Project #12 Unravelling the Primary Photoprotection Pathways in - - PowerPoint PPT Presentation

Unravelling the Primary Photoprotection Pathways in Model DNA systems

• Dr. Tom Oliver & Dr. Carmen Galan

Project #12

Bristol Chemical Synthesis Doctoral Training Centre Brainstorming Session

Friday 4th December 2015

DNA Nomenclature Primer

• DNA is essential for cell growth, function and development
• Comprised from specifjc sequences of deoxyribonucleic acids

nucleobase nucleoside nucleotide

DNA nucleobases Polynucleotide π-stacking Double helix (Primary structure) H-bonding and π-stacking DNA ribose

Nucleobases vs Nucleotides

• 90% of thymine molecules

return to S0 within 1 ps (1 ps = 1x10-12 s)

• When the sugar and

phosphate groups are attached, branching into the

1nπ* state is enhanced

signifjcantly

• For (dT)n, 10% of molecules

decay on a nanosecond timescale (~1x10-9 s)

Deoxythymidine monophosphate

DNA Photoinduced Damage

• Photoinduced lesions and reactions are correlated with the

absorption spectrum of DNA bases

• What are the links between DNA structure and damage?

1) What is the extent of delocalisation?

• When DNA is photoexcited, how many

nucleobases are excited?

• What is the length scale of delocalisation,

i.e. 2-8 bases?

• How fast does energy transfer between

adjacent moieties?

• What causes the excited states to

localise?

– Solvent re-organisation? – Base, sugar or phosphate vibrations?

G T A C

A C A C T A C A A T G T T G C A A T G T A T T G C A A C A T T G T A G T

Incoherent sequential hopping Super-exchange through-bond tunneling

• How far do h+ and e- migrate?
• Does it matter where charge-

transfer is initiated?

• DNA as a molecular wire?

2) What is the Charge-Transport Mechanism?

Time Resolved Spectroscopies

Signal = (Pump+Probe) – Probe Probe

Probe wavelength / 104 cm-1 Pump-probe time delay / fs

Negative features: excited states Positive features: ground states

Multidimensional Optical Spectroscopy

• Optical analogue of 2D NMR: correlate optical

absorption and emission

Absorption Spectra

UV absorption spectra FTIR absorption spectra

2D Electronic-Vibrational Spectroscopy

• Connect energy and structural landscapes with 2D electronic-

vibrational spectroscopy

• Use the vibrations as a “tag” for the physical location of energy
• Monitor evolution of the system with increasing pump-probe

time delay, T

Original paper: TAA Oliver et al., Proc. Natl. Acad. Sci. 111, 10061 (2014).

Model systems

Hairpins or Dumbbells

• Includes π-stacking and H-bonding
• Can vary sequence/no. base pairs

DNA primary structures: Difficult to extract mechanistic details

Di-/oligo-/poly-nucleotides

• Conformationally fmoppy, no π-stacking
• Not representative of primary structure

Oligonucleotide Synthesis Using

Phosphoramidites

Oligonucleotide phophoramidite synthesis review: Wei, Tetrahedron, 69, 3615 (2013)

Oligonucleotide Synthesis Using

Phosphoramidites

Oligonucleotide phophoramidite synthesis review: Wei, Tetrahedron, 69, 3615 (2013)

Oligonucleotide Synthesis Using

Phosphoramidites

Oligonucleotide phophoramidite synthesis review: Wei, Tetrahedron, 69, 3615 (2013)

15 ¡

Duplex Synthesis

Duplex Synthesis: Letsinger and Wu, JACS, 117, 7323 (1995).

Target 1

L ¡= ¡ ¡ ¡ ¡

O NH O HN

DMTO NH OP HN DMT, Dimethoxytrityl N CN

via ¡

Duplex Synthesis

Target 1

• What linkers will make good caps for the hairpin?
• How will you selectively couple the two
• ligonucleotides to the linker? I.e. avoid the

following products:

Dumbbell Synthesis

Target 2

• How will you alter the synthesis to cap the duplex

making a rigid dumbbell?

Vibrational Tagged Dumbbells

Target 3

• Specifjc IR tags are required on terminal/specifjc

nucleotides for “tag” experiments

• IR active functional group can be put on the sugar
• r DNA nucleobase
• The vibrational needs to be distinguishable from

current infrared active vibrations

CO amino ring breath (RB) CO CO amino CO RB

Electron Injecting Linkers

• What linkers could be used to inject electrons into

the duplex sequence?

• This requires the linker to be a good electron donor,

which upon irradiation (that does not excite DNA, > 310 nm) generating a radical anion

• The anion radical oxidises the adjacent nucleobase,

injecting electrons in the DNA sequence

Target 4

Electron Injecting linker: Lewis et al., JACS, 124, 14020 (2002)

Specifjcally Sequenced Dumbbells

Target 5

• Through sequential phosphoramidite reactions,

specifjc sequences of polynucleotides will be synthesised

• Think of strategies that ensure the correct sequence

is assembled in the fjnal dumbbell

¡ ¡

Gl Glyco-T co-Tools

• ols – ¡Galan ¡Research ¡Strategy ¡

¡ ¡

Bio-­‑Inspired ¡nanoprobes ¡for ¡ glycobiology ¡research ¡ Novel ¡methodologies ¡for ¡

• ligosaccharide ¡synthesis ¡

and ¡modified ¡nucleo?des ¡

Glycan

• Angew. ¡Chem. ¡Int. ¡Ed. ¡2015, ¡54, ¡14719 ¡
• Chem. ¡Commun. ¡2015, ¡51, ¡8939 ¡
• Angew. ¡Chem. ¡Int. ¡Ed. ¡2014, ¡53, ¡8190 ¡
• Chem. ¡Commun. ¡2013, ¡49, ¡4217 ¡
• Angew. ¡Chem. ¡Int. ¡Ed. ¡2012, ¡51, ¡9152 ¡
• Chem. ¡Commun. ¡2011, ¡47, ¡4526 ¡
• Adv. ¡Synth. ¡Cat. ¡2011, ¡353, ¡2593 ¡

¡

• Bioorg. ¡Med. ¡Chem. ¡LeR. ¡2015 ¡in ¡press ¡
• Angew. ¡Chem. ¡Int. ¡Ed. ¡2014, ¡53, ¡810 ¡
• Org. ¡Biomol. ¡Chem. ¡2012, ¡10, ¡7091 ¡
• Chem. ¡Commun. ¡(2010) ¡46 ¡(47), ¡8968 ¡

¡ ¡

Funding ¡

Oliver Group Research Interests

Primary Photoprotection Pathways of DNA

• Excited state delocalisation
• Charge-transfer mechanisms
• Infmuence of protein

environment on protection mechanism

• J. Chem. Phys., 142, 174202 (2015)

Design Principles of Natural and Artifjcial Photosynthesis

• Understand molecular mechanisms

underlying energy transfer in natural light harvesting

• Connect spatial morphology with

ultrafast properties of nanomaterial and photovoltaic materials

• J. Phys. Chem. B, 118, 5382 (2014)
• Nat. Phys. 9, 744 (2013)

Development of New Optical Spectroscopies

• PNAS, 111, 10061 (2014)
• J. Phys. Chem. B, 119, 11428 (2015)

Slides available from: http://taaoliver.com/bristol-chemical- synthesis-cdt/