US 11,981,702 B2
Compounds for fluorescence sensing of duplex formation
Byron W. Purse, San Diego, CA (US); Dillon Burns, San Diego, CA (US); Kristine Teppang, San Diego, CA (US); Raymond Lee, San Diego, CA (US); and Melissa Lokensgard, San Diego, CA (US)
Assigned to San Diego State University (SDSU) Foundation, San Diego, CA (US)
Filed by San Diego State University Research Foundation, San Diego, CA (US)
Filed on Sep. 13, 2022, as Appl. No. 17/943,682.
Application 17/943,682 is a continuation of application No. 16/346,708, granted, now 11,447,519, previously published as PCT/US2017/060776, filed on Nov. 9, 2017.
Claims priority of provisional application 62/533,897, filed on Jul. 18, 2017.
Claims priority of provisional application 62/420,347, filed on Nov. 10, 2016.
Prior Publication US 2023/0094737 A1, Mar. 30, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. C07H 19/24 (2006.01); C09K 11/06 (2006.01); C12Q 1/68 (2018.01); C12Q 1/682 (2018.01); C12Q 1/686 (2018.01); G01N 21/77 (2006.01)
CPC C07H 19/24 (2013.01) [C09K 11/06 (2013.01); C12Q 1/682 (2013.01); C12Q 1/686 (2013.01); G01N 21/77 (2013.01); C09K 2211/1018 (2013.01); G01N 2021/7786 (2013.01)] 20 Claims
 
1. A compound of Formula I:

OG Complex Work Unit Chemistry
wherein
R is OR1, or NR2R3, wherein R is at the ortho, meta, meta', or para position relative to the NH substituent of Formula I;
X is O, C═O, NR4, S, S═O, or S(═O)2;
Gx is a moiety of Formula X1 or X2;

OG Complex Work Unit Chemistry
Y is H, OH, halo, or Me;
Z is OH, O(dimethoxytrityl), guanidinium, phosphate, diphosphate, triphosphate, phosphoramidite, phosphorothioate, or —O2P(═O)(3′ -X1A) wherein Formula X1A is,

OG Complex Work Unit Chemistry
Rz is H, —P(N(R4)2)(OCH2CH2CN), or —O2P(═O)(5′-X1A);
R1 is CH2CH3 or (C3-C12)alkyl wherein alkyl is optionally branched;
R2 and R3 are each independently CH3, CH2CH3, or (C3-C12)alkyl wherein alkyl is optionally branched;
R4 is H, CH3, or CH2CH3, CH(CH3)2;
each Q is independently H, CH3, CH2CH3, (C3-C12)alkyl wherein alkyl is optionally branched, or —(CH2CH2O)n(C1-C4)alkyl where n is 1-20, and when Q is not H the carbon of the CH—Q bond is a stereocenter having an (R)-configuration, or an (5)-configuration;
RA is H, CH3, CH2CH3, (C3-C12)alkyl wherein alkyl is optionally branched, or an amide bond to X2A wherein Formula X2A is:

OG Complex Work Unit Chemistry
RB is H, CH3, CH2CH3, (C3-C12)alkyl wherein alkyl is optionally branched, or a protecting group;
RC is OH, OCH3, OCH2CH3, O(C3-C12)alkyl wherein alkyl is optionally branched, or an amide bond to X2A;
each J is independently O or S, and when J is S the phosphorous stereocenter has an (R)-configuration, or an (S)-configuration;
each W is independently adenine (A), thymine (T), cytosine (C), guanine (G), or Formula IA, wherein Formula IA is,

OG Complex Work Unit Chemistry
and
d is 1 to about 50.