protein–DNA recognition and adduct-mimic studies

Design note: Include native-base, positional and opposite-base controls. Protect halogenated and thio analogs from unnecessary UV and oxidizing conditions.

DNA Damage & Lesion Models — oxidative, hydroxy, deamination, dihydro and adduct mimics for repair, bypass and recognition studies.

Best forrepair mapping
Readoutexcision / bypass
Design focussequence context
QC focusLC-MS
Category Modification Code Primary Effect Typical Application
Oxidative Lesion 8-Oxo-2′-dG [8-oxo-dG] Classic oxidative guanine lesion BER studies, polymerase fidelity and mispairing
Oxidative Lesion 8-Oxo-2′-dA [8-oxo-dA] Oxidative adenine lesion Repair recognition and polymerase bypass
Hydroxy Lesion 5-Hydroxy-2′-deoxycytidine [5-OH-dC] Oxidative cytidine lesion Repair mapping and lesion recognition
Hydroxy Lesion 5-Hydroxymethyl-2′-dU [5-hme-dU] Hydroxymethyl-modified uracil Stability, recognition and H-bond studies
Deamination Product 2′-Deoxyxanthosine [dX] Deamination/oxidation product with altered pairing Mispairing and polymerase-fidelity studies
Adduct Etheno-2′-dA [ε-dA] Exocyclic adenine adduct Polymerase bypass and adduct-recognition studies
Dihydro Base 5,6-Dihydrothymidine [5,6-DH-dT] Reduced base with loss of aromaticity Stacking, ΔG and structural perturbation studies
Dihydro Base 5,6-Dihydro-2′-dU [5,6-DH-dU] Reduced uracil analog Folding and conformational studies
Adduct C4-(1,2,4-Triazol-1-yl)-2′-dU [C4-Tz-dU] Heteroaryl C4 adduct H-bond and stacking perturbation studies

Design note: For repair assays, define the strand, position, opposite base and sequence context carefully. Compare lesion-containing duplexes with lesion-free and opposite-base controls.

Backbone & Structural Variants — sugar, linkage, isomer and abasic mimics for geometry, flexibility and recognition studies.

Best forgeometry tests
ReadoutTm / CD / enzyme
Design focusanalog window
QC focussequence map
Category Modification Code Primary Effect Typical Application
Sugar Variant Aracytidine [araC] 2′-arabinosyl sugar pucker change Backbone geometry and enzyme-recognition studies
Sugar / Isomer 2′-Deoxypseudouridine [ψ-dU] C-linked uracil isomer in DNA Pairing and structural-effect studies
RNA Isomer Pseudouridine ribo [ψ-rU] RNA pseudouridine RNA folding, RNA-protein and translation-effect models
Methylated Base 5-Methyluridine ribo [5-Me-U] RNA m5U stability and stacking change RNA modification and recognition studies
Fluorescent Sugar Variant 2-AP-2′-O-methylriboside [2-AP-2′-OMe-r] Fluorescent base with 2′-OMe sugar RNA folding with nuclease-resistant reporter placement
Linkage Variant 2′–5′ Linked dN [2′-5′-Link-dN] Non-canonical phosphodiester linkage Backbone geometry, folding and protein-contact studies
Zebularine Analog rZebularine [rZeb] RNA cytidine analog Enzyme recognition and cytidine analog SAR
Zebularine Analog Zebularine-deoxy-5-methyl [dZeb-5-Me] Deoxy zebularine plus methyl context Stability, recognition and methyl-context SAR studies
Abasic Mimic Pyrrolidine [Pyr] Stable abasic-site mimic that removes coding information Repair recognition, flexibility, stacking and coding-effect studies

Design note: Keep stabilizing modifications outside the analog window when the goal is to measure the local effect of a sugar, linkage or abasic mimic.

Application-Centered Design

Match the Analog to the Experimental Readout

A successful SAR study links each modification to a measurable output and matched control set.

Select an application goal to view design recommendations

Recommended Analogs

8-oxo-dG, ε-dA, dX, 5-F-dU, deaza/aza bases and thio bases.

Design Focus

Place the analog at the extension site and compare matched native and opposite-base controls.

Readouts

Primer extension, misincorporation spectra, stopped-flow kinetics and LC-MS product mapping.

Recommended Analogs

8-oxo-dG, 5-OH-dC, dX, ε-dA, Pyr and dihydro bases.

Design Focus

Use defined sequence contexts and position series around recognition motifs.

Readouts

Excision assays, BER/NER enzyme panels, PAGE, HPLC and LC-MS verification.

Recommended Analogs

7-deaza-dA/dG, 3-deaza-dA, N4-Et-dC, halogenated bases and abasic mimics.

Design Focus

Map contacts at the footprint while preserving surrounding binding-site geometry.

Readouts

EMSA, SPR, BLI, footprinting, cleavage mapping and binding kinetics.

Recommended Analogs

2-AP, pyrrolo-dC, BODIPY-TR-X, pyrene cap and sugar/linkage variants.

