Energetics and Dynamics of the Non-Natural Fluorescent 4AP:DAP Base pair
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1 Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2018 Energetics and Dynamics of the Non-Natural Fluorescent 4AP:DAP Base pair Mohit Chawla, 1 Ida Autiero, 1 Romina Oliva, 2, Luigi Cavallo 1 1 King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal , Saudi Arabia. 2 Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I , Naples, Italy luigi.cavallo@kaust.edu.sa S1
2 Table S1: Population of the first 10 clusters (on 2000 total snapshot, each from 100 ps of the last 200 ns of simulation). Cluster 4AP (63 clusters) AT (71 clusters) Table S2: Average interaction energy of the central, top (at 5 direction) and bottom (3 direction) H-bonded base pairs of the modified 4AP and natural/un-modified AT duplex. The single point interaction energies have been calculated at RIMP2/aug-cc-pVTZ level of theory for the three most populated clusters derived from the MD simulations. 4AP-duplex AT-duplex AT along the 5 direction Central pair AT along the 3 direction S2
3 Figure S1: Plot between the experimental temperature, T m, and the calculated H-bonding energies in vacuo and in water for all the studied base pairs in cww orientation. Figure S2: Base pair structure of 4AP:DAP cww geometry with the protonated N5 atom, shown by circle. S3
4 Figure S3: Root mean square deviation (RMSD) computed considering separately the base atoms (left panels) and the backbone atoms (right panels) of each residue in the central position (4AP: a,e and AT: b, f ) and the whole strands A and B (4AP: c, g and AT: d, h), always excluding the capping pairs. Black lines refer to the strand containing 4AP or A, while red lines refer to the strand containing DAP or T. S4
5 Figure S4: Distribution of the χ angles of the central bases in the 4AP (top) and AT (bottom) duplexes. S5
6 Figure S5: Evolution of the distances between atoms involved into the base pair H-bonds in position 7A-7B with time (4AP: top panel and AT: bottom panel). S6
7 Figure S6: Evolution of the C1 -C1 distances between the central and the neighboring base pairs (4AP: top panel and AT: bottom panel). Red line, central 4AP-DAP or A-T pair. Black lines and green lines, A6-T8 and A8-T6 pairs both in the 4AP and AT duplexes. S7
8 Figure S7: Root mean square fluctuation (RMSF) computed per residues (strand A in black and strand B in red) considering all the atoms and plotted as interacting pairs. 4AP: top panel and AT: bottom panel. S8
9 Figure S8: Left: cluster distribution among simulation time, 4AP (top panel) and AT (bottom panel). Right: Cluster size distribution for 4AP (black) and AT (red). S9
10 XYZ coordinates of the QM optimized base pairing geometries: In Water optimized coordinates for the studied base pairs: 4AP:DAP cww 38 4ap-dap SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C N N C N C H H H H H H H H H H AP:A cww 39 S10
11 4ap-A SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C N C N C H H H H N C N N C H H H H C H AP:G cww 40 4ap-G SCF Done: A.U. C C N C N C S11
12 C C C C O C O H H H H H H C N C C H H N C O H N H H N N C H C H H H AP:C cww 37 4ap-C SCF Done: A.U. C C N C N C C C C C O C S12
13 O H H H H H H C C N C N C H H H H H H H H N C O H AP:U cww 36 4ap-U SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N S13
14 C C H H H H H H N C O H O H AP:U1 cww 36 4ap-U1 SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O S14
15 H O H AP:T cww 39 4ap-T SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O O H C H H H AP:T1 cww 39 S15
16 4ap-T1 SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O O H C H H H GC cww 35 GC-gd3bj SCF Done: A.U. C N C O N S16
17 C N C C C N C N N C C C O N C N H H H H H H H H H H H H H H Coordinates of the In Gas Phase optimized structures: 4AP:DAP cww 38 4ap-nos SCF Done: A.U. C C N C N C C C C C O C O S17
18 H H H H H H C C N C N N C N C H H H H H H H H H H AP:A cww 39 4ap-A SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C N C S18
19 N C H H H H N C N N C H H H H C H AP:G cww 40 4ap-G SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C N C C H H N C O H S19
20 N H H N N C H C H H H AP:C cww 37 4ap-C SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C N C H H H H H H H H N S20
21 C O H AP:U cww 36 4ap-U SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O H O H AP:U1 cww 36 4ap-U1 SCF Done: A.U. C C S21
22 N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O H O H AP:T cww 39 4ap-T SCF Done: A.U. C C N C N C C C C C O C O S22
23 H H H H H H C C N C C H H H H H H N C O O H C H H H AP:T1 cww 39 4ap-T1 SCF Done: A.U. C C N C N C C C C C O C O H H H H H H S23
24 C C N C C H H H H H H N C O O H C H H H Optimized structures of the 4AP base pairing with DAP and natural bases in tww geometries: In Water optimized structures: 4AP:DAP tww 38 4ap-dap-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N S24
25 C N N C N C H H H H H H H H H H AP:A tww 39 4ap-A-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C N C N C H H H H N C S25
26 N N C H H H H C H AP:G tww 40 4ap-G-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C N C C H H N C O H N H H N N C H C S26
27 H H H AP:C tww 37 4ap-C-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C N C H H H H H H H H N C O H AP:U tww 36 S27
28 4ap-U-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O H O H AP:U1 tww 36 4ap-U1-trans SCF Done: A.U. C C N C N C C C S28
29 C C O C O H H H H H H C C N C C H H H H H H N C O H O H AP:T tww 39 4ap-T-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H S29
30 H C C N C C H H H H H H N C O O H C H H H AP:T1 tww 39 4ap-T1-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H S30
31 H H H H H N C O O H C H H H ig:c tww 35 igc-s SCF Done: A.U. C N C C C N C N C C C N C N H H H H H H H H C H H H H N C O O N S31
32 N H H ic:g tww: 35 GiC-s SCF Done: A.U. C O N C N C C N C N N C C C O N C N H H H H H H H H H H C H H H H C N In gas phase optimized geometries for tww base pairs: 4AP:DAP tww S32
33 38 4ap-dap-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C N N C N C H H H H H H H H H H AP:A tww 39 4ap-A-trans SCF Done: A.U. C C N C N S33
34 C C C C C O C O H H H H H H C N C N C H H H H N C N N C H H H H C H AP:G tww 40 4ap-G-trans SCF Done: A.U. C C N C N C C C C C O S34
35 C O H H H H H H C N C C H H N C O H N H H N N C H C H H H AP:C tww 37 4ap-C-trans SCF Done: A.U. C C N C N C C C C C O C O H H H S35
36 H H H C C N C N C H H H H H H H H N C O H AP:U tww 36 4ap-U-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C S36
37 H H H H H H N C O H O H AP:U1 tww 36 4ap-U1-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C S37
38 O H O H AP:T tww 39 4ap-T-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O O H C H H H S38
39 4AP:T1 tww 39 4ap-T1-trans SCF Done: A.U. C C N C N C C C C C O C O H H H H H H C C N C C H H H H H H N C O O H C H H H ig:c tww 35 igc SCF Done: A.U. C N C C S39
40 C N C N C C C N C N H H H H H H H H C H H H H N C O O N N H H ic:g tww 35 GiC SCF Done: A.U. C O N C N C C N C N N C C S40
41 C O N C N H H H H H H H H H H C H H H H C N A:T tww 36 AT-trans-gd3bj SCF Done: A.U. C N C N C C C N N C N C N C O N C O C C H H H S41
42 H H H H H H H H H C H H H S42
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