DNA ChemistryDavid Peters Baran Group Meeting06/02/17

N

N NH

NNH2

HN

N NH

NO

H2N

N

NH

HN

NH

HN

NH

O OO

O ONH2Me

adenine guanine cytosine thymine uracil

The Basics…

Purines Pyrimidines

O

HO

NHO

N

N

N

H2N

O

HO

NO

N

N

N

H2N

NH

N

N

N

NH2 POO

O

Nucleobase Nucleoside(adenosine)(guanidine)(cytidine)

(thymidine)(uridine)

Nucleotide(adenosine monophosphate)

(di-, tri-)(AMP, ADP, ATP)

O

HO OH

HOOH O

HO

HOOH

D-ribosfuranose 2’-deoxy-D-ribofuranose

OH

N

N

NN

NH2

O

OOPOH

O

HNO

O MeN

O

OOPOH

O

NH

NN

OH2N

N

OOPO

OH

NNH2

ON

O

HOOPO

OHO

5’3’

Oligonucelotide

OH OH

O

HO

NHO

N

N

N

H2N

O

HO

NO

N

N

N

H2N

POO

O

DeoxynucleotideDeoxynucleoside

O NO

N

N

N

H2N

PO

OO OH

Cyclic Adenosine Monophosphate (cAMP)

WHAT DOES DNA STAND FOR?!

Topics Included: DNA building blocks, DNA structures, chemical stability/succeptibility, relevant enzymatic processes, DNA modifications/bioconjugation, Levaraging DNA: base pairing, chemical diversity, and stereochemical environment

Topics Breiefly Discussed: oligonucleotide drugs, chemical etiology, non-natural DNA

Topics Not Included: RNA, nucleoside chemistry (O’Hara, 2012; Gianatassio, 2013), nucleotide synthesis, oligonucleotide synthesis, sequencing, nucleobase synthesis, prebiotic chemsitry

Selected History1869 - Friedrich Miescher identifies “nuclein” from white blood cells1919 - Phoebus Levene identifies components as base, nucleoside and nucleotide1935 - Klein and Thannhauser isolate single nucleotides from degraded DNA1937 - First X-ray diffraction showing DNA as a regular structure1944 - Avery-MacLeod-McCarty experiment published – DNA as ‘transforming principle’1950 - Chargaff published on species specificity and G/C and A/T ratios (Chargaff’s Rule)1952 - Hershy-Chase experiment confirms DNA’s role as genetic material1952 - Franklin X-ray photographs are taken (A- and B-DNA)1953 - Watson and Crick elucidated structure of DNA1977 - Frederick Sanger develops dideoxy method of sequencing1985 - PCR is invented1994 - First gene therapy is approved by FDA2003 - Human Genome project declared complete

Contents

Fun Facts!!- A person has roughly 3x109 bases pairs! - All of your DNA would go across the solar system…twice- ~ 3% of your DNA is gene encoding- ~ 8% of your DNA is viral DNA- You’re DNA is 99.9% similar to everyone elses- There is a Potato Genome Project- DNA is a flame retardant (phosphoric acid and ammonia)- You shouldn’t combine dinosaur and frog DNA

D_______________N_______________A_______________- 2’-deoxy is important for stability- first found in the center of cells- pka is about 1.5

DNA ChemistryDavid Peters

NN

N

N N

NN

N

N O

N

NN

O

N

NN

O

O MeH

H

H H

HH

HH

Sug

Sug

SugSug

NN

O

O Me

H

Sug

N

N

NN

N H

H

Sug

N

N

NN

ON

NN

O

NH

H

H HH

Sug

H

Sug

Watson-Crick Pairing

Hoogsteen Pairing

A-T

A-T G-C

G-C+

A-type DNA B-type DNA Z-type DNA

Rotation Sense left left right

Helix Diameter 25.5 Å 23.7 Å 17.4 Å

Rise/Base 2.3 Å 3.32 Å 3.8 Å

Rotation/Base 33.6º 35.9º -30º

Bases/Turn ~11 ~10 12

Base Pair Tilt +19º -1.2º -9º

Propeller Twist +18º +16º ~0º

Helix Axis Location major groove through base pairs minor groove

Sugar Conformation C3’-endo C2’-endo C:2’-endo, G:2’-exo

Glycosyl-Base Bond anti anti anti (C), syn (G)

O

O

NO

N

N

N

H2N

anti (B-DNA) syn (Z-DNA)

