Adenine

Guanine

Cytosine

Thymine

5΄

3΄

DNA Backbone and Bases

BaseO

HO

O

O

P

O

BaseOP OO

O O

O

O

BaseOPO OO

HOCH2Base

O

NN

NN

NH2

N NH

NN

O

NH2

N

N

NH2

O

NH

N

O

O

H3C

(A) (C)

(G) (T)

CC

CC

NN

O

O

H

H

H

CH3

T

3´

5´

CC

CC

NNH

H

O H

H

H

H

NC

NN N

NC

CC

C

HN

CH H

HN

NCC

C C

N

NC

N

O

A

G H

5´

3´

base pairingbetween 2 strands

duplex formation

Watson-Crick pairing

Strand 1 Strand 2

TG

G

T

T

C

A

G C

A

C

A C

G

3´5´

5´ 3´

J.D. Watson, F.H. Crick Nature 1953, 171, 737

W. Fuller, et al

J. Mol. Biol. 1965, 12, 60

(X-ray of DNA fibers at

75% relative humidity)

3 Common Helical Duplexes

A.H.J. Wang, et al

Nature 1979, 282, 680

(CGCGCG in high salt conc.)

A-Form B-Form Z-Form

R. Langridge, et al

J. Mol. Biol. 1960, 2, 19

(X-ray of DNA fibers at

92% relative humidity)

Duplexes in the gas-phase

• V. Gabelica and E. DePauw, Int. J. Mass Spectrom. 2002, 219, 151.

• P.D. Schnier, J.S. Klassen, E.F. Strittmatter and E.R. Williams,J. Am.Chem. Soc. 1998, 120, 9605-9613.

Higher Ea for complimentary duplexes and Ea correlated to –∆Hd in solutionEvidence of Watson-Crick pairing in vacuo

CID yields correlate with number of GC pairs and ∆Hdiss in solutionSuggests structure conserved in gas phase

• M. Rueda, S.G. Kalko, F.J. Luque, M. Orozco J. Am. Chem. Soc. 2003, 125, 8007

Gas-phase MD simulations indicate 12- and 16-mer duplexes retain major

conformational features as the double helix in aqueous solution

Instrumental Details

ESISource

IonFunnel

DriftCell MS Detector

Ion Funnel

DriftCell

Ion Optics

QuadAnalyzer

DetectorTo PumpTo PumpTo Pump

To Pump

Ion Funnel

DriftCell

Ion Optics

QuadAnalyzer

DetectorTo PumpTo PumpTo Pump

To Pump Drift Cell

Ion funnelDetector

Quad

ESIsource

Drift cell

in out

E

~5 torr He

Get shape information from ion mobility

Arrival Time Distribution(ATD)

arrival time

Smaller cross-section

Largercross-section

Molecular Dynamics

Structures Collision Cross-Sections (σ)

ATDs Collision Cross-Sections (σ)

CompareCompare

Experimental Method:

Theoretical Method:

Experiment vs. Theory

H+

Cu+

Na+

Cu+

(2Cu-H)+(3Cu-2H)+

500 600 700 800 900 1000 1100 1200 1300 1400m/z

Duplex

Single-Strand

dCG dCG

dCG+Cu MALDI-TOF Mass Spectrum

Cu+ duplex formation favored over Na+, H+

ATDs for M+(dCG dCG)

1050 1200 1350 1500 1650

arrival time (µs)

Cu+, Ag+

[Zn2+ - H]+ , [Cd2+ - H]+

Li+, Na+, K+

σ expt = 230, 252 Å2

σ expt = 228 Å2[Ca2+- H]+

[Mg2+ - H]+

Cu+

Na+

observed for

[Ni2+- H]+ , [Co2+ - H]+ , [Fe2+- H]+

[Mn2+ - H]+ , [Cr2+- H]+

ATDs for M+(dCG dCG)

1050 1200 1350 1500 1650arrival time (µs)

Ag+

1050 1200 1350 1500 1650arrival time (µs)