Design Focus

Avoid terminal quenching and choose positions that report local structural transitions.

Readouts

Steady-state fluorescence, stopped-flow fluorescence, FRET, UV melt and CD.
Production Workflow

Workflow for SAR Oligonucleotide Studies

A clear workflow connects hypothesis, analog choice, positional design, synthesis, QC and assay-ready delivery.

?

Define Question

Choose pairing, stacking, repair, binding, photochemistry or geometry as the primary readout.

A

Select Analog

Match the base analog or lesion to the chemical feature being tested.

±

Build Controls

Design native, positional, opposite-base, scrambled and duplex/ss controls.

QC

Synthesize & Verify

Purify by HPLC/UPLC or PAGE and verify identity by LC-MS where compatible.

→

Deliver Format

Provide tubes, duplexes, normalized plates and documentation for assay execution.

Analytical QC & Manufacturing

QC Strategy for SAR Oligo Modifications

SAR experiments are only interpretable when the analog identity, purity, position and handling conditions are well controlled.

Analytical Control Matrix

QC packages may include HPLC/UPLC purity, LC-MS identity, OD260 concentration, duplex annealing support, Tm guidance, CoA, plate maps and custom documentation.

HPLC / UPLC

Purity assessment and cleanup for modified, lesion-bearing and fluorescent oligos.

LC-MS

Identity confirmation for analog incorporation and lesion-specific mass.

Handling Controls

Light shielding, oxidant control and minimized UV exposure for labile analogs.

Assay Formatting

Annealed duplexes, plates, concentration normalization and matched control sets.

Labile Analogs

Halogenated and thio bases may require reduced UV, oxygen or oxidant exposure.

Publication Support

Document sequence context, analog position, lot/QC and full control outcomes.

Supply Paths

RUO, scale-up and GMP-like documentation paths can be supported.

FAQ

Which analogs are best to monitor stacking or base flipping?
2-aminopurine and pyrrolo-dC are classic environment-sensitive reporters. Place them internally and compare against native-base controls at the same position.
Do halogenated bases increase or decrease Tm?
It depends on sequence context. 5-Br, 5-I and 5-F can shift Tm through electronics, sterics and photochemistry, so matched native and positional controls are recommended.
Where should lesion mimics go for repair assays?
Place the lesion within a defined sequence context near the recognition motif and include upstream/downstream positional controls. Confirm analog identity by LC-MS.
Can SAR analogs be combined with LNA or PS backbones?
Usually yes, but placement matters. Stabilizing modifications should be kept outside the analog window when the goal is to measure the analog’s local effect.
What purification and QC are recommended?
HPLC/UPLC purification with LC-MS confirmation is standard. Labile analogs such as 5-I and thio bases should be protected from unnecessary light or oxidants.
What information is needed for a quote?
 Provide sequence, analog position, target readout, required controls, scale, purification, plate or tube format and QC requirements.
More FAQ'sAll FAQ's
Before Requesting a Quote

Information Helpful for SAR Oligos

Question
pairing, repair, binding
Sequence
5′→3′ and position
Analog
2-AP, 8-oxo, deaza
Controls
native, swap, duplex
Format
tube, duplex, plate
QC
HPLC, LC-MS, CoA
Contact & Quote Request

Need help choosing SAR oligo modifications?

Share your sequence, structural question, analog position, assay readout, control set, scale, purification and QC needs. Bio-Synthesis can help recommend analogs, placement, spacers and documentation for clear interpretation.
Request a Quote Speak to a Scientist

Need help before quoting?

Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)
SAR

Analog Selection Review

Compare fluorescent reporters, halogenated bases, deaza/aza variants, thio bases, lesions and sugar/linkage variants for your specific readout.

2-AP Pyrrolo-dC 7-Deaza 8-oxo
QC

Control & QC Package

Plan native-base controls, positional controls, matched duplexes, HPLC/UPLC purification and LC-MS identity confirmation.

Native control Duplex HPLC LC-MS
Recommended Reading

Recommended Reading & Literature References

Use this section to support scientific credibility while keeping the page focused on base analog selection, SAR design, repair readouts and analytical verification.

  1. Ward DC, Reich E, Stryer L. Fluorescence studies of nucleotides and polynucleotides. Journal of Biological Chemistry. 1969.
  2. Rachofsky EL, Osman R, Ross JBA. Probing structure and dynamics of DNA with 2-aminopurine. Biochemistry. 2001.
  3. David SS, O’Shea VL, Kundu S. Base-excision repair of oxidative DNA damage. Nature. 2007.
  4. Friedberg EC. Suffering in silence: the tolerance of DNA damage. Nature Reviews Molecular Cell Biology. 2005.
  5. Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chemical Reviews. 2010.

Suggested page note: References are provided for scientific background. Final SAR oligo design should be evaluated within sequence context, analog position, assay readout, control design, purification method and QC requirements.

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