O

O

NONN

NNH2

O

O

NO

NH

NH2

OO

O

NO

HN

NH2

O

Structural Parameters

Conformational Considerations

- 99% of DNA base pairs- N-N/N-O distances: 0.28 to 0.30 nm

OBaseHO

OBaseHO

OBaseHO

C2’-endo C3’-endo C2’-exo

Propeller Twist

A T - results in greater base-base overlap

- 1% of DNA base pairing- disclosed 10 years later- relevant in G-quadruplex

A-DNA B-DNA Z-DNA- observed when dehydrated- natural in bacterial endospores and some viral capsids

- first in artificial GC repeats- Forced by m5C- Implicated in gene regulation

- majority of natural DNAAG

Sugar Puckers

Inclination

Garret, Grisham, Biochemistry, 4th Ed., 2010.Neidle, Principles of Nucleic Acid Structure, 1st Ed., 2008.

Baran Group Meeting06/02/17

DNA ChemistryDavid Peters

Bent B-DNA- A•T propellor twist 5-7º greater than G•C- properly spaced Poly-A’s cuase kink/bend in helix- implication in seq. recognition

Other Structures Solvation- must be 30% w/w water to maintain B-DNA - many spheres of solvation – 3 defined in some sequences- solvation ordered in minor groove (H-bonding bases)- “spine of hydration” (left; blue = 1st sphere, yellow = 2nd)- solvation less orded in major groove – disperse negaitve charge along phosphates- ester oxygens don’t usually participate in H-bonding- ring oxygens occasionally participate in H-bonding- A•T promotes minor groove H-bonding – entropic driving force for protein bindingN

NN

NO

N

NN

N N

O

N

N

N N

NO

N

NN

NN

O

NH

HH

H

H

HH

H

H

H

H

HSugSug

SugSug

M+n

N

NN

NN

NH

NN

NO

NN

N O

N

Base Hydration/Water Networks

OH

H OH

HO

HHOH

H

H H

Sugar Sugar

NNO

N

OH H

OH

HH H

HH

O HH

OH

HOH

HOH

H

H

H NHN

O

OMe

OH

H

OH

H

Sugar

Major Groove

Minor Groove

Metal Binding in Solvation- Na+ and K+ lay in minor groove replacing waters (exact position disputed)- exactly locating metals is difficult – Tl+ helps- Mg2+ plays a major role in solvation of major groove – serves as counterion to posphates- Mg2+ exists as hexahydrate – associated waters H-bond

Mg2+OH2H2O

H2O

H2O

OH2H2OBase

O

O

OPO

O

O

OP

O

O

G-Quadruplexes- discovered in 1962 by X-ray diffraction- important structure in aptamer technology- thought to play important role in gene regulation- G-rich telomeres form these – imporant in cancer biology- can be from 1,2,3, or 4 strands (examples above)- propensity to form/type dependent on sequence and metal ions available

DNA’s Happy Place: Stability

Holliday Junction- 4 stranded, 4 armed structure- intermediate in chromosomal recombination and bouble-strand break repair- symmetrical sequences can slide at juntion- unsemmetrica sequenced cannot – uses in nanotechnology/DNA Origami

BaseO

O

OPO

O

O

OH OH

DNA vs. RNA

- RNA is more hydrolytically labile- hydrol. results in 2’ or 3’ phosphate- Thymine in DNA; Uracil in RNA- deamination of C is U (that’s a problem…)- base pairing and larger structure is the same

N

NH

HN

NH

O O

ONH2

OHNH3

Rate: 7 x 10-13/sec

- overall stability is a combination of solvent, pH, and ionic strength- base pair H-bonding contributes very little (-3 kcal/mol/bp)- equally as many H-bonds available w/ water in ssDNA- pi-stacking contributes majority of stablilization (-16 to -51 kcal/mol/bp)- colder = more stable- pH around neutral is best (pH<11 = denatured)- Denatured ≠ Decomposition- Tm dependent on above cond. (and G/C content)

N

S

SOMe

dTPT3 dNaM2nd

order1storder

ssDNAdsDNA

J. Mol. Biol. 2007, 365.

Niedle, 2008. (see above)

Baran Group Meeting06/02/17

DNA ChemistryDavid Peters

DNA’s Unhappy Place: Degradation

MetalsRule of Thumb: If it’s not Mg2+, Ca2+, Na+, or K+ its going to do something bad.Hud, Nucleic Acid-Metal ion Interactions, 2009.

