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1 Supplemental Material Sensitivity of Hydrogen Bonds of DNA and RNA to Hydration, as Gauged by 1 JNH Measurements in Ethanol Water Mixtures Marlon N. Manalo, Xiangming Kong, and Andy LiWang* Texas A&M University Department of Biochemistry & Biophysics College Station, TX Corresponding author: Andy LiWang ( ; andy liwang@tamu.edu) Corresponding address: 2128 TAMU, College Station, TX Key Words. DNA, ethanol, hydration, hydrogen bond length, NMR, RNA.
2 Supplemental Table 1. 1 JNH values of DNA and RNA at different mol % ethanol. a DNA RNA Sample, residue 0% 5% 8% 0% 8% 1, T7/U ± ± ± ± ± 0.7 1, T8/U ± ± ± ± ± 0.5 1, G ± ± ± ± ± 0.6 1, G ± ± ± ± ± 0.5 1, G ± ± ± ± ± 0.5 2, T3/U ± ± ± 0.0 NA c ± 0.6 2, T4/U ± ± ± ± ± 0.6 2, T5/U ± ± ± ± ± 0.4 2, T6/U ± 0.6 NA c NA c ± ± 0.4 2, G ± 0.7 NA c NA c ± ± 0.7 3, T7/U ± ± ± ± ± 0.7 3, T8/U ± ± ± 0.3 NA b NA b 3, T9/U ± ± ± 0.3 NA b NA b 3, T10/U ± ± ± 0.1 NA b NA b 3, G ± ± ± ± ± 0.4 4, T3/U ± ± 0.3 NA c ± ± 0.7 4, T5/U5 NA b NA b NA b NA b NA b 4, T7/U7 NA b NA b NA b NA b NA b 4, T9/U ± ± ± 0.4 NA b NA b 4, G ± 0.8 NA c NA c ± 0.4 NA b 5, T5/U ± ± ± ± ± 0.4 5, T7/U ± ± ± ± ± 0.8 5, G ± 0.2 NA c NA c NA b ± 0.7 5, G ± ± ± 0.1 NA b ± 0.4 5, G ± ± ± ± 0.7 NA c a Values are given in Hz and represent averages of 3 16 data sets. Each experiment took about two days to acquire (see main text for details). The number of data sets collected for a particular sample depended on the sample concentration, which varied between mm duplex. The DNA sequences for 1, 2, 3, 4, and 5 are d(cgcgaattcgcg)2, d(cgttttaaaacg)2, d(cgaaaattttcg)2, d(cgtatatatacg)2, and d(cgcgtatacgcg)2. For each DNA there is an isosequential RNA. b Could not determine 1 JNH due to resonance overlap. c Could not determine 1 JNH due to poor signal to noise. S2
3 Supplemental Table 2. Imino chemical shifts of DNA and RNA at different mol % ethanol. a DNA RNA Sample, DNA residue 0% 5% 8% 0% 8% 1, T , T , G , G , G , T , T , T , T , G , T , T , T , T , G , T , T NA b NA b NA b 4, T NA b NA b NA b 4, T NA b 4, G NA c NA c NA b 5, T , T , G d d d e 5, G e 5, G d d d a Values are given in parts per million relative to internal DSS. The sequences are defined in the caption of Supplemental Table 1. b Could not determine chemical shift due to resonance overlap. c Could not determine chemical shift due to poor signal to noise. d Chemical shifts were assigned according to Patel et al. e Chemical shift is tentatively assigned. Patel, D. J.; Ikuta, S.; Kozlowski, S. A.; Itakura, K.; (1983) Proc. Natl. Acad. Sci. USA, 47, S3
4 Supplemental Table 3. Melting temperatures (Tm) of DNA and RNA at different mol % ethanol. a DNA/RNA 0% 5% 8% 10% 15% sample 1 67 (67) 57 (60) (42) 39 (38) (43) 43 (38) (47) 36 (43) NA b (NA) b NA b (NA) b NA b NA b a Tm values are given in C. All samples contained 2.5 μm duplex DNA, 125 mm NaCl, 50 mm NaH2PO 4, 0.75 mm EDTA, ph 7. The sequences are defined in the caption of Supplemental Table 1. Values for RNA are given in parenthesis. b Could not determine Tm since melting profile did not follow a two state melting transition. S4
5 Supplemental Table 4. Changes in energy, ΔE for a 0.01 Å decrease from the fully optimized N1 N3 distance of isolated A:T, A:U, and G:C base pairs. Base pair Fully optimized N1 N3 (Å) ΔE (cal/mol) A:T A:U G:C Density functional theory calculations were carried out at the BPW91 level with counterpoise correction as implemented in Gaussian03. Geometry optimizations were performed with the basis sets 6 31G(d) on all heavy atoms (C, N, O) and hydrogen atoms bound to carbon, but with 6 31G(d,p) on hydrogen atoms bound to nitrogen. Gaussian 03, Revision C.02, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian, Inc., Wallingford CT, S5