Cd2+

Cu+

Zn2+

3d10 4d10

230 Å2

252 Å2257 Å2

226 Å2

227Å2

253 Å2

228 Å2

258 Å2

Theoretical Structure for Na+(dCG dCG)

Na+

PO4 groups

σtheory = 231 Å2

σexpt = 228 Å2

Na+ binds to O on each base

No Watson-Crick pairing

guanine

cytosine

DFT Structures for Cu+(dCG dCG)

Cu+ binds to O on both cytosines

σtheory = 257 Å2

σexpt = 252 Å2

Watson-Crick structureCu+ binds to O on all 4 bases

Cu+

σtheory = 238 Å2

σexpt = 230 Å2

+ ~1 kcal/mol

Summary - metals

d10 metals promote Watson-Crick duplexes, other metals do not

Cu+ > Ag+ >> Zn2+ > Cd2+

dAT Watson-Crick duplexes not observed

[6-mer]3-

[8-mer + Na]4-

[10-mer]5-

[14-mer]7-

658 Å2

σEXPT = 716 Å2

dCG 6, 8, 10, 14dCG 6, 8, 10, 14--mer duplex ATDsmer duplex ATDs

σEXPT = 430 Å2

arrival time

σEXPT = 1000 Å2

536 Å2

σEXPT = 536 Å2

658 Å2

[6-mer]3-

[8-mer + Na]4-

[10-mer]5-

[14-mer]7-

658 Å2

σEXPT = 716 Å2

σEXPT = 430 Å2

arrival time

σEXPT = 1000 Å2

536 Å2

σEXPT = 536 Å2

658 Å2

σGlob = 440 Å2

σGlob = 541 Å2

σGlob = 605 Å2

σGlob = 830 Å2

Theory

dCG 6, 8, 10, 14dCG 6, 8, 10, 14--mer duplex ATDsmer duplex ATDs

σexpt = 430 Å2

[6[6--mer]mer]33-- and [8and [8--mer + Na]mer + Na]44-- Theoretical StructuresTheoretical Structures

σglob = 541 Å2

dCGCGCG(6-mer)

dCGCGCGCG(8-mer)

σglob = 440 Å2

σexpt = 536 Å2

Na+

If the 8-mer duplex is placed in water it remains helical

300K dynamics for 10 ns

Na+

[8[8--mer + Na]mer + Na]44-- 300K Dynamics300K Dynamics

0.5 1 21.5

0.5 1 21.5

0 0.5 1 21.5

Cro

ss-S

ectio

n (Å

2 )C

ross

-Sec

tion

(Å2 )

time (ns)

time (ns)

time (ns)

0

740

720

700

680

660

640

0

Cro

ss-S

ectio

n (Å

2 )

610

710

690

670

650

630

700

680

660

640

600

620

solution helix

solvent-free helix

A-Helix

σexpt = 667 Å2

[8[8--mer + Na]mer + Na]44-- SolventSolvent--Free HelicesFree Helices

B-Helix Z-Helix

σB = 653 Å2 σZ = 654 Å2

7 WC pairs 8 WC pairs

σA = 671 Å2

7 WC pairs

Small amount of the helical form remains in the gas phase on expt time scale

Na+

σexpt = 718 Å2

σA = 734 Å2 σB = 783 Å2

σ = 640 Å2

σZ = 763 Å2

B-Helix Z-HelixA-Helix

globular

[10[10--mer]mer]55-- Theoretical StructuresTheoretical Structures

8 WC pairs 8 WC pairs 10 WC pairs

σexpt = 1002 Å2

σA = 1016 Å2 σB = 1034 Å2

σ = 850 Å2

σZ = 1035Å2

B-Helix Z-HelixA-Helix

globular

[14[14--mer]mer]77-- Theoretical StructuresTheoretical Structures

12 WC pairs 12 WC pairs 14 WC pairs

-90

-60

-30

0

30

60

90

200 220 240 260 280 300 320

λ (nm)

ellip

ticity

(mde

g)

Circular Dichroism Spectrum of the dCG 14-mer in ESI Solution

(50:50 H2O/MeOH, 2%NH4OH)