GGH3N

PtClClH3N

H3NPt

OHClH3N

H3NPt

H3N

- cisplatnin targets G,G repeats- binds to N7 of G- large conformational change and extrahelical bases- signals for apoptosis

CellDeath

Interstrand Binding

Intrastrand Binding- Metal ion invades helix or binds during denaturation- flips bases (syn) or makes helix “breathe”- Pt2+, Ag+, Hg2+

Stabilizing Other Conformations- metal binding can stabilize non-B-DNA structures- can inhibit recognition and/or make succeptible to other chemical modification- [Co(NH3)6]3+ and Zn2+ polyamine complexes stabilize Z-DNA w/ phosphate binding- Pt2+, Ag+, Hg2+ all stabilize quadruplexes and triplexes by bridging non- cannonical baise pairing

Miscelaneous- PbII, ZnII, CdII hydroxides cleave phosphodiesters- Pt2+ facilitates deamination of C (MeC→T)- OsO4 and MnO4

- oxidize 5,6 bond of pyrimidines

Depurination- nucleotides are naturally succeptible to this at low pH- Metals have high affinity for N7 of purine bases- Metal binding retards depurination at low pH & accelerates it at high pH- ex: PtII(dien) depurination of G pH<4 (slower) pH>4 (faster)- Pt2+, Ag+, Zn2+, Co2+, Ni2+, Cu2+, Pd2+

Radicals- radical reactions generally result in cleavage of glycosidic bond- can cause phosphodiester cleavage, abasic sites- electron rich nucleobases are most sensitive (G)- fenton chemistry most implicated in biological systems- ribose H-atom abstraction - most radicals can participate- Cu+, Fe2+, Mn5+-oxo, [Ru(bipy)3]2+/h!, ROOH

Fe2+ Fe3+HOOH HO OH+ ++

Fe3+ Fe2+HOOH HOO H+ ++

Intercalating Agents

N

Ph

NH2

H2NMe

Br

OH

OHO

O

OMe O

O

OOH

OH

NH2

OHMe

General- main degradation is depurination (pH 4)- faster under acidic conditions and higher heat- abasic sites strand cleave faster under basic cond.- thermal denaturation is sequence dependent - chemical denaturants: ureas, DMSO, formamide, propylene glycol- denatured DNA is more succeptible- pH 1 = phosphodiester cleavage

ethidiumbromide

doxorubicin(Adriamycin)

- usually flat, cationic, fused aromatic tricycles- lengthening (~3.4 Å) and unwinding (~26º) of helix- interactions in major/minor groove increase affinity- sequence insensitive- easy entry = dynamic DNA- increases chemical liability & modulates gene regualtion

Alkylation- any strong alkyl electrophile (most carcinogens are alkylators)- act mainly at phosphate, guanine-N7, adenine-N3- generally leads depurination - mutation results from mispairing or unfixed sites replicating- Duocarmycin recognizes 5’-AAAAA sequences and alkylating A-N3- dimethylsulfate, nitrogen mustards, acrylates, most things in the lab

NH

N

O

O

O

MeO OMe

NH

MeO

MeO

MeO

Photochemistry- well documented intrastrand pyrimidine dimers (254 nm)- guanine oxidation at 266 nm- photosensitizers (S) lead to a variety of reactivity

S S*O2 1O2

G+

S+ + O2–

5’-H abstr.

HO

sugar/basechemistry

HN

NO

O Me

Sug Sug

MeO

ON

NH

HN

N N

NO

H2NOH

[O] [H]

HN

N N

HN

O

H2NO HN

N NH

CHO

NHO

H2NSugSug

Sug

HN

NO

O Me

SugSug

O

NN

OH

MeCPD (6,4)-photoproduct

8-oxo-gaunine FAPy-G

Duocarmycin

O

OOP

OO

O

OH

H OH

OOP

O

OOHO

O

– H2O

(after depurination)

Chem. Rev. 1998, 1109.

Chem. Rev. 1998, 1109.

Baran Group Meeting06/02/17

DNA ChemistryDavid Peters

ENZYMATIC PROCESSES

BaseO

OH

OP

BaseO

OO

O

O

O PO

OO

BaseO

OH

O PO

OO P

O

O

BaseO

O

O

H

Mg2+Mg2+

B

Polymerase

Template Strand

5’

3’

Free 3’-OH

Extending Strand

Extending Strand

- PPi

- Nucleic acids duplexes are antiparallel- synthesized strand grows from 5’ to 3’- many polymerases in each organism- DNA and RNA polymerase acts similarly

- RNA polymerases selects for NTPs over dNTPs- fidelity is controlled by KINETICS- RNA plays many roles (stay tuned!)

