Table 2.

List of HMGBs that directly interact with RNA in vitro. If evidence was found, RNA and DNA binding preferences with affinities are listed followed by references. Unknown = UK.

HMGB protein (species)	HMGBs Bind RNA in vitro		DNA Binding in vitro
	Preferred RNA Ligands, [binding affinity] (reference)	Less preferred RNA ligands, [binding affinity] (reference)	DNA Ligands, [binding affinity] (reference)
Sox2, (human)	dsRNA elements including: stem loops with internal bulges, [~10–80 nM]; tRNAleu, [27 nM]; riboswitch, [26 nM], EVF2 lncRNA (Cajigas et al., 2021; Holmes et al., 2020; Hou et al., 2020; Tung et al., 2010)	ssRNA, [500 nM] (Holmes et al., 2020)	consensus dsDNA, [0.4–15 nM]; nucleosomal DNA, [0.3–1.4 nM]; non-consensus dsDNA, [550 nM] (Holmes et al., 2020; Moosa et al., 2018; Palasingam et al., 2009; Scaffidi & Bianchi, 2001; Soufi et al., 2015)
Sox Family HMGB domains, (human)	RNA 4way-junction, [1.6–96 nM]; Stem loop w/ internal bulge, [6.9–360 nM]; ES2 lncRNA fragment, [1.5–100 nM]; TERRA G-quadruplex, [0.2–130 nM] (Hamilton et al., 2022)	UK	consensus dsDNA, [0.5–31 nM]; non-consensus dsDNA, [310– 1200 nM] (Connor et al., 1994; Hamilton et al., 2022; Mertin et al., 1999; Palasingam et al., 2009)
Sox30, (human)	RNA 4way-junction, [990 nM]; ES2 lncRNA fragment, [910 nM]; TERRA G-quadruplex, [460 nM] (Hamilton et al., 2022)	Stem loop w/ internal bulge, [3100 nM] (Hamilton et al., 2022)	consensus dsDNA, [72 nM]; non-consensus dsDNA, [≥5000 nM] (Hamilton et al., 2022)
LEF1, (human)	RNA 4way-junction, [89 nM], ES2 lncRNA fragment, [61 nM], TERRA G-quadruplex, [4.1 nM] (Hamilton et al., 2022)	Stem loop w/ internal bulge, [630 nM] (Hamilton et al., 2022)	consensus dsDNA, [1–1.6 nM]; non-consensus dsDNA, [1000 nM] (Giese et al., 1991; Hamilton et al., 2022)
TCF7, (human)	dsRNA elements containing stem loop with internal bulge, [100–500 nM] (Lee & Jeong, 2004; Park et al., 2005)	dsRNA elements with stem loop with internal bulges (Lee et al., 2005)	UK
TFAM, (human)	RNA:DNA 4WJ, [300 nM]; RNA 4WJ, [279 and 99 nM]; tRNA, [71 nM]; Hybrid DNA:RNA and RNA G-quadruplexes, [1–2 nM] (Brown et al., 2015; Lyonnais et al., 2017)	ssRNA (poly AC or U), dsRNA, dsRNA hairpin loops, linear dsRNA/DNA hybrids (Brown et al., 2015)	consensus dsDNA, [0.3–9 nM]; non-consensus dsDNA [100 nM]; DNA 4WJ, [63 nM] (Brown et al., 2015; Lyonnais et al., 2017)
HMGD, (fly)	TAR RNA, [29 nM]; dsRNA stem loop, [36 nM]; linear dsRNA, [70 nM]; bulged dsRNA, [53 nM] (Arimondo et al., 2000)	ssRNA (Arimondo et al., 2000)	dsDNA and bulged DNA, [~85 nM]; DNA microcircle, [~1 nM] (Payet & Travers, 1997)
HMGB1, (human)	dsRNA elements including stem loops and internal bulges, siRNA, poly (I:C) (Bell et al., 2008; Choi et al., 2020; Lee et al., 2012; Oh & Lee, 2014; Yanai et al., 2009; Yu et al., 2015)	E. coli tRNA (Yu et al., 2015)	4WJ DNA; DNA minicircles, [0.01–5 nM]; semicatenated DNA, [~0.16 pm]; ssDNA; cruciform DNA; supercoiled DNA; Z-DNA (Gaillard & Strauss, 2000; Jaouen et al., 2005; Webb et al., 2001; Webb & Thomas, 1999)
HMGB2, (human)	LRP1-AS ncRNA (Yamanaka et al., 2015)	LRP1-mRNA (Yamanaka et al., 2015)	chromium damaged DNA, [1 nM]; dsDNA, [610 nM] semicatenated DNA, (Gaillard & Strauss, 2000; Wang et al., 1997; Yoshioka et al., 1999)
HMGB3, (human)	HIV-1 Tat mRNA containing dsRNA elements, including stem loops and internal bulges (Khoury et al., 2021)	UK	UK
MAEL, (mouse, bombyx)	RNA 4WJ, [640 nM]; ssRNA, [130–220] (Chen et al., 2015; Genzor & Bortvin, 2015)	dsRNA, RNA hairpins, ssRNA (Genzor & Bortvin, 2015)	DNA 4wj, [14 nM] (Genzor & Bortvin, 2015)
CsHMG, (plant)	poly (U) and poly (G) RNA (de Souza et al., 2012)	poly (AU) RNA (de Souza et al., 2012)	dsDNA (de Souza et al., 2012)
DssRP, (fly)	poly (U) and poly (G) RNA (Hsu et al., 1993)	poly (A) or poly (C) RNA (Hsu et al., 1993)	ssDNA (Hsu et al., 1993)