6 Manalo et al. Supplemental Figure 1. One dimensional 1 1 echo spectra of the DNA and RNA samples in water (left hand column) and 8 mol % ethanol (right hand column). Residues for which 1JNH were not measured are labeled with asterisks. Spectra were acquired using the 1 1 echo sequence (Sklenár, V. and Bax, A. (1987) J. Magn. Reson., 74, ). S6
7 Supplemental Figure 2. Melting temperatures of DNA and RNA as a function of ethanol concentration. The solid and open symbols are used for DNA and RNA, respectively. Circles, squares, diamonds, and triangles correspond to data for 1, 2, 3, and 4. The solid lines are linear fits to the DNA data and all have r 2 > The melting profile for 5 was not two state and thus no Tm for that sample is reported. S7
8 Supplemental Figure 3. Line widths of imino protons of DNA and RNA measured in water versus those measured in 8 mol % ethanol. Data for the DNA and RNA are plotted using solid and open circles, respectively. In 8 mol % ethanol, the line widths increase on average by 0.9 ± 1.5 and 2.0 ± 3.4 Hz, respectively, for the imino protons of DNA and RNA. A paired Student s t test yields P values of 0.01 and 0.03 for the DNA and RNA data. The increase in line widths suggests an increase in solvent exchange (Nonin et al., 1995). Nonin, S., Leroy, J.-L. and Gueron, M. (1995) Biochemistry, 34, S8
9 Supplemental Figure 4. Differences in the chemical shifts of imino protons of (a) DNA and (b) RNA measured in 8 mol % ethanol and water. The definitions of the symbols and colors are the same as those in Figure 4 of the manuscript. The chemical shifts were measured from the spectra shown in Supplemental Figure 1. The imino protons of the Gs of the DNA and RNA shift downfield upon the addition of ethanol by 25 ± 15 and 41 ± 28 ppb with paired Student s t test P values of and 0.005, respectively. The imino protons of the Us of the RNA shift downfield by 29 ± 46 ppb (P = 0.042). In contrast, the imino protons of the Ts of the DNA duplexes shift upfield by 8 ± 13 ppb (P = 0.037). Chemical shifts of imino protons are largely influenced not only by hydrogenbonding, but also by the ringcurrent fields of neighboring bases: hydrogen bonding and base stacking cause down (Dingley et al., 1999) and upfield shifts (Patel and Tonelli, 1974), respectively. Thus, downfield shifts could be induced by shorter hydrogen bonds, reduced base stacking, or both. Dingley, A. J., Masse, J. E., Peterson, R. D., Barfield, M., Feigon, J. and Grzesiek, S. (1999) J. Am. Chem. Soc., 121, Patel, D. J. and Tonelli, A. E. (1974) Proc. Natl. Acad. Sci. USA, 71, S9
10 For a general introduction to Gaussian and Gaussian input files, please see Exploring Chemistry with Electronic Structure Methods (Second edition) by James B. Foresman and Æleen Frisch; Copyright 1993, , Gaussian, Inc.: Pittsburgh, PA. 1. Gaussian input file for full geometry optimization of an AT base pair #p bpw91/gen opt counterpoise=2 AT opt with CP correction 0 1 H N C N C C C O C H O C H H H N C N C C C N C N H C H H H N H H H H H H S10
11 C N O g(d) **** g(d,p) **** g(d) **** S11
12 2. Gaussian input file for geometry optimization of an AT base pair with constrained N1 N3 distance #p bpw91/gen opt=modredund counterpoise=2 AT opt with CP correction, NN A 0 1 H N C N C C C O C H O C H H H N C N C C C N C N H C H H H N H H H H H H * B 1 S12
13 2 F F C N O g(d) **** g(d,p) **** g(d) **** S13
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