Transcription

Replication- complex process utilizing many protiens and complexes- chemically dangerous process- error rate: 1/107 bases

Polymerases

E + DNA E•DNA E•DNA•dNTP E*•DNA•dNTP E*•DNA+1•PPi

E•DNA+1

1 2 3 4

5

E•DNA+1•PPi

- fidelity is controlled by KINETICS- editing domains/machinery also contribute- many DNA polymerases - various roles

- Correct Pair: step 3 is rate limiting - Incorrect Pair: step 4 is rate limiting

Biochemistry 2004, 14317.

For mRNA:- template strand is “anti-sense”- coding strand/RNA transcript are “sense”

DNA Repair

N

N N

NOMe

H2NSug

HN

N N

NO

H2NSug

MGMT

HN

NO

O Me

Sug Sug

MeO

ON

NH photolyaseh" HN

NO

O Me

Sug Sug

MeO

ON

NHFADH–MTHF

N

NO

O

Sug

Me2x

- humans lack photolyase; rely on nucleotide excission repair- catalytic in cofactors

Chem. Rev. 2003, 2203.

- Methyl guanosine methyl transferase- common damage from smoking - stoichiometric in MGMT – extremely energy expensive

glycosylase

APnuclease;

lyase

polymerase;ligase

Base Excission Repair- major repair pathway for many types of damage/mispairs- can also involve invasive polymerase- repairs: 8-oxo-G, Fapy-G, 3-Me-A, 7-Me-G, xanthine, hypoxyxanthine, U (T-derived), etc.- implicated in some cancers

Mg2+

BaseO

O

OP

BaseO

OO

O

O

O H

HO HHB

Nucleases- break nucleic acid polymers - DNase (left) is selective for DNA, and RNase (not pictured) for RNA- some have Zn2+ sites- exonucleases cleave at ends of chain- endo nucleases cleave mid-chain- RNase is EVERYWHERE!- restriction nucleases (bacterial) used extensively in molecular biology- usually guided or sequence specific - play roles in gene regulation and repair

Baran Group Meeting06/02/17

DNA ChemistryDavid Peters

Random Primed Labeling

denature/anneal primer

polymerase/labeled dNTPs

3’ 5’

repeat/denature

Labeled ssDNA

denature/anneal primer

3’ 5’

End Labeled DNA

N

NO

HN

O

HO

OO PO

OO P

O

OO P

O

O

O3’

N

NO

HN

O

HO

OPO

O

TdT (enzyme)ssDNA, Co2+

PCR Labeling

Terminal TransferaseLabeling

Enzymatic Labeling

- also: dual enzyme Nick Translation Labeling- RPL can be used for 32P labeling- control labeled [dNTP] for RPL and NTL- no site selectivity in RPL and NTL- PCR labeling possible from RNA (MLLV reverse transcriptase)- end labeling doesn’t affect hybridization

Chemcial Labeling

HN

NO

NH2

HN

NO

NH2

SO3

NaHSO3 HN

NO

Nu

SO3

Nu HN

NO

Nu- amine and hydrazide nucleophiles common- water competes- disrupts pairing (3% labeling ideal)

Bisulfite Conjugation

HN

N N

NO

H2N

HN

N N

NO

H2NNHRHN

N N

NO

H2NBr

NBSpH 9.60 ºC

NH2R50 ºC

O5’

OPO

OO

5’OP

NHR

OEDC, NH2R

0.1 M imidazolepH 6.0

Bromine Activation

- G: C8- C: C5- A: hard

Carbodiimide 5’ Phosphate Conjuagtionreacts via:phosphor-imidazolide

NH2

O NH

HN

N N

NO

H2NN

O

NHNNHHN

S

O N2

O NH

NHHN

S

O

NH

HN S

O

HNNO2

N3

NHHN

S

O

HNNO2

N N

HNO2N

O

O

O

O

OO OO

N

HN

HN

N

OO

O

OMe Me

DNA

DNA

psoralen-PEG3-biotin

dsDNAh! 365 nm

TRIS pH 7.4

HN

NH

S O

HN

NH

S O

HN

NH

S O

N

HNO2N

HN

NH

S O

NH

sunlamp DNA

“photobiotin”

pH 7.0

p-aminobenzoylbiocytin

NaNO2HCl; NaOH ssDNA

Biotin Labeling

- intercalaton based- pairing disruptive

HN

HN

S

O

Post Incorporation Modifications

N

N

NH2

OO

HO

OO PO

OO P

O

OO P

O

Opolymerase

NN

N

HN

SO

O

CuBr, N3RNa(ascorbate)

Chem. Eur. J. 2015, 16091.