-90

-60

-30

0

30

60

90

200 220 240 260 280 300 320

λ (nm)

ellip

ticity

(mde

g)

Circular Dichroism Spectrum of the dCG 14-mer in ESI Solution

(50:50 H2O/MeOH, 2%NH4OH)

(ideal)

B-Form

R.R. Sinden, DNA Structure and Function

R.R. Sinden, DNA Structure and Function

-90

-60

-30

0

30

60

90

200 220 240 260 280 300 320

λ (nm)

ellip

ticity

(mde

g)

Circular Dichroism Spectrum of the dCG 14-mer in ESI Solution

(50:50 H2O/MeOH, 2%NH4OH)

(ideal)

B-Form

Z-Form

-90

-60

-30

0

30

60

90

200 220 240 260 280 300 320

λ (nm)

ellip

ticity

(mde

g)

Circular Dichroism Spectrum of the dCG 14-mer in ESI Solution

(50:50 H2O/MeOH, 2%NH4OH)

(ideal)

A-Form

B-Form

Z-Form

J.H. Riazance, et al. Nuc. Acids Res. 1985, 13, 4983

∴ have B form in solution

B-Form A-Form

solvent-free

ESI spray

dehydrate

Ion funnel

dehydrate

solution after spray

~ A-Form

Solution vs. Solvent-Free Structures

k

~ A-Form globular

k is stronglysize dependent

ATDATDdGAGAGAGAGA dGAGAGAGAGA •• dTCTCTCTCTCdTCTCTCTCTC

[10[10--mer]mer]55--

400 500 600 700 800

arrival time (µs)

σexpt = 741 Å2

σexpt = 741 Å2

σA = 750 Å2 σB = 838 Å2

σ = 719 Å2

B-HelixA-Helix

globular

Theoretical StructuresTheoretical StructuresdGAGAGAGAGA dGAGAGAGAGA •• dTCTCTCTCTCdTCTCTCTCTC

[10[10--mer]mer]55--

dTC strand

dGA strand

450arrival time (µs)

550 650 750 850 950

ATD for dATATATATAT duplexATD for dATATATATAT duplex[10[10--mer]mer]55--

IE = 13eV

IE = 44eV

IE = 89eV

758 Å21126 Å2

916 Å2819 Å2

700

750

800

850

900

950

0 100 200 300 400 500 600 700 800 900 1000

dAT 10-mer (A-form) Theoretical Structures

σtheory = 920 Å2

σtheory = 750 Å2σexpt = 819 Å2

σexpt = 916 Å2

σtheory = 820 Å2

σexpt = 756 Å2

time (ps)

cros

s-se

ctio

n (Å

2 )

arrival time (µs)

Assign peaks in ATDAssign peaks in ATD

IE =44eV

dATdAT [10[10--mer]mer]55--

ATD for dCGCGATATATCGCG duplex

arrival time (µs)

IE = 13eV

IE = 44eV

IE = 89eV

450 550 650 750 850 950

1006 Å2

1157 Å2

[14[14--mer]mer]77--

σ = 1006 Å2

σ = 1157 Å2

ATD for dCGCGATATATCGCG duplex

IE = 13eV

1006 Å2

1157 Å2

[14[14--mer]mer]77--

σ = 1006 Å2

σ = 1157 Å2

σtheory = 1000 Å2

(fraying?)

(A or B helix)

dATATCGCGCGATAT ATD

400

arrival time (µs)

500 600 700 800 900

σEXPT = 1123 Å2

[14[14--mer]mer]77--

Summary

• W-C pairing enhanced in dinucleotides cationized by d10 metals

• Duplexes retain helical structures on ms time scale in the gas phase

size dependency – onset of helicity at 8-mer length

base dependency – AT pairs preferentially broken over CG pairs

unidentified conformational family in AT containing

duplexes with σexpt = 1120 – 1160Å2

ManuelDFT calculations

ErinMALDI-TOF

AlessandraESI

JenMD calculations