Bioconjugate Chem. 2012, 1382. NN

N NR

NN

NN3

CuSO4, THPTA, Na(ascorbate)

NNH

R- one pot bisfunctionalization

Hermanson, Bioconjugate Techniques, 3rd Ed., 2013.

Baran Group Meeting06/02/17

DNA ChemistryDavid Peters Baran Group Meeting

FQ

Q

F

DNA-Templated Asymmetric Catalysis (stereochemical)Biosensors (base pairing)- achiral metal catalyst associated/bound to double helix- mostly use undefined DNA sequences (st-DNA)- reaction scope extremely limited currently- scale limitations

Intercalative Binding Groove Binding

Covalent Binding

Reaction Examples:

MM

M

Solid-Support

M

M

M

M

N NHN N

R

N

N N

N

Me

Me

NH

N

HN

NMeN

NHNN

R

N

N

M

LigandlessN N

O

HN

HN

N

OPPh2

Sug

- utilizes ion binding G-quadruplexes

- recycling 10x- flow application- scaled to 1 mmol- SiO2 & cellulose

Hoeschst LigandR = 3,5-OMe-Ph or 1-naphthyl

n

NN

n = 2 or 3Terpyridine

NO

R

RR = p-OMePh; 73% eeR = Ph; 37% ee

ONCu(II), st-DNA,1,10-phen.

MOPS (pH 6.5)5ºC

R1

O

N2

SO2R2

OSO2R2

R1Cu(II), st-DNA,

terpyridine

MOPS (pH 6.5)5ºC

R1 = H, MeR2 = Ph, p-Tol, 2-Pyr16-84% ee

NO

PhMOPS (pH 6.5)

5ºC

Cu(II), [DNA],4,4’-bipy

st-DNA: 98% eeGC oligo: 86% ee

GACT oligo: 78% ee

O

RN

NMeNuH+

O

RN

NMe

Cu(II), st-DNA,4,4’-bipy

MOPS (pH 6.5)5ºC

- R = Ar, alk.- Nu = CH(CO2Me)2, indole CH2(CN)CO2R, MeNO2- 62 to 91% ee

CO2R

O

CO2R

OF

MES (pH 5.5)5ºC

R = Me, i-Pr, t-Bu22 to 70% ee

Other Reactions:- Pd/Ir allylic amination- chiral sulfoxide formation- epoxide resolution - L-DNA = other antipode

General- Utilizes high specificity of base pairing- oligos synthesized for specific purpose- FRET or fluorophore/quencher pair - microarray bound = parallel detection- point-of-care diagnostics- metals, DNA, RNA, protiens

Idealistically: fast, highly specific detection of analytes at very low concentrations

ACS Appl. Mater. Interfaces 2013, 11741.- gold nanorods (GNR) = generalized- oligo with 1 modification = easier- hairpin = higher selectivity- can discriminate SNP (3x higher LOD)- 0.3 nM LOD (fluorescence)- 10 nM LOD (colorimetric)

Deoxyribozymes (diversity)- no known natural DNAzymes; lots of ribozymes known- nearly all catalyze bioorganic reactions- in vitro selection necessary; cannot predict 1º→2º→Function- libraries synthesied; hits amplified- Selection = 1014 tested simultaneously; Cominatorial = 103

- “coverage” decreases with length BUT longer sequences yield better hits- Rate accelerations beyond “effective concentration” effects (105 to 1010)

constant(RNA)

variable(DNA)

constant(DNA)

NH

HN

NHO

NH

HN

NHOi. PCRii. streptavidin

iii. cleavage

NH

HN

NHO

NH

HN

NHO +

discard

repeat

Reactions catalyzed:- RNA cleavage- DNA cleavage (oxidative)- RNA ligation (3’ or 2’-branched)- DNA ligation- DNA posphorylation- DNA capping (adenylation)- DNA depurination- Nucleopeptide linking

A GTC C

AG

CCG

G

G

AGC A

8-17 Deoxyribozyme- metal ions needed for activity- Pb2+ dependent RNA cleavage- Zn2+ and Mg2+ = cyclic phosphate- pH dependent

BaseO

OOP

OO

O

OHGen. Base

Cu(II), st-DNA,4,4’-bipy

Selectfluor

Silverman, Chem. Commun. 2008, 3467.

Arseniyadis, Org. Biomol. Chem. 2017, ASAP.

ACIE 2005, 3230.

Chem. Sci. 2013, 2013.

Synlett. 2007, 1153.

Chem. Comm. 2006, 635.

ACIE 2007, 9308.

DNA ChemistryDavid Peters

BaseO

O

OP

BaseO

OO

O

O

OR

OR

R= CH3 orOMe

N

O Base

PO OMe2N

O

N

O Base

NBase

O

NH

ONH

N

O

O

Base

OBase

O

O

OBase

O

OPO O

MorpholinoPhosphoramidateTricyclo DNA Peptide Nucleic Acid

2’-O-alkyl-RNA

BaseO

NH

OP

BaseO

NHO

O

O

BaseO

O

OP

BaseO

OO

O

O

O

O

N3’-P5’-phosphoramidate

Locked Nucleic Acid

BaseO

O

OP

BaseO

OMeO

O

O

BaseO

O

OP

BaseO

OS

O

O

Phosphorothioate

Methylphosphonate

BaseO

O

OP

BaseO

OO

O

O

F

F

2’-Fluoro DNA

BaseO

OP

OO

O Base

O

Cyclohexene Nucleic Acid

mRNA

RNase H

Protein

pre-mRNA

X

miRNA4

RISC

RISC

53

2

16

1. Aptamers

2. Anti miRNA

3. RISC Recruiting

4. Splice Switching

5. miRNA Mimic

6. Gapmers

- specificity for single protein- modulate activity/binding of target

- decoy of mRNA targeted by native miRNA- UPREGULATION

- ds-oligo mimics siRNA- recuits RISC machinery to cleave target mRNA

- blocks splicing sites durring pre-mRNA modification

- blocks translation by forming duplex (miRNA-like)

- DNA capped with stable variants (see left) at 3’ and 5’- DNA/RNA duplex recuits RNase H causing cleavage

Oligonucleotide Therapeutic MOAsOligonucleotide Therapeutics (base pairing)- Utilizes base recognition specificity to target specific genes- Challenges: entry/uptake, RNase resistance, toxicity, afinity, high specificity- Area for chemical inovation to overcome these challenges

Watts, Nature Biotech. 2017, 238.Ludnin, Human Gene Therapy 2015, 475. Bruice, Chem. Rev. 2012, 1284.

Good Reviews/Perspectives:

Key Points On This Topic- also known as “ASOs” or “antisense drugs” - claimed dianophore and pharmacophore separation – has not been true- biggest issue to address has been toxicity: specificity and ADME- complexity has risen as a result of poor efficacy

splice switching

improved uptakenuclease stability

Tm increases

reduces toxicityvery popular

- phosphate changes introduce stereocenter- Sp more resistant to nuclease- Rp higher binding afinity

- stereorandom > stereopure (only one)- selective orders may be beneficial- # of isomers = 2n-1

Stereochemsitry

18-mer = 217 = 131072 isomers!!Connectivity

PAST

CURRENT

Conjugation

ONH

Oligo

OHO

HOO

OH

NHAcOligo

3

3’GalNAc

5’PUFA

PUFA

GalNAc

Baran Group Meeting06/02/17

splice switching

stops phosphotases

DNA ChemistryDavid Peters

DNA Origami (base pairing) Related Topics Worthy of Their Own Meeting:- Nucleic Acid Chemical Etiology (concept, design, synthesis)- Oligonucleotides- Nucleobases

Chemical EtiologyAsks the qustion: Why are nucleic acids the they are and not otherwise?

Experimental Set-Up:1. Use chemical reasoning to propose alternatives to natural nucleic acid components2. Synthesize those alternatives 3. Study their properties with respect to nucleic acid functions as we know them4. Compare the to natural nucelic acids (NA)Assumptions Made:- NA’s originated from a “combinatorial” process w/ respect to functional and informational storage abilities- selection took place in the domain of sugar based oligonucleotides- reasoned component constitutions must be similar to those of natural NAs- the reasoned components were available- must contain a nucleobase (or derivative) and have capacity for pairing in any fashion

Eschenmoser, Science 1999, 2118.

10ºC unitTmestimatednot investigated

A8•T8 A12•T12

Baran Group Meeting06/02/17

“Keys”

Nature 2009, 73.Nature 2006